| 1 | scRNA-seq Can Identify Different Cell Populations in Ovarian Cancer Bulk RNA-seq Experiments. (Gabrilovich S, Devor E, Cardillo N, Bender D, Goodheart M, Gonzalez-Bosquet J) Int J Mol Sci 2025 Aug 04;26(15) |
| 4 | Hepatocyte reporter cells and integrated metabolomic and transcriptomic analyses reveal insights into hepatocyte changes in offspring of pregnancies with obesity. (Kozlovich SY, Pan AY, McIntosh JJ, Palatnik A, Jia S, Hessner MJ, Nghiem-Rao TH) Sci Rep 2025 Jul 25;15(1):27041 |
| 1 | Novel insights into post-myocardial infarction cardiac remodeling through algorithmic detection of cell-type composition shifts. (Gural B, Kirkland L, Hockett A, Sandroni P, Zhang J, Rosa-Garrido M, Swift SK, Chapski DJ, Flinn MA, O'Meara CC, Vondriska TM, Patterson M, Jensen BC, Rau CD) PLoS Genet 2025 Jul;21(7):e1011807 |
| 1 | Transcriptomic Analysis of Localized High-risk Prostate Cancer Improves Prognostication and Identifies Benefit from Adding Docetaxel to Definitive Radiotherapy with Androgen Suppression in the NRG Oncology/RTOG 0521 Phase 3 Trial. (Phillips RM, Proudfoot JA, Davicioni E, Liu Y, Spratt DE, Simko JM, Den RB, Pollack A, Rosenthal SA, Sartor AO, Sweeney CJ, Attard G, Longoria L, Patel S, Straza MW, Efstathiou JA, Shah AB, Hoffman KE, Rodgers JP, Sandler HM, Feng FY, Tran PT) Eur Urol Oncol 2025 Aug;8(4):968-976 1 Citation |
| 2 | Amprenavir Mitigates Pepsin-Induced Transcriptomic Changes in Normal and Precancerous Esophageal Cells. (Ergun P, Samuels TL, Mathison AJ, Liu T, Jin VX, Johnston N) Int J Mol Sci 2025 Jun 26;26(13) |
| 1 | Examination of an iPSC model of human eye development reveals progressive emergence of critical embryonic cell types. (Replogle MR, Ma X, Lin CW, Semina EV) Sci Rep 2025 Jul 02;15(1):23009 1 Citation |
| 1 | Polyclonal plasma cell (PolyPC) signature as a key indicator for predicting the progression of MGUS to multiple myeloma. (Sun F, Cheng Y, Ma C, Xu H, Bailey C, Mery D, Ashby TC, Alapat D, Li Y, Young KH, Al Hadidi S, Thanendrarajan S, Schinke C, Zangari M, van Rhee F, Tricot G, Shaughnessy JD Jr, Zhan F) Cancer Biomark 2025 Jun;42(6):18758592251344936 |
| 2 | Molecular inflammatory expression profiles associated with the frequency of pain in individuals with sickle cell disease. (Mucalo Katunaric L, Jia S, Singh A, Roethle MF, Panepinto JA, Brousseau DC, Hessner MJ, Brandow AM) Blood Adv 2025 Aug 12;9(15):3790-3800 1 Citation |
| 1 | Enhancing risk stratification and treatment decision in multiple myeloma with SKY92 gene expression profiling in real-world data. (Biran N, Dhakal B, Niesvizky R, Lentzsch S, Bhutani D, McKay JT, Vesole DH, Nooka A, Paul B, Hari PN, D'Ambrosi S, Kuiper R, van Vliet M, Siegel D, Usmani SZ, van Rhee F) Br J Haematol 2025 Jun;206(6):1642-1653 |
| 3 | A realistic FastQ-based framework FastQDesign for ScRNA-seq study design issues. (Wang Y, Chen YG, Ahn KW, Lin CW) Commun Biol 2025 Apr 02;8(1):547 1 Citation |
| 1 | Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods. (Tercan B, Apolonio VH, Chagas VS, Wong CK, Lee JA, Yau C, Benz CC, Stuart JM, Karlberg BJ, Ellrott K, Grewal JK, Jones SJM, Cancer Genome Atlas Analysis Network, Zenklusen JC, Robertson AG, Laird PW, Cherniack AD, Castro MAA) STAR Protoc 2025 Jun 20;6(2):103681 |
| 1 | Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions. (Gromer KD, Chen SY, Gadhvi G, Feng L, Shearn C, Antala S, Wechsler JB, Cuda CM, Mack CL, Sokol RJ, Janssen WJ, Green RM, Perlman H, Winter DR, Taylor SA) Front Immunol 2025;16:1506195 1 Citation |
| 1 | Network-based meta-analysis and confirmation of genes ATP1A2, FXYD1, and ADCY3 associated with cAMP signaling in breast tumors compared to corresponding normal marginal tissues. (Torki Z, Ghavi D, Foruzandeh Z, Zeinali Sehrig F, Hashemi S, Alivand MR, Pornour M) Cell Mol Biol (Noisy-le-grand) 2024 Nov 27;70(11):16-30 1 Citation |
| 1 | Intrinsic adaptive plasticity in mouse and human sensory neurons. (McIlvried LA, Del Rosario JS, Pullen MY, Wangzhou A, Sheahan TD, Shepherd AJ, Slivicki RA, Lemen JA, Price TJ, Copits BA, Gereau RW 4th) J Gen Physiol 2025 Jan 06;157(1) 4 Citations |
| 1 | A luminal non-coding RNA-based genomic classifier confirms favourable outcomes in patients with clinically organ-confined bladder cancer treated with radical cystectomy. (de Jong JJ, Proudfoot JA, Daneshmand S, Svatek RS, Narayan V, Gibb EA, Davicioni E, Joshi S, Dahmen A, Li R, Inman BA, Shah P, Chaplin I, Wright J, Lotan Y) BJU Int 2025 Apr;135(4):648-656 1 Citation |
| 1 | Identification of shared gene expression programs activated in multiple modes of torpor across vertebrate clades. (Weir K, Vega N, Busa VF, Sajdak B, Kallestad L, Merriman D, Palczewski K, Carroll J, Blackshaw S) Sci Rep 2024 Oct 17;14(1):24360 |
| 3 | Global Transcriptomic Analysis of Topical Sodium Alginate Protection against Peptic Damage in an In Vitro Model of Treatment-Resistant Gastroesophageal Reflux Disease. (Ergun P, Samuels TL, Mathison AJ, Plehhova K, Coyle C, Horvath L, Johnston N) Int J Mol Sci 2024 Oct 05;25(19) 4 Citations |
| 3 | Temporally resolved early bone morphogenetic protein-driven transcriptional cascade during human amnion specification. (Sekulovski N, Wettstein JC, Carleton AE, Juga LN, Taniguchi LE, Ma X, Rao S, Schmidt JK, Golos TG, Lin CW, Taniguchi K) Elife 2024 Jul 25;12 |
| 1 | Transcriptomic diversity of innate lymphoid cells in human lymph nodes compared to BM and spleen. (Hashemi E, McCarthy C, Rao S, Malarkannan S) Commun Biol 2024 Jun 25;7(1):769 2 Citations |
| 1 | Surveillance with dual noninvasive testing for acute cellular rejection after heart transplantation: Outcomes from the Surveillance HeartCare Outcomes Registry. (Khush K, Hall S, Kao A, Raval N, Dhingra R, Shah P, Bellumkonda L, Ravichandran A, Van Bakel A, Uriel N, Patel S, Pinney S, DePasquale E, Baran DA, Pinney K, Oreschak K, Kobulnik J, Shen L, Teuteberg J) J Heart Lung Transplant 2024 Sep;43(9):1409-1421 15 Citations |
| 6 | Transcriptomic-Based Microenvironment Classification Reveals Precision Medicine Strategies for Pancreatic Ductal Adenocarcinoma. (George B, Kudryashova O, Kravets A, Thalji S, Malarkannan S, Kurzrock R, Chernyavskaya E, Gusakova M, Kravchenko D, Tychinin D, Savin E, Alekseeva L, Butusova A, Bagaev A, Shin N, Brown JH, Sethi I, Wang D, Taylor B, McFall T, Kamgar M, Hall WA, Erickson B, Christians KK, Evans DB, Tsai S) Gastroenterology 2024 May;166(5):859-871.e3 16 Citations |
| 1 | Pan-cancer analysis of TIM-3 transcriptomic expression reveals high levels in pancreatic cancer and interpatient heterogeneity. (Lim J, Kurzrock R, Nishizaki D, Miyashita H, Adashek JJ, Lee S, Pabla S, Nesline M, Conroy JM, DePietro P, Lippman SM, Kato S) Cancer Med 2024 Jan;13(1):e6844 7 Citations |
| 4 | Unfavorable transcriptome profiles and social disadvantage in hematopoietic cell transplantation: a CIBMTR analysis. (Taylor MR, Cole SW, Strom J, Brazauskas R, Baker KS, Phelan R, Buchbinder D, Hamilton B, Schoemans H, Shaw BE, Sharma A, Bhatt NS, Badawy SM, Winestone LE, Preussler JM, Mayo S, Jamani K, Nishihori T, Lee MA, Knight JM) Blood Adv 2023 Nov 28;7(22):6830-6838 8 Citations |
| 2 | Mild and moderate chronic hypercapnia elicit distinct transcriptomic responses of immune function in cardiorespiratory nuclei. (Grams KJ, Neumueller SE, Mouradian GC Jr, Burgraff NJ, Hodges MR, Pan L, Forster HV) Physiol Genomics 2023 Nov 01;55(11):487-503 |
| 3 | Robustness of single-cell RNA-seq for identifying differentially expressed genes. (Liu Y, Huang J, Pandey R, Liu P, Therani B, Qiu Q, Rao S, Geurts AM, Cowley AW Jr, Greene AS, Liang M) BMC Genomics 2023 Jul 03;24(1):371 6 Citations |
| 2 | A gene signature can predict risk of MGUS progressing to multiple myeloma. (Sun F, Cheng Y, Ying J, Mery D, Al Hadidi S, Wanchai V, Siegel ER, Xu H, Gai D, Ashby TC, Bailey C, Chen JR, Schinke C, Thanendrarajan S, Zangari M, Janz S, Barlogie B, Van Rhee F, Tricot G, Shaughnessy JD Jr, Zhan F) J Hematol Oncol 2023 Jun 29;16(1):70 7 Citations |
| 1 | Multi-omics cannot replace sample size in genome-wide association studies. (Baranger DAA, Hatoum AS, Polimanti R, Gelernter J, Edenberg HJ, Bogdan R, Agrawal A) Genes Brain Behav 2023 Dec;22(6):e12846 4 Citations |
| 1 | Transcriptome Profiling of the Hippocampal Seizure Network Implicates a Role for Wnt Signaling during Epileptogenesis in a Mouse Model of Temporal Lobe Epilepsy. (Mardones MD, Gupta K) Int J Mol Sci 2022 Oct 10;23(19) 8 Citations |
| 1 | Methods for Isolating and Defining Single-Cell Transcriptomes of Tissue-Resident Human NK Cells. (Hashemi E, Mei A, Wang D, Khalil M, Malarkannan S) Methods Mol Biol 2022;2463:103-116 |
| 1 | A de novo paradigm for male infertility. (Oud MS, Smits RM, Smith HE, Mastrorosa FK, Holt GS, Houston BJ, de Vries PF, Alobaidi BKS, Batty LE, Ismail H, Greenwood J, Sheth H, Mikulasova A, Astuti GDN, Gilissen C, McEleny K, Turner H, Coxhead J, Cockell S, Braat DDM, Fleischer K, D'Hauwers KWM, Schaafsma E, Genetics of Male Infertility Initiative (GEMINI) consortium, Nagirnaja L, Conrad DF, Friedrich C, Kliesch S, Aston KI, Riera-Escamilla A, Krausz C, Gonzaga-Jauregui C, Santibanez-Koref M, Elliott DJ, Vissers LELM, Tüttelmann F, O'Bryan MK, Ramos L, Xavier MJ, van der Heijden GW, Veltman JA) Nat Commun 2022 Jan 10;13(1):154 61 Citations |
| 2 | Donor T-Cell Repertoire Profiling in Recipient Lymphoid and Parenchyma Organs Reveals GVHD Pathogenesis at Clonal Levels After Bone Marrow Transplantation in Mice. (Wu Y, Fu J, Wang H, Yu XZ) Front Immunol 2021;12:778996 4 Citations |
| 1 | Disruption of Circadian Rhythms by Ambient Light during Neurodevelopment Leads to Autistic-like Molecular and Behavioral Alterations in Adult Mice. (Fang K, Liu D, Pathak SS, Yang B, Li J, Karthikeyan R, Chao OY, Yang YM, Jin VX, Cao R) Cells 2021 Nov 26;10(12) 20 Citations |
| 1 | Enhanced metastatic risk assessment in cutaneous squamous cell carcinoma with the 40-gene expression profile test. (Ibrahim SF, Kasprzak JM, Hall MA, Fitzgerald AL, Siegel JJ, Kurley SJ, Covington KR, Goldberg MS, Farberg AS, Trotter SC, Reed K, Brodland DG, Koyfman SA, Somani AK, Arron ST, Wysong A) Future Oncol 2022 Mar;18(7):833-847 33 Citations |
| 1 | Integrative analysis of DNA methylation and gene expression profiles to identify biomarkers of glioblastoma. (Alivand MR, Najafi S, Esmaeili S, Rahmanpour D, Zhaleh H, Rahmati Y) Cancer Genet 2021 Nov;258-259:135-150 14 Citations |
| 1 | Single-Cell Transcriptomics Reveals a Conserved Metaplasia Program in Pancreatic Injury. (Ma Z, Lytle NK, Chen B, Jyotsana N, Novak SW, Cho CJ, Caplan L, Ben-Levy O, Neininger AC, Burnette DT, Trinh VQ, Tan MCB, Patterson EA, Arrojo E Drigo R, Giraddi RR, Ramos C, Means AL, Matsumoto I, Manor U, Mills JC, Goldenring JR, Lau KS, Wahl GM, DelGiorno KE) Gastroenterology 2022 Feb;162(2):604-620.e20 68 Citations |
| 1 | A gene expression-based model predicts outcome in children with intermediate-risk classical Hodgkin lymphoma. (Johnston RL, Mottok A, Chan FC, Jiang A, Diepstra A, Visser L, Telenius A, Gascoyne RD, Friedman DL, Schwartz CL, Kelly KM, Scott DW, Horton TM, Steidl C) Blood 2022 Feb 10;139(6):889-893 14 Citations |
| 1 | A multimodal cell census and atlas of the mammalian primary motor cortex. (BRAIN Initiative Cell Census Network (BICCN)) Nature 2021 Oct;598(7879):86-102 334 Citations |
| 2 | Multi-omics mapping of human papillomavirus integration sites illuminates novel cervical cancer target genes. (Iden M, Tsaih SW, Huang YW, Liu P, Xiao M, Flister MJ, Rader JS) Br J Cancer 2021 Nov;125(10):1408-1419 17 Citations |
| 1 | Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression. (Mo A, Nagpal S, Gettler K, Haritunians T, Giri M, Haberman Y, Karns R, Prince J, Arafat D, Hsu NY, Chuang LS, Argmann C, Kasarskis A, Suarez-Farinas M, Gotman N, Mengesha E, Venkateswaran S, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, LeLeiko NS, Heyman MB, Griffiths AM, Patel AS, Noe JD, Davis Thomas S, Aronow BJ, Walters TD, McGovern DPB, Hyams JS, Kugathasan S, Cho JH, Denson LA, Gibson G) Am J Hum Genet 2021 Sep 02;108(9):1765-1779 10 Citations |
| 2 | Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease. (Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson DW, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PE, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP) PLoS Genet 2021 Jul;17(7):e1009679 21 Citations |
| 1 | The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer. (Delgir S, Ilkhani K, Safi A, Rahmati Y, Montazari V, Zaynali-Khasraghi Z, Seif F, Bastami M, Alivand MR) BMC Med Genomics 2021 Jul 07;14(1):180 20 Citations |
| 1 | Immunophenotype-associated gene signature in ductal breast tumors varies by receptor subtype, but the expression of individual signature genes remains consistent. (Behring M, Ye Y, Elkholy A, Bajpai P, Agarwal S, Kim HG, Ojesina AI, Wiener HW, Manne U, Shrestha S, Vazquez AI) Cancer Med 2021 Aug;10(16):5712-5720 7 Citations |
| 1 | A 95-gene signature stratifies recurrence risk of invasive disease in ER-positive, HER2-negative, node-negative breast cancer with intermediate 21-gene signature recurrence scores. (Fujii T, Masuda H, Cheng YC, Yang F, Sahin AA, Naoi Y, Matsunaga Y, Raghavendra A, Sinha AK, Fernandez JRE, James A, Yamagishi K, Matsushima T, Schuetz R, Tripathy D, Tada S, Jackson RS, Noguchi S, Nakamura S, Acoba JD, Ueno NT) Breast Cancer Res Treat 2021 Sep;189(2):455-461 8 Citations |
| 1 | Expression Analysis of VDR-Related LncRNAs in Autism Spectrum Disorder. (Ghafouri-Fard S, Eghtedarian R, Hussen BM, Motevaseli E, Arsang-Jang S, Taheri M) J Mol Neurosci 2021 Jul;71(7):1403-1409 12 Citations |
| 1 | GATA4 Controls Epithelial Morphogenesis in the Developing Stomach to Promote Establishment of Glandular Columnar Epithelium. (DeLaForest A, Kohlnhofer BM, Franklin OD, Stavniichuk R, Thompson CA, Pulakanti K, Rao S, Battle MA) Cell Mol Gastroenterol Hepatol 2021;12(4):1391-1413 10 Citations |
| 1 | Clonally Focused Public and Private T Cells in Resected Brain Tissue From Surgeries to Treat Children With Intractable Seizures. (Chang JW, Reyes SD, Faure-Kumar E, Lam SK, Lawlor MW, Leventer RJ, Lew SM, Lockhart PJ, Pope K, Weiner HL, Salamon N, Vinters HV, Mathern GW, Fallah A, Owens GC) Front Immunol 2021;12:664344 12 Citations |
| 1 | Single-cell RNA sequencing of mouse islets exposed to proinflammatory cytokines. (Stancill JS, Kasmani MY, Khatun A, Cui W, Corbett JA) Life Sci Alliance 2021 Jun;4(6) 29 Citations |
| 1 | E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation. (Schauder DM, Shen J, Chen Y, Kasmani MY, Kudek MR, Burns R, Cui W) Proc Natl Acad Sci U S A 2021 Apr 20;118(16) 25 Citations |
| 1 | A 10-gene prognostic signature points to LIMCH1 and HLA-DQB1 as important players in aggressive cervical cancer disease. (Halle MK, Sødal M, Forsse D, Engerud H, Woie K, Lura NG, Wagner-Larsen KS, Trovik J, Bertelsen BI, Haldorsen IS, Ojesina AI, Krakstad C) Br J Cancer 2021 May;124(10):1690-1698 24 Citations |
| 1 | Altered expression of lncRNAs in autism spectrum disorder. (Tamizkar KH, Ghafouri-Fard S, Omrani MD, Pouresmaeili F, Arsang-Jang S, Taheri M) Metab Brain Dis 2021 Jun;36(5):983-990 9 Citations |
| 1 | Expression Signature of lncRNAs and mRNAs in Sevoflurane-Induced Mouse Brain Injury: Implication of Involvement of Wide Molecular Networks and Pathways. (Jiang C, Arzua T, Yan Y, Bai X) Int J Mol Sci 2021 Jan 30;22(3) 10 Citations |
| 1 | Cancer of Unknown Primary in the Molecular Era. (Kato S, Alsafar A, Walavalkar V, Hainsworth J, Kurzrock R) Trends Cancer 2021 May;7(5):465-477 58 Citations |
| 1 | Clinical characteristics of testicular extramedullary involvement in multiple myeloma. (Mohan M, Yarlagadda N, Szabo A, Singh A, Pina Oviedo S, Schinke C) Am J Hematol 2021 Mar 01;96(3):E77-E81 3 Citations |
| 1 | Exuberant fibroblast activity compromises lung function via ADAMTS4. (Boyd DF, Allen EK, Randolph AG, Guo XJ, Weng Y, Sanders CJ, Bajracharya R, Lee NK, Guy CS, Vogel P, Guan W, Li Y, Liu X, Novak T, Newhams MM, Fabrizio TP, Wohlgemuth N, Mourani PM, PALISI Pediatric Intensive Care Influenza (PICFLU) Investigators, Wight TN, Schultz-Cherry S, Cormier SA, Shaw-Saliba K, Pekosz A, Rothman RE, Chen KF, Yang Z, Webby RJ, Zhong N, Crawford JC, Thomas PG) Nature 2020 Nov;587(7834):466-471 148 Citations |
| 1 | Cell type specific gene expression profiling reveals a role for complement component C3 in neutrophil responses to tissue damage. (Houseright RA, Rosowski EE, Lam PY, Tauzin SJM, Mulvaney O, Dewey CN, Huttenlocher A) Sci Rep 2020 Sep 24;10(1):15716 14 Citations |
| 2 | The 3D genomic landscape of differential response to EGFR/HER2 inhibition in endocrine-resistant breast cancer cells. (Yang Y, Choppavarapu L, Fang K, Naeini AS, Nosirov B, Li J, Yang K, He Z, Zhou Y, Schiff R, Li R, Hu Y, Wang J, Jin VX) Biochim Biophys Acta Gene Regul Mech 2020 Nov;1863(11):194631 13 Citations |
| 1 | Transcriptomics and solid tumors: The next frontier in precision cancer medicine. (Tsimberidou AM, Fountzilas E, Bleris L, Kurzrock R) Semin Cancer Biol 2022 Sep;84:50-59 68 Citations |
| 1 | Relationship closeness buffers the effects of perceived stress on transcriptomic indicators of cellular stress and biological aging marker p16INK4a. (Rentscher KE, Carroll JE, Cole SW, Repetti RL, Robles TF) Aging (Albany NY) 2020 Jul 26;12(16):16476-16490 11 Citations |
| 1 | Cell Lineage-Based Stratification for Glioblastoma. (Wang Z, Sun D, Chen YJ, Xie X, Shi Y, Tabar V, Brennan CW, Bale TA, Jayewickreme CD, Laks DR, Alcantara Llaguno S, Parada LF) Cancer Cell 2020 Sep 14;38(3):366-379.e8 79 Citations |
| 1 | Comparative Pathway Integrator: A Framework of Meta-Analytic Integration of Multiple Transcriptomic Studies for Consensual and Differential Pathway Analysis. (Zeng X, Zong W, Lin CW, Fang Z, Ma T, Lewis DA, Enwright JF, Tseng GC) Genes (Basel) 2020 Jun 24;11(6) 7 Citations |
| 1 | Epigenomics-based identification of oestrogen-regulated long noncoding RNAs in ER+ breast cancer. (Zhang Z, Yu W, Tang D, Zhou Y, Bi M, Wang H, Zheng Y, Chen M, Li L, Xu X, Zhang W, Tao H, Jin VX, Liu Z, Chen L) RNA Biol 2020 Nov;17(11):1590-1602 11 Citations |
| 1 | Dynamic Characterization of Structural, Molecular, and Electrophysiological Phenotypes of Human-Induced Pluripotent Stem Cell-Derived Cerebral Organoids, and Comparison with Fetal and Adult Gene Profiles. (Logan S, Arzua T, Yan Y, Jiang C, Liu X, Yu LK, Liu QS, Bai X) Cells 2020 May 23;9(5) 38 Citations |
| 1 | In silico identification of MAPK14-related lncRNAs and assessment of their expression in breast cancer samples. (Dashti S, Taherian-Esfahani Z, Kholghi-Oskooei V, Noroozi R, Arsang-Jang S, Ghafouri-Fard S, Taheri M) Sci Rep 2020 May 20;10(1):8316 25 Citations |
| 4 | Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature. (Yang C, Siebert JR, Burns R, Zheng Y, Mei A, Bonacci B, Wang D, Urrutia RA, Riese MJ, Rao S, Carlson KS, Thakar MS, Malarkannan S) Elife 2020 May 14;9 21 Citations |
| 1 | Identification of Serum miRNA Signature and Establishment of a Nomogram for Risk Stratification in Patients With Pancreatic Ductal Adenocarcinoma. (Kandimalla R, Shimura T, Mallik S, Sonohara F, Tsai S, Evans DB, Kim SC, Baba H, Kodera Y, Von Hoff D, Chen X, Goel A) Ann Surg 2022 Jan 01;275(1):e229-e237 19 Citations |
| 1 | Eosinophil accumulation in postnatal lung is specific to the primary septation phase of development. (Loffredo LF, Coden ME, Jeong BM, Walker MT, Anekalla KR, Doan TC, Rodriguez R, Browning M, Nam K, Lee JJ, Abdala-Valencia H, Berdnikovs S) Sci Rep 2020 Mar 10;10(1):4425 26 Citations |
| 1 | RNA Sequencing Analysis of Induced Pluripotent Stem Cell-Derived Cardiomyocytes From Congenital Heart Disease Patients. (Kitani T, Tian L, Zhang T, Itzhaki I, Zhang JZ, Ma N, Liu C, Rhee JW, Romfh AW, Lui GK, Wu JC) Circ Res 2020 Mar 27;126(7):923-925 20 Citations |
| 2 | Integrative pathway enrichment analysis of multivariate omics data. (Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, PCAWG Consortium) Nat Commun 2020 Feb 05;11(1):735 153 Citations |
| 1 | Dysregulation of autophagy-related lncRNAs in peripheral blood of coronary artery disease patients. (Ebadi N, Ghafouri-Fard S, Taheri M, Arsang-Jang S, Parsa SA, Omrani MD) Eur J Pharmacol 2020 Jan 15;867:172852 16 Citations |
| 1 | Transcriptome-based molecular staging of human stem cell-derived retinal organoids uncovers accelerated photoreceptor differentiation by 9-cis retinal. (Kaya KD, Chen HY, Brooks MJ, Kelley RA, Shimada H, Nagashima K, de Val N, Drinnan CT, Gieser L, Kruczek K, Erceg S, Li T, Lukovic D, Adlakha YK, Welby E, Swaroop A) Mol Vis 2019;25:663-678 65 Citations |
| 1 | AAV-Mediated Gene Transfer Restores a Normal Muscle Transcriptome in a Canine Model of X-Linked Myotubular Myopathy. (Dupont JB, Guo J, Renaud-Gabardos E, Poulard K, Latournerie V, Lawlor MW, Grange RW, Gray JT, Buj-Bello A, Childers MK, Mack DL) Mol Ther 2020 Feb 05;28(2):382-393 21 Citations |
| 1 | Integrating multi-platform genomic datasets for kidney renal clear cell carcinoma subtyping using stacked denoising autoencoders. (Gu T, Zhao X) Sci Rep 2019 Nov 13;9(1):16668 10 Citations |
| 1 | Effects of Spaceflight on Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Structure and Function. (Wnorowski A, Sharma A, Chen H, Wu H, Shao NY, Sayed N, Liu C, Countryman S, Stodieck LS, Rubins KH, Wu SM, Lee PHU, Wu JC) Stem Cell Reports 2019 Dec 10;13(6):960-969 82 Citations |
| 1 | Integrated pan-cancer gene expression and drug sensitivity analysis reveals SLFN11 mRNA as a solid tumor biomarker predictive of sensitivity to DNA-damaging chemotherapy. (Shee K, Wells JD, Jiang A, Miller TW) PLoS One 2019;14(11):e0224267 38 Citations |
| 2 | Genome-wide differential expression profiling of lncRNAs and mRNAs associated with early diabetic cardiomyopathy. (Pant T, Dhanasekaran A, Bai X, Zhao M, Thorp EB, Forbess JM, Bosnjak ZJ, Ge ZD) Sci Rep 2019 Oct 25;9(1):15345 27 Citations |
| 1 | A Transcriptionally Definable Subgroup of Triple-Negative Breast and Ovarian Cancer Samples Shows Sensitivity to HSP90 Inhibition. (Shee K, Wells JD, Ung M, Hampsch RA, Traphagen NA, Yang W, Liu SC, Zeldenrust MA, Wang L, Kalari KR, Yu J, Boughey JC, Demidenko E, Kettenbach AN, Cheng C, Goetz MP, Miller TW) Clin Cancer Res 2020 Jan 01;26(1):159-170 1 Citation |
| 1 | CXCR5+PD-1+ follicular helper CD8 T cells control B cell tolerance. (Chen Y, Yu M, Zheng Y, Fu G, Xin G, Zhu W, Luo L, Burns R, Li QZ, Dent AL, Zhu N, Cui W, Malherbe L, Wen R, Wang D) Nat Commun 2019 Sep 27;10(1):4415 67 Citations |
| 1 | Prediction and management of CAD risk based on genetic stratification. (Roberts R, Campillo A, Schmitt M) Trends Cardiovasc Med 2020 Aug;30(6):328-334 18 Citations |
| 1 | Nicotinamide nucleotide transhydrogenase expression analysis in multiple sclerosis patients. (Eftekharian MM, Taheri M, Arsang-Jang S, Komaki A, Ghafouri-Fard S) Int J Neurosci 2019 Dec;129(12):1256-1260 5 Citations |
| 1 | A single-cell transcriptome atlas of the adult human retina. (Lukowski SW, Lo CY, Sharov AA, Nguyen Q, Fang L, Hung SS, Zhu L, Zhang T, Grünert U, Nguyen T, Senabouth A, Jabbari JS, Welby E, Sowden JC, Waugh HS, Mackey A, Pollock G, Lamb TD, Wang PY, Hewitt AW, Gillies MC, Powell JE, Wong RC) EMBO J 2019 Sep 16;38(18):e100811 226 Citations |
| 1 | Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models. (Olson RJ, Hopp K, Wells H, Smith JM, Furtado J, Constans MM, Escobar DL, Geurts AM, Torres VE, Harris PC) J Am Soc Nephrol 2019 Nov;30(11):2113-2127 41 Citations |
| 1 | Abrupt involution induces inflammation, estrogenic signaling, and hyperplasia linking lack of breastfeeding with increased risk of breast cancer. (Basree MM, Shinde N, Koivisto C, Cuitino M, Kladney R, Zhang J, Stephens J, Palettas M, Zhang A, Kim HK, Acero-Bedoya S, Trimboli A, Stover DG, Ludwig T, Ganju R, Weng D, Shields P, Freudenheim J, Leone GW, Sizemore GM, Majumder S, Ramaswamy B) Breast Cancer Res 2019 Jul 17;21(1):80 36 Citations |
| 6 | The p52 isoform of SHC1 is a key driver of breast cancer initiation. (Wright KD, Miller BS, El-Meanawy S, Tsaih SW, Banerjee A, Geurts AM, Sheinin Y, Sun Y, Kalyanaraman B, Rui H, Flister MJ, Sorokin A) Breast Cancer Res 2019 Jun 15;21(1):74 40 Citations |
| 1 | Regionally specified human pluripotent stem cell-derived astrocytes exhibit different molecular signatures and functional properties. (Bradley RA, Shireman J, McFalls C, Choi J, Canfield SG, Dong Y, Liu K, Lisota B, Jones JR, Petersen A, Bhattacharyya A, Palecek SP, Shusta EV, Kendziorski C, Zhang SC) Development 2019 Jul 08;146(13) 54 Citations |
| 1 | Expression analysis of vitamin D receptor-associated lncRNAs in epileptic patients. (Mazdeh M, Zamani M, Eftekharian MM, Komaki A, Arsang-Jang S, Taheri M, Ghafouri-Fard S) Metab Brain Dis 2019 Oct;34(5):1457-1465 18 Citations |
| 3 | Neuronatin is a modifier of estrogen receptor-positive breast cancer incidence and outcome. (Plasterer C, Tsaih SW, Peck AR, Chervoneva I, O'Meara C, Sun Y, Lemke A, Murphy D, Smith J, Ran S, Kovatich AJ, Hooke JA, Shriver CD, Hu H, Mitchell EP, Bergom C, Joshi A, Auer P, Prokop J, Rui H, Flister MJ) Breast Cancer Res Treat 2019 Aug;177(1):77-91 5 Citations |
| 1 | Clinical Relevance of Noncoding Adenosine-to-Inosine RNA Editing in Multiple Human Cancers. (Gu T, Fu AQ, Bolt MJ, White KP) JCO Clin Cancer Inform 2019 Jun;3:1-8 10 Citations |
| 1 | Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity. (Jarjour NN, Schwarzkopf EA, Bradstreet TR, Shchukina I, Lin CC, Huang SC, Lai CW, Cook ME, Taneja R, Stappenbeck TS, Randolph GJ, Artyomov MN, Urban JF Jr, Edelson BT) Nat Immunol 2019 Jun;20(6):687-700 61 Citations |
| 1 | Diagnosing and Managing Sepsis by Probing the Host Response to Infection: Advances, Opportunities, and Challenges. (Gunsolus IL, Sweeney TE, Liesenfeld O, Ledeboer NA) J Clin Microbiol 2019 Jul;57(7) 53 Citations |
| 1 | Molecular profiling of cancer patients enables personalized combination therapy: the I-PREDICT study. (Sicklick JK, Kato S, Okamura R, Schwaederle M, Hahn ME, Williams CB, De P, Krie A, Piccioni DE, Miller VA, Ross JS, Benson A, Webster J, Stephens PJ, Lee JJ, Fanta PT, Lippman SM, Leyland-Jones B, Kurzrock R) Nat Med 2019 May;25(5):744-750 547 Citations |
| 1 | Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial. (Rodon J, Soria JC, Berger R, Miller WH, Rubin E, Kugel A, Tsimberidou A, Saintigny P, Ackerstein A, Braña I, Loriot Y, Afshar M, Miller V, Wunder F, Bresson C, Martini JF, Raynaud J, Mendelsohn J, Batist G, Onn A, Tabernero J, Schilsky RL, Lazar V, Lee JJ, Kurzrock R) Nat Med 2019 May;25(5):751-758 448 Citations |
| 3 | Identification of a Rat Mammary Tumor Risk Locus That Is Syntenic with the Commonly Amplified 8q12.1 and 8q22.1 Regions in Human Breast Cancer Patients. (Plasterer C, Tsaih SW, Lemke A, Schilling R, Dwinell M, Rau A, Auer P, Rui H, Flister MJ) G3 (Bethesda) 2019 May 07;9(5):1739-1743 6 Citations |
| 1 | RNA Splicing of the BHC80 Gene Contributes to Neuroendocrine Prostate Cancer Progression. (Li Y, Xie N, Chen R, Lee AR, Lovnicki J, Morrison EA, Fazli L, Zhang Q, Musselman CA, Wang Y, Huang J, Gleave ME, Collins C, Dong X) Eur Urol 2019 Aug;76(2):157-166 24 Citations |
| 2 | Mature IgDlow/- B cells maintain tolerance by promoting regulatory T cell homeostasis. (Ray A, Khalil MI, Pulakanti KL, Burns RT, Gurski CJ, Basu S, Wang D, Rao S, Dittel BN) Nat Commun 2019 Jan 14;10(1):190 27 Citations |
| 1 | Metaplastic breast cancers: Genomic profiling, mutational burden and tumor-infiltrating lymphocytes. (Tray N, Taff J, Singh B, Suh J, Ngo N, Kwa M, Troxel AB, Chae YK, Kurzrock R, Patel SP, Sharon E, Denkert C, Ross JS, Adams S) Breast 2019 Apr;44:29-32 48 Citations |
| 1 | Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. (Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, Braun T, Novak E, Bauman L, Collins MH, Mo A, Rosen MJ, Bonkowski E, Gotman N, Marquis A, Nistel M, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, Leleiko NS, Heyman MB, Grifiths AM, Patel AS, Noe JD, Aronow BJ, Kugathasan S, Walters TD, Gibson G, Thomas SD, Mollen K, Shen-Orr S, Huttenhower C, Xavier RJ, Hyams JS, Denson LA) Nat Commun 2019 Jan 03;10(1):38 255 Citations |
| 1 | Exploring drivers of gene expression in the Cancer Genome Atlas. (Rau A, Flister M, Rui H, Auer PL) Bioinformatics 2019 Jan 01;35(1):62-68 21 Citations |
| 2 | Microarray analysis of long non-coding RNA and mRNA expression profiles in diabetic cardiomyopathy using human induced pluripotent stem cell-derived cardiomyocytes. (Pant T, Mishra MK, Bai X, Ge ZD, Bosnjak ZJ, Dhanasekaran A) Diab Vasc Dis Res 2019 Jan;16(1):57-68 16 Citations |
| 1 | Upregulation of FOXM1 leads to diminished drug sensitivity in myeloma. (Gu C, Jing X, Holman C, Sompallae R, Zhan F, Tricot G, Yang Y, Janz S) BMC Cancer 2018 Nov 21;18(1):1152 24 Citations |
| 1 | Analysis of Circulating Tumor DNA and Clinical Correlates in Patients with Esophageal, Gastroesophageal Junction, and Gastric Adenocarcinoma. (Kato S, Okamura R, Baumgartner JM, Patel H, Leichman L, Kelly K, Sicklick JK, Fanta PT, Lippman SM, Kurzrock R) Clin Cancer Res 2018 Dec 15;24(24):6248-6256 106 Citations |
| 1 | MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis. (Ma T, Huo Z, Kuo A, Zhu L, Fang Z, Zeng X, Lin CW, Liu S, Wang L, Liu P, Rahman T, Chang LC, Kim S, Li J, Park Y, Song C, Oesterreich S, Sibille E, Tseng GC) Bioinformatics 2019 May 01;35(9):1597-1599 26 Citations |
| 1 | Signaling network between the dysregulated expression of microRNAs and mRNAs in propofol-induced developmental neurotoxicity in mice. (Jiang C, Logan S, Yan Y, Inagaki Y, Arzua T, Ma P, Lu S, Bosnjak ZJ, Bai X) Sci Rep 2018 Sep 21;8(1):14172 16 Citations |
| 1 | Robust interferon signature and suppressed tissue repair gene expression in synovial tissue from patients with postinfectious, Borrelia burgdorferi-induced Lyme arthritis. (Lochhead RB, Arvikar SL, Aversa JM, Sadreyev RI, Strle K, Steere AC) Cell Microbiol 2019 Feb;21(2):e12954 38 Citations |
| 1 | Strategy for Tumor-Selective Disruption of Androgen Receptor Function in the Spectrum of Prostate Cancer. (Rosati R, Polin L, Ducker C, Li J, Bao X, Selvakumar D, Kim S, Xhabija B, Larsen M, McFall T, Huang Y, Kidder BL, Fribley A, Saxton J, Kakuta H, Shaw P, Ratnam M) Clin Cancer Res 2018 Dec 15;24(24):6509-6522 15 Citations |
| 1 | Epigenetic and Transcriptomic Profiling of Mammary Gland Development and Tumor Models Disclose Regulators of Cell State Plasticity. (Dravis C, Chung CY, Lytle NK, Herrera-Valdez J, Luna G, Trejo CL, Reya T, Wahl GM) Cancer Cell 2018 Sep 10;34(3):466-482.e6 102 Citations |
| 1 | Expression of TNF- and HNRNPL-related Immunoregulatory Long Non-coding RNA (THRIL) in Acute Myeloid Leukemia: Is There Any Correlation? (Sayad A, Hajifathali A, Omrani MD, Arsang-Jang S, Hamidieh AA, Taheri M) Iran J Allergy Asthma Immunol 2018 Jun;17(3):274-280 11 Citations |
| 1 | The impact of pharmacokinetic gene profiles across human cancers. (Zimmermann MT, Therneau TM, Kocher JA) BMC Cancer 2018 May 21;18(1):577 3 Citations |
| 2 | A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. (Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R) Cancer Cell 2018 Apr 09;33(4):690-705.e9 475 Citations |
| 3 | Transcriptomic analysis reveals inflammatory and metabolic pathways that are regulated by renal perfusion pressure in the outer medulla of Dahl-S rats. (Evans LC, Dayton A, Yang C, Liu P, Kurth T, Ahn KW, Komas S, Stingo FC, Laud PW, Vannucci M, Liang M, Cowley AW Jr) Physiol Genomics 2018 Jun 01;50(6):440-447 12 Citations |
| 1 | A hedgehog pathway-dependent gene signature is associated with poor clinical outcomes in Luminal A breast cancer. (Rudolph M, Sizemore ST, Lu Y, Teng KY, Basree MM, Reinbolt R, Timmers CD, Leone G, Ostrowski MC, Majumder S, Ramaswamy B) Breast Cancer Res Treat 2018 Jun;169(3):457-467 8 Citations |
| 1 | P300 Acetyltransferase Mediates Stiffness-Induced Activation of Hepatic Stellate Cells Into Tumor-Promoting Myofibroblasts. (Dou C, Liu Z, Tu K, Zhang H, Chen C, Yaqoob U, Wang Y, Wen J, van Deursen J, Sicard D, Tschumperlin D, Zou H, Huang WC, Urrutia R, Shah VH, Kang N) Gastroenterology 2018 Jun;154(8):2209-2221.e14 194 Citations |
| 1 | Clinical and Genomic Correlates of Neutrophil Reactive Oxygen Species Production in Pediatric Patients With Crohn's Disease. (Denson LA, Jurickova I, Karns R, Shaw KA, Cutler DJ, Okou DT, Dodd A, Quinn K, Mondal K, Aronow BJ, Haberman Y, Linn A, Price A, Bezold R, Lake K, Jackson K, Walters TD, Griffiths A, Baldassano RN, Noe JD, Hyams JS, Crandall WV, Kirschner BS, Heyman MB, Snapper S, Guthery SL, Dubinsky MC, Leleiko NS, Otley AR, Xavier RJ, Stevens C, Daly MJ, Zwick ME, Kugathasan S) Gastroenterology 2018 Jun;154(8):2097-2110 75 Citations |
| 1 | Long ncRNA Landscape in the Ileum of Treatment-Naive Early-Onset Crohn Disease. (Haberman Y, BenShoshan M, Di Segni A, Dexheimer PJ, Braun T, Weiss B, Walters TD, Baldassano RN, Noe JD, Markowitz J, Rosh J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Kellermayer R, Patel A, Otley A, Steiner SJ, Gulati AS, Guthery SL, LeLeiko N, Moulton D, Kirschner BS, Snapper S, Avivi C, Barshack I, Oliva-Hemker M, Cohen SA, Keljo DJ, Ziring D, Anikster Y, Aronow B, Hyams JS, Kugathasan S, Denson LA) Inflamm Bowel Dis 2018 Jan 18;24(2):346-360 56 Citations |
| 1 | Transcriptomic signatures of cellular and humoral immune responses in older adults after seasonal influenza vaccination identified by data-driven clustering. (Voigt EA, Grill DE, Zimmermann MT, Simon WL, Ovsyannikova IG, Kennedy RB, Poland GA) Sci Rep 2018 Jan 15;8(1):739 24 Citations |
| 4 | Modulation of the diet and gastrointestinal microbiota normalizes systemic inflammation and β-cell chemokine expression associated with autoimmune diabetes susceptibility. (Henschel AM, Cabrera SM, Kaldunski ML, Jia S, Geoffrey R, Roethle MF, Lam V, Chen YG, Wang X, Salzman NH, Hessner MJ) PLoS One 2018;13(1):e0190351 25 Citations |
| 1 | Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle-Related Transcription and Attenuated Androgen Response. (Horning AM, Wang Y, Lin CK, Louie AD, Jadhav RR, Hung CN, Wang CM, Lin CL, Kirma NB, Liss MA, Kumar AP, Sun L, Liu Z, Chao WT, Wang Q, Jin VX, Chen CL, Huang TH) Cancer Res 2018 Feb 15;78(4):853-864 91 Citations |
| 1 | HDACis (class I), cancer stem cell, and phytochemicals: Cancer therapy and prevention implications. (Bayat S, Shekari Khaniani M, Choupani J, Alivand MR, Mansoori Derakhshan S) Biomed Pharmacother 2018 Jan;97:1445-1453 38 Citations |
| 1 | Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells. (Welby E, Lakowski J, Di Foggia V, Budinger D, Gonzalez-Cordero A, Lun ATL, Epstein M, Patel A, Cuevas E, Kruczek K, Naeem A, Minneci F, Hubank M, Jones DT, Marioni JC, Ali RR, Sowden JC) Stem Cell Reports 2017 Dec 12;9(6):1898-1915 85 Citations |
| 1 | Ottogi Inhibits Wnt/β-catenin Signaling by Regulating Cell Membrane Trafficking of Frizzled8. (Kim HT, Lee MS, Jeong YM, Ro H, Kim DI, Shin YH, Kim JE, Hwang KS, Choi JH, Bahn M, Lee JJ, Lee SH, Bae YK, Lee JS, Choi JK, Kim NS, Yeo CY, Kim CH) Sci Rep 2017 Oct 16;7(1):13278 4 Citations |
| 1 | Gene Expression Profiling and Heterogeneity of Nonspecific Orbital Inflammation Affecting the Lacrimal Gland. (Rosenbaum JT, Choi D, Harrington CA, Wilson DJ, Grossniklaus HE, Sibley CH, Salek SS, Ng JD, Dailey RA, Steele EA, Hayek B, Craven CM, Edward DP, Maktabi AMY, Al Hussain H, White VA, Dolman PJ, Czyz CN, Foster JA, Harris GJ, Bee YS, Tse DT, Alabiad CR, Dubovy SR, Kazim M, Selva D, Yeatts RP, Korn BS, Kikkawa DO, Silkiss RZ, Sivak-Callcott JA, Stauffer P, Planck SR) JAMA Ophthalmol 2017 Nov 01;135(11):1156-1162 33 Citations |
| 1 | Functional characterization of zebrafish orthologs of the human Beta 3-Glucosyltransferase B3GLCT gene mutated in Peters Plus Syndrome. (Weh E, Takeuchi H, Muheisen S, Haltiwanger RS, Semina EV) PLoS One 2017;12(9):e0184903 14 Citations |
| 1 | Analysis of the whole transcriptome from gingivo-buccal squamous cell carcinoma reveals deregulated immune landscape and suggests targets for immunotherapy. (Singh R, De Sarkar N, Sarkar S, Roy R, Chattopadhyay E, Ray A, Biswas NK, Maitra A, Roy B) PLoS One 2017;12(9):e0183606 6 Citations |
| 1 | Patient- and Cell Type-Specific Heterogeneity of Metformin Response. (Asiedu MK, Barron M, Aubry MC, Wigle DA) Basic Clin Pharmacol Toxicol 2018 Feb;122(2):214-222 14 Citations |
| 1 | The diversity in the expression profile of caveolin II transcripts, considering its new transcript in breast cancer. (Ariana M, Arabi N, Pornour M, Vaseghi H, Ganji SM, Alivand MR, Salari M, Akbari ME) J Cell Biochem 2018 Feb;119(2):2168-2178 11 Citations |
| 3 | Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer. (Palatnik A, Ye S, Kendziorski C, Iden M, Zigman JS, Hessner MJ, Rader JS) PLoS One 2017;12(8):e0181242 10 Citations |
| 1 | Platelets reduce anoikis and promote metastasis by activating YAP1 signaling. (Haemmerle M, Taylor ML, Gutschner T, Pradeep S, Cho MS, Sheng J, Lyons YM, Nagaraja AS, Dood RL, Wen Y, Mangala LS, Hansen JM, Rupaimoole R, Gharpure KM, Rodriguez-Aguayo C, Yim SY, Lee JS, Ivan C, Hu W, Lopez-Berestein G, Wong ST, Karlan BY, Levine DA, Liu J, Afshar-Kharghan V, Sood AK) Nat Commun 2017 Aug 21;8(1):310 218 Citations |
| 1 | Unconventional MAPK-GSK-3β Pathway Behind Atypical Epithelial-Mesenchymal Transition In Hepatocellular Carcinoma. (Parveen S, Vedagiri D, Nair HG, Parthasarathy H, Harshan KH) Sci Rep 2017 Aug 18;7(1):8842 4 Citations |
| 1 | Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease. (Marigorta UM, Denson LA, Hyams JS, Mondal K, Prince J, Walters TD, Griffiths A, Noe JD, Crandall WV, Rosh JR, Mack DR, Kellermayer R, Heyman MB, Baker SS, Stephens MC, Baldassano RN, Markowitz JF, Kim MO, Dubinsky MC, Cho J, Aronow BJ, Kugathasan S, Gibson G) Nat Genet 2017 Oct;49(10):1517-1521 132 Citations |
| 1 | Frequency of mononuclear diploid cardiomyocytes underlies natural variation in heart regeneration. (Patterson M, Barske L, Van Handel B, Rau CD, Gan P, Sharma A, Parikh S, Denholtz M, Huang Y, Yamaguchi Y, Shen H, Allayee H, Crump JG, Force TI, Lien CL, Makita T, Lusis AJ, Kumar SR, Sucov HM) Nat Genet 2017 Sep;49(9):1346-1353 260 Citations |
| 1 | Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. (Leung W, Shaffer CD, Chen EJ, Quisenberry TJ, Ko K, Braverman JM, Giarla TC, Mortimer NT, Reed LK, Smith ST, Robic S, McCartha SR, Perry DR, Prescod LM, Sheppard ZA, Saville KJ, McClish A, Morlock EA, Sochor VR, Stanton B, Veysey-White IC, Revie D, Jimenez LA, Palomino JJ, Patao MD, Patao SM, Himelblau ET, Campbell JD, Hertz AL, McEvilly MF, Wagner AR, Youngblom J, Bedi B, Bettincourt J, Duso E, Her M, Hilton W, House S, Karimi M, Kumimoto K, Lee R, Lopez D, Odisho G, Prasad R, Robbins HL, Sandhu T, Selfridge T, Tsukashima K, Yosif H, Kokan NP, Britt L, Zoellner A, Spana EP, Chlebina BT, Chong I, Friedman H, Mammo DA, Ng CL, Nikam VS, Schwartz NU, Xu TQ, Burg MG, Batten SM, Corbeill LM, Enoch E, Ensign JJ, Franks ME, Haiker B, Ingles JA, Kirkland LD, Lorenz-Guertin JM, Matthews J, Mittig CM, Monsma N, Olson KJ, Perez-Aragon G, Ramic A, Ramirez JR, Scheiber C, Schneider PA, Schultz DE, Simon M, Spencer E, Wernette AC, Wykle ME, Zavala-Arellano E, McDonald MJ, Ostby K, Wendland P, DiAngelo JR, Ceasrine AM, Cox AH, Docherty JEB, Gingras RM, Grieb SM, Pavia MJ, Personius CL, Polak GL, Beach DL, Cerritos HL, Horansky EA, Sharif KA, Moran R, Parrish S, Bickford K, Bland J, Broussard J, Campbell K, Deibel KE, Forka R, Lemke MC, Nelson MB, O'Keeffe C, Ramey SM, Schmidt L, Villegas P, Jones CJ, Christ SL, Mamari S, Rinaldi AS, Stity G, Hark AT, Scheuerman M, Silver Key SC, McRae BD, Haberman AS, Asinof S, Carrington H, Drumm K, Embry T, McGuire R, Miller-Foreman D, Rosen S, Safa N, Schultz D, Segal M, Shevin Y, Svoronos P, Vuong T, Skuse G, Paetkau DW, Bridgman RK, Brown CM, Carroll AR, Gifford FM, Gillespie JB, Herman SE, Holtcamp KL, Host MA, Hussey G, Kramer DM, Lawrence JQ, Martin MM, Niemiec EN, O'Reilly AP, Pahl OA, Quintana G, Rettie EAS, Richardson TL, Rodriguez AE, Rodriguez MO, Schiraldi L, Smith JJ, Sugrue KF, Suriano LJ, Takach KE, Vasquez AM, Velez X, Villafuerte EJ, Vives LT, Zellmer VR, Hauke J, Hauser CR, Barker K, Cannon L, Parsamian P, Parsons S, Wichman Z, Bazinet CW, Johnson DE, Bangura A, Black JA, Chevee V, Einsteen SA, Hilton SK, Kollmer M, Nadendla R, Stamm J, Fafara-Thompson AE, Gygi AM, Ogawa EE, Van Camp M, Kocsisova Z, Leatherman JL, Modahl CM, Rubin MR, Apiz-Saab SS, Arias-Mejias SM, Carrion-Ortiz CF, Claudio-Vazquez PN, Espada-Green DM, Feliciano-Camacho M, Gonzalez-Bonilla KM, Taboas-Arroyo M, Vargas-Franco D, Montañez-Gonzalez R, Perez-Otero J, Rivera-Burgos M, Rivera-Rosario FJ, Eisler HL, Alexander J, Begley SK, Gabbard D, Allen RJ, Aung WY, Barshop WD, Boozalis A, Chu VP, Davis JS, Duggal RN, Franklin R, Gavinski K, Gebreyesus H, Gong HZ, Greenstein RA, Guo AD, Hanson C, Homa KE, Hsu SC, Huang Y, Huo L, Jacobs S, Jia S, Jung KL, Wai-Chee Kong S, Kroll MR, Lee BM, Lee PF, Levine KM, Li AS, Liu C, Liu MM, Lousararian AP, Lowery PB, Mallya AP, Marcus JE, Ng PC, Nguyen HP, Patel R, Precht H, Rastogi S, Sarezky JM, Schefkind A, Schultz MB, Shen D, Skorupa T, Spies NC, Stancu G, Vivian Tsang HM, Turski AL, Venkat R, Waldman LE, Wang K, Wang T, Wei JW, Wu DY, Xiong DD, Yu J, Zhou K, McNeil GP, Fernandez RW, Menzies PG, Gu T, Buhler J, Mardis ER, Elgin SCR) G3 (Bethesda) 2017 Aug 07;7(8):2439-2460 16 Citations |
| 1 | Cytomegalovirus Late Protein pUL31 Alters Pre-rRNA Expression and Nuclear Organization during Infection. (Westdorp KN, Sand A, Moorman NJ, Terhune SS) J Virol 2017 Sep 15;91(18) 15 Citations |
| 1 | Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns. (Tang B, Zhou Y, Wang CM, Huang TH, Jin VX) Sci Rep 2017 Jun 15;7(1):3626 18 Citations |
| 1 | Discovery of Stromal Regulatory Networks that Suppress Ras-Sensitized Epithelial Cell Proliferation. (Liu H, Dowdle JA, Khurshid S, Sullivan NJ, Bertos N, Rambani K, Mair M, Daniel P, Wheeler E, Tang X, Toth K, Lause M, Harrigan ME, Eiring K, Sullivan C, Sullivan MJ, Chang SW, Srivastava S, Conway JS, Kladney R, McElroy J, Bae S, Lu Y, Tofigh A, Saleh SMI, Fernandez SA, Parvin JD, Coppola V, Macrae ER, Majumder S, Shapiro CL, Yee LD, Ramaswamy B, Hallett M, Ostrowski MC, Park M, Chamberlin HM, Leone G) Dev Cell 2017 May 22;41(4):392-407.e6 25 Citations |
| 1 | Oscillating expression of interleukin-16 in multiple myeloma is associated with proliferation, clonogenic growth, and PI3K/NFKB/MAPK activation. (Templin J, Atanackovic D, Hasche D, Radhakrishnan SV, Luetkens T) Oncotarget 2017 Jul 25;8(30):49253-49263 13 Citations |
| 1 | Manufacturing Differences Affect Human Bone Marrow Stromal Cell Characteristics and Function: Comparison of Production Methods and Products from Multiple Centers. (Liu S, de Castro LF, Jin P, Civini S, Ren J, Reems JA, Cancelas J, Nayak R, Shaw G, O'Brien T, McKenna DH, Armant M, Silberstein L, Gee AP, Hei DJ, Hematti P, Kuznetsov SA, Robey PG, Stroncek DF) Sci Rep 2017 Apr 27;7:46731 69 Citations |
| 1 | Targeting the PIM protein kinases for the treatment of a T-cell acute lymphoblastic leukemia subset. (Padi SKR, Luevano LA, An N, Pandey R, Singh N, Song JH, Aster JC, Yu XZ, Mehrotra S, Kraft AS) Oncotarget 2017 May 02;8(18):30199-30216 37 Citations |
| 1 | Overexpression of EZH2 in multiple myeloma is associated with poor prognosis and dysregulation of cell cycle control. (Pawlyn C, Bright MD, Buros AF, Stein CK, Walters Z, Aronson LI, Mirabella F, Jones JR, Kaiser MF, Walker BA, Jackson GH, Clarke PA, Bergsagel PL, Workman P, Chesi M, Morgan GJ, Davies FE) Blood Cancer J 2017 Mar 31;7(3):e549 89 Citations |
| 1 | The regulation of tumor-suppressive microRNA, miR-126, in chronic lymphocytic leukemia. (Guinn D, Lehman A, Fabian C, Yu L, Maddocks K, Andritsos LA, Jones JA, Flynn JM, Jaglowski SM, Woyach JA, Byrd JC, Johnson AJ) Cancer Med 2017 Apr;6(4):778-787 15 Citations |
| 2 | Gene expression profiling of patient-derived pancreatic cancer xenografts predicts sensitivity to the BET bromodomain inhibitor JQ1: implications for individualized medicine efforts. (Bian B, Bigonnet M, Gayet O, Loncle C, Maignan A, Gilabert M, Moutardier V, Garcia S, Turrini O, Delpero JR, Giovannini M, Grandval P, Gasmi M, Ouaissi M, Secq V, Poizat F, Nicolle R, Blum Y, Marisa L, Rubis M, Raoul JL, Bradner JE, Qi J, Lomberk G, Urrutia R, Saul A, Dusetti N, Iovanna J) EMBO Mol Med 2017 Apr;9(4):482-497 61 Citations |
| 1 | Longitudinal analysis of hepatic transcriptome and serum metabolome demonstrates altered lipid metabolism following the onset of hyperglycemia in spontaneously diabetic biobreeding rats. (Regnell SE, Hessner MJ, Jia S, Åkesson L, Stenlund H, Moritz T, La Torre D, Lernmark Å) PLoS One 2017;12(2):e0171372 5 Citations |
| 1 | Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes. (Gao S, Wolanyk N, Chen Y, Jia S, Hessner MJ, Wang X) BMC Med Genomics 2017 Jan 31;10(1):7 7 Citations |
| 3 | Cancer cell chemokines direct chemotaxis of activated stellate cells in pancreatic ductal adenocarcinoma. (Roy I, Boyle KA, Vonderhaar EP, Zimmerman NP, Gorse E, Mackinnon AC, Hwang RF, Franco-Barraza J, Cukierman E, Tsai S, Evans DB, Dwinell MB) Lab Invest 2017 Mar;97(3):302-317 28 Citations |
| 1 | Pathway-Structured Predictive Model for Cancer Survival Prediction: A Two-Stage Approach. (Zhang X, Li Y, Akinyemiju T, Ojesina AI, Buckhaults P, Liu N, Xu B, Yi N) Genetics 2017 Jan;205(1):89-100 33 Citations |
| 1 | Tgif1 and Tgif2 Repress Expression of the RabGAP Evi5l. (Anderson AE, Taniguchi K, Hao Y, Melhuish TA, Shah A, Turner SD, Sutherland AE, Wotton D) Mol Cell Biol 2017 Mar 01;37(5) 14 Citations |
| 1 | Dickkopf-1 promotes hematopoietic regeneration via direct and niche-mediated mechanisms. (Himburg HA, Doan PL, Quarmyne M, Yan X, Sasine J, Zhao L, Hancock GV, Kan J, Pohl KA, Tran E, Chao NJ, Harris JR, Chute JP) Nat Med 2017 Jan;23(1):91-99 68 Citations |
| 1 | Targeted myocardial gene expression in failing hearts by RNA sequencing. (Dhar K, Moulton AM, Rome E, Qiu F, Kittrell J, Raichlin E, Zolty R, Um JY, Moulton MJ, Basma H, Anderson DR, Eudy JD, Lowes BD) J Transl Med 2016 Nov 25;14(1):327 23 Citations |
| 1 | Role of CTGF in Sensitivity to Hyperthermia in Ovarian and Uterine Cancers. (Hatakeyama H, Wu SY, Lyons YA, Pradeep S, Wang W, Huang Q, Court KA, Liu T, Nie S, Rodriguez-Aguayo C, Shen F, Huang Y, Hisamatsu T, Mitamura T, Jennings N, Shim J, Dorniak PL, Mangala LS, Petrillo M, Petyuk VA, Schepmoes AA, Shukla AK, Torres-Lugo M, Lee JS, Rodland KD, Fagotti A, Lopez-Berestein G, Li C, Sood AK) Cell Rep 2016 Nov 01;17(6):1621-1631 22 Citations |
| 1 | E2F-2 Promotes Nuclear Condensation and Enucleation of Terminally Differentiated Erythroblasts. (Swartz KL, Wood SN, Murthy T, Ramirez O, Qin G, Pillai MM, Rao S, Minella AC) Mol Cell Biol 2017 Jan 01;37(1) 25 Citations |
| 1 | Growth and maturation of heart valves leads to changes in endothelial cell distribution, impaired function, decreased metabolism and reduced cell proliferation. (Anstine LJ, Bobba C, Ghadiali S, Lincoln J) J Mol Cell Cardiol 2016 Nov;100:72-82 34 Citations |
| 1 | Radiogenomics: A systems biology approach to understanding genetic risk factors for radiotherapy toxicity? (Herskind C, Talbot CJ, Kerns SL, Veldwijk MR, Rosenstein BS, West CM) Cancer Lett 2016 Nov 01;382(1):95-109 68 Citations |
| 2 | The cohesin subunit Rad21 is a negative regulator of hematopoietic self-renewal through epigenetic repression of Hoxa7 and Hoxa9. (Fisher JB, Peterson J, Reimer M, Stelloh C, Pulakanti K, Gerbec ZJ, Abel AM, Strouse JM, Strouse C, McNulty M, Malarkannan S, Crispino JD, Milanovich S, Rao S) Leukemia 2017 Mar;31(3):712-719 49 Citations |
| 1 | Transcriptome Profiling of Patient-Specific Human iPSC-Cardiomyocytes Predicts Individual Drug Safety and Efficacy Responses In Vitro. (Matsa E, Burridge PW, Yu KH, Ahrens JH, Termglinchan V, Wu H, Liu C, Shukla P, Sayed N, Churko JM, Shao N, Woo NA, Chao AS, Gold JD, Karakikes I, Snyder MP, Wu JC) Cell Stem Cell 2016 Sep 01;19(3):311-25 132 Citations |
| 1 | Whole Transcriptome Profiling Identifies CD93 and Other Plasma Cell Survival Factor Genes Associated with Measles-Specific Antibody Response after Vaccination. (Haralambieva IH, Zimmermann MT, Ovsyannikova IG, Grill DE, Oberg AL, Kennedy RB, Poland GA) PLoS One 2016;11(8):e0160970 23 Citations |
| 1 | Genomic Landscape of Malignant Mesotheliomas. (Kato S, Tomson BN, Buys TP, Elkin SK, Carter JL, Kurzrock R) Mol Cancer Ther 2016 Oct;15(10):2498-2507 73 Citations |
| 1 | Potential cerebral malaria therapy: intramuscular arteether and vitamin D co-administration. (Dwivedi H, Singh SK, Chauhan BS, Gunjan S, Tripathi R) Parasitology 2016 Oct;143(12):1557-68 14 Citations |
| 1 | Predisposition to treatment response in major depressive episode: A peripheral blood gene coexpression network analysis. (Belzeaux R, Lin CW, Ding Y, Bergon A, Ibrahim EC, Turecki G, Tseng G, Sibille E) J Psychiatr Res 2016 Oct;81:119-26 28 Citations |
| 2 | Asymmetric Cancer Hallmarks in Breast Tumors on Different Sides of the Body. (Campoy EM, Laurito SR, Branham MT, Urrutia G, Mathison A, Gago F, Orozco J, Urrutia R, Mayorga LS, Roqué M) PLoS One 2016;11(7):e0157416 7 Citations |
| 1 | Transcriptional signatures of influenza A/H1N1-specific IgG memory-like B cell response in older individuals. (Haralambieva IH, Ovsyannikova IG, Kennedy RB, Zimmermann MT, Grill DE, Oberg AL, Poland GA) Vaccine 2016 Jul 25;34(34):3993-4002 28 Citations |
| 1 | Cell-Cycle Gene Alterations in 4,864 Tumors Analyzed by Next-Generation Sequencing: Implications for Targeted Therapeutics. (Helsten T, Kato S, Schwaederle M, Tomson BN, Buys TP, Elkin SK, Carter JL, Kurzrock R) Mol Cancer Ther 2016 Jul;15(7):1682-90 38 Citations |
| 1 | Cancer Therapy Directed by Comprehensive Genomic Profiling: A Single Center Study. (Wheler JJ, Janku F, Naing A, Li Y, Stephen B, Zinner R, Subbiah V, Fu S, Karp D, Falchook GS, Tsimberidou AM, Piha-Paul S, Anderson R, Ke D, Miller V, Yelensky R, Lee JJ, Hong DS, Kurzrock R) Cancer Res 2016 Jul 01;76(13):3690-701 204 Citations |
| 1 | MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis. (Kim S, Lin CW, Tseng GC) Bioinformatics 2016 Jul 01;32(13):1966-73 35 Citations |
| 1 | Transcription Profile in Sporadic Multiple Symmetric Lipomatosis Reveals Differential Expression at the Level of Adipose Tissue-Derived Stem Cells. (Prantl L, Schreml J, Gehmert S, Klein S, Bai X, Zeitler K, Schreml S, Alt E, Gehmert S, Felthaus O) Plast Reconstr Surg 2016 Apr;137(4):1181-1190 22 Citations |
| 2 | Mechanosensory and ATP Release Deficits following Keratin14-Cre-Mediated TRPA1 Deletion Despite Absence of TRPA1 in Murine Keratinocytes. (Zappia KJ, Garrison SR, Palygin O, Weyer AD, Barabas ME, Lawlor MW, Staruschenko A, Stucky CL) PLoS One 2016;11(3):e0151602 24 Citations |
| 2 | Ndufc2 Gene Inhibition Is Associated With Mitochondrial Dysfunction and Increased Stroke Susceptibility in an Animal Model of Complex Human Disease. (Rubattu S, Di Castro S, Schulz H, Geurts AM, Cotugno M, Bianchi F, Maatz H, Hummel O, Falak S, Stanzione R, Marchitti S, Scarpino S, Giusti B, Kura A, Gensini GF, Peyvandi F, Mannucci PM, Rasura M, Sciarretta S, Dwinell MR, Hubner N, Volpe M) J Am Heart Assoc 2016 Feb 17;5(2) 47 Citations |
| 1 | Precision Oncology: The UC San Diego Moores Cancer Center PREDICT Experience. (Schwaederle M, Parker BA, Schwab RB, Daniels GA, Piccioni DE, Kesari S, Helsten TL, Bazhenova LA, Romero J, Fanta PT, Lippman SM, Kurzrock R) Mol Cancer Ther 2016 Apr;15(4):743-52 159 Citations |
| 1 | Variants in TRIM22 That Affect NOD2 Signaling Are Associated With Very-Early-Onset Inflammatory Bowel Disease. (Li Q, Lee CH, Peters LA, Mastropaolo LA, Thoeni C, Elkadri A, Schwerd T, Zhu J, Zhang B, Zhao Y, Hao K, Dinarzo A, Hoffman G, Kidd BA, Murchie R, Al Adham Z, Guo C, Kotlarz D, Cutz E, Walters TD, Shouval DS, Curran M, Dobrin R, Brodmerkel C, Snapper SB, Klein C, Brumell JH, Hu M, Nanan R, Snanter-Nanan B, Wong M, Le Deist F, Haddad E, Roifman CM, Deslandres C, Griffiths AM, Gaskin KJ, Uhlig HH, Schadt EE, Muise AM) Gastroenterology 2016 May;150(5):1196-1207 98 Citations |
| 1 | Precision medicine: lessons learned from the SHIVA trial. (Tsimberidou AM, Kurzrock R) Lancet Oncol 2015 Dec;16(16):e579-80 51 Citations |
| 2 | Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis. (Li W, Turner A, Aggarwal P, Matter A, Storvick E, Arnett DK, Broeckel U) BMC Genomics 2015 Dec 16;16:1069 75 Citations |
| 1 | Genetic Architectures of Quantitative Variation in RNA Editing Pathways. (Gu T, Gatti DM, Srivastava A, Snyder EM, Raghupathy N, Simecek P, Svenson KL, Dotu I, Chuang JH, Keller MP, Attie AD, Braun RE, Churchill GA) Genetics 2016 Feb;202(2):787-98 18 Citations |
| 1 | NCCN Oncology Research Program's Investigator Steering Committee and NCCN Best Practices Committee Molecular Profiling Surveys. (Kurzrock R, Colevas AD, Olszanski A, Akerley W, Arteaga CL, Carson WE 3rd, Clark JW, DiPersio JF, Ettinger DS, Morgan RJ Jr, Schwartzberg LS, Venook AP, Gocke CD, Tait J, Stewart FM) J Natl Compr Canc Netw 2015 Nov;13(11):1337-46 23 Citations |
| 1 | Molecular inimitability amongst tumors: implications for precision cancer medicine in the age of personalized oncology. (Patel SP, Schwaederle M, Daniels GA, Fanta PT, Schwab RB, Shimabukuro KA, Kesari S, Piccioni DE, Bazhenova LA, Helsten TL, Lippman SM, Parker BA, Kurzrock R) Oncotarget 2015 Oct 20;6(32):32602-9 16 Citations |
| 1 | Sequence and expression variations in 23 genes involved in mitochondrial and non-mitochondrial apoptotic pathways and risk of oral leukoplakia and cancer. (Datta S, Ray A, Singh R, Mondal P, Basu A, De Sarkar N, Majumder M, Maiti G, Baral A, Jha GN, Mukhopadhyay I, Panda C, Chowdhury S, Ghosh S, Roychoudhury S, Roy B) Mitochondrion 2015 Nov;25:28-33 12 Citations |
| 1 | The FGFR Landscape in Cancer: Analysis of 4,853 Tumors by Next-Generation Sequencing. (Helsten T, Elkin S, Arthur E, Tomson BN, Carter J, Kurzrock R) Clin Cancer Res 2016 Jan 01;22(1):259-67 670 Citations |
| 1 | The Role of the Immune Response in the Pathogenesis of Thyroid Eye Disease: A Reassessment. (Rosenbaum JT, Choi D, Wong A, Wilson DJ, Grossniklaus HE, Harrington CA, Dailey RA, Ng JD, Steele EA, Czyz CN, Foster JA, Tse D, Alabiad C, Dubovy S, Parekh PK, Harris GJ, Kazim M, Patel PJ, White VA, Dolman PJ, Edward DP, Alkatan HM, Al Hussain H, Selva D, Yeatts RP, Korn BS, Kikkawa DO, Stauffer P, Planck SR) PLoS One 2015;10(9):e0137654 19 Citations |
| 4 | Low Socioeconomic Status, Adverse Gene Expression Profiles, and Clinical Outcomes in Hematopoietic Stem Cell Transplant Recipients. (Knight JM, Rizzo JD, Logan BR, Wang T, Arevalo JM, Ma J, Cole SW) Clin Cancer Res 2016 Jan 01;22(1):69-78 76 Citations |
| 1 | Genomic landscape of salivary gland tumors. (Kato S, Elkin SK, Schwaederle M, Tomson BN, Helsten T, Carter JL, Kurzrock R) Oncotarget 2015 Sep 22;6(28):25631-45 46 Citations |
| 4 | Gene Expression in Experimental Aortic Coarctation and Repair: Candidate Genes for Therapeutic Intervention? (LaDisa JF Jr, Bozdag S, Olson J, Ramchandran R, Kersten JR, Eddinger TJ) PLoS One 2015;10(7):e0133356 8 Citations |
| 1 | Genomic Profiling of Cancers of Unknown Primary Site: The Next Steps. (Cobain EF, Chinnaiyan AM, Kurzrock R, Baker LH) JAMA Oncol 2015 Jul;1(4):542 1 Citation |
| 1 | Orbital pseudotumor can be a localized form of granulomatosis with polyangiitis as revealed by gene expression profiling. (Rosenbaum JT, Choi D, Wilson DJ, Grossniklaus HE, Harrington CA, Sibley CH, Dailey RA, Ng JD, Steele EA, Czyz CN, Foster JA, Tse D, Alabiad C, Dubovy S, Parekh PK, Harris GJ, Kazim M, Patel PJ, White VA, Dolman PJ, Korn BS, Kikkawa DO, Edward DP, Alkatan HM, al-Hussain H, Yeatts RP, Selva D, Stauffer P, Planck SR) Exp Mol Pathol 2015 Oct;99(2):271-8 35 Citations |
| 1 | Nebulin deficiency in adult muscle causes sarcomere defects and muscle-type-dependent changes in trophicity: novel insights in nemaline myopathy. (Li F, Buck D, De Winter J, Kolb J, Meng H, Birch C, Slater R, Escobar YN, Smith JE 3rd, Yang L, Konhilas J, Lawlor MW, Ottenheijm C, Granzier HL) Hum Mol Genet 2015 Sep 15;24(18):5219-33 57 Citations |
| 1 | Microarray Determination of the Expression of Drug Transporters in Humans and Animal Species Used for the Investigation of Nasal Absorption. (Al-Ghabeish M, Scheetz T, Assem M, Donovan MD) Mol Pharm 2015 Aug 03;12(8):2742-54 21 Citations |
| 1 | HTR7 Mediates Serotonergic Acute and Chronic Itch. (Morita T, McClain SP, Batia LM, Pellegrino M, Wilson SR, Kienzler MA, Lyman K, Olsen AS, Wong JF, Stucky CL, Brem RB, Bautista DM) Neuron 2015 Jul 01;87(1):124-38 155 Citations |
| 1 | deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies. (Chu C, Fang Z, Hua X, Yang Y, Chen E, Cowley AW Jr, Liang M, Liu P, Lu Y) BMC Genomics 2015 Jun 13;16(1):455 15 Citations |
| 1 | Fibrosis, gene expression and orbital inflammatory disease. (Rosenbaum JT, Choi D, Wilson DJ, Grossniklaus HE, Harrington CA, Dailey RA, Ng JD, Steele EA, Czyz CN, Foster JA, Tse D, Alabiad C, Dubovy S, Parekh P, Harris GJ, Kazim M, Patel P, White V, Dolman P, Edward DP, Alkatan H, Al Hussain H, Selva D, Yeatts P, Korn B, Kikkawa D, Stauffer P, Planck SR) Br J Ophthalmol 2015 Oct;99(10):1424-9 32 Citations |
| 1 | Renal systems biology of patients with systemic inflammatory response syndrome. (Tsalik EL, Willig LK, Rice BJ, van Velkinburgh JC, Mohney RP, McDunn JE, Dinwiddie DL, Miller NA, Mayer ES, Glickman SW, Jaehne AK, Glew RH, Sopori ML, Otero RM, Harrod KS, Cairns CB, Fowler VG, Rivers EP, Woods CW, Kingsmore SF, Langley RJ) Kidney Int 2015 Oct;88(4):804-14 48 Citations |
| 1 | MicroRNA-135b Regulates Leucine Zipper Tumor Suppressor 1 in Cutaneous Squamous Cell Carcinoma. (Olasz EB, Seline LN, Schock AM, Duncan NE, Lopez A, Lazar J, Flister MJ, Lu Y, Liu P, Sokumbi O, Harwood CA, Proby CM, Neuburg M, Lazarova Z) PLoS One 2015;10(5):e0125412 32 Citations |
| 1 | Challenges in initiating and conducting personalized cancer therapy trials: perspectives from WINTHER, a Worldwide Innovative Network (WIN) Consortium trial. (Rodon J, Soria JC, Berger R, Batist G, Tsimberidou A, Bresson C, Lee JJ, Rubin E, Onn A, Schilsky RL, Miller WH, Eggermont AM, Mendelsohn J, Lazar V, Kurzrock R) Ann Oncol 2015 Aug;26(8):1791-8 68 Citations |
| 1 | Hypermethylation of BDNF and SST Genes in the Orbital Frontal Cortex of Older Individuals: A Putative Mechanism for Declining Gene Expression with Age. (McKinney BC, Lin CW, Oh H, Tseng GC, Lewis DA, Sibille E) Neuropsychopharmacology 2015 Oct;40(11):2604-13 25 Citations |
| 1 | Parallel Gene Expression Changes in Sarcoidosis Involving the Lacrimal Gland, Orbital Tissue, or Blood. (Rosenbaum JT, Choi D, Wilson DJ, Grossniklaus HE, Harrington CA, Sibley CH, Dailey RA, Ng JD, Steele EA, Czyz CN, Foster JA, Tse D, Alabiad C, Dubovy S, Parekh P, Harris GJ, Kazim M, Patel P, White V, Dolman P, Korn BS, Kikkawa D, Edward DP, Alkatan H, Al-Hussain H, Yeatts RP, Selva D, Stauffer P, Planck SR) JAMA Ophthalmol 2015 Jul;133(7):770-7 32 Citations |
| 1 | The tumor virus landscape of AIDS-related lymphomas. (Arvey A, Ojesina AI, Pedamallu CS, Ballon G, Jung J, Duke F, Leoncini L, De Falco G, Bressman E, Tam W, Chadburn A, Meyerson M, Cesarman E) Blood 2015 May 14;125(20):e14-22 67 Citations |
| 1 | Tumor profiling of gastric and esophageal carcinoma reveal different treatment options. (Miura JT, Xiu J, Thomas J, George B, Carron BR, Tsai S, Johnston FM, Turaga KK, Gamblin TC) Cancer Biol Ther 2015;16(5):764-9 20 Citations |
| 2 | Mesenchymal condensation-dependent accumulation of collagen VI stabilizes organ-specific cell fates during embryonic tooth formation. (Mammoto T, Mammoto A, Jiang A, Jiang E, Hashmi B, Ingber DE) Dev Dyn 2015 Jun;244(6):713-23 23 Citations |
| 1 | A survey of computational methods in transcriptome-wide alternative splicing analysis. (Wang J, Ye Z, Huang TH, Shi H, Jin V) Biomol Concepts 2015 Mar;6(1):59-66 17 Citations |
| 1 | Up-regulation of silent information regulator 2 (Sir2) is associated with amphotericin B resistance in clinical isolates of Leishmania donovani. (Purkait B, Singh R, Wasnik K, Das S, Kumar A, Paine M, Dikhit M, Singh D, Sardar AH, Ghosh AK, Das P) J Antimicrob Chemother 2015 May;70(5):1343-56 29 Citations |
| 1 | Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity. (Chiu IM, Barrett LB, Williams EK, Strochlic DE, Lee S, Weyer AD, Lou S, Bryman GS, Roberson DP, Ghasemlou N, Piccoli C, Ahat E, Wang V, Cobos EJ, Stucky CL, Ma Q, Liberles SD, Woolf CJ) Elife 2014 Dec 19;3 192 Citations |
| 1 | Targeted exon sequencing in Usher syndrome type I. (Bujakowska KM, Consugar M, Place E, Harper S, Lena J, Taub DG, White J, Navarro-Gomez D, Weigel DiFranco C, Farkas MH, Gai X, Berson EL, Pierce EA) Invest Ophthalmol Vis Sci 2014 Dec 02;55(12):8488-96 20 Citations |
| 3 | Maternal diet during gestation and lactation modifies the severity of salt-induced hypertension and renal injury in Dahl salt-sensitive rats. (Geurts AM, Mattson DL, Liu P, Cabacungan E, Skelton MM, Kurth TM, Yang C, Endres BT, Klotz J, Liang M, Cowley AW Jr) Hypertension 2015 Feb;65(2):447-55 60 Citations |
| 1 | Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. (Verma H, Kumar R, Oldach P, Sangwan N, Khurana JP, Gilbert JA, Lal R) BMC Genomics 2014 Nov 23;15(1):1014 67 Citations |
| 1 | Genetic interference with peroxisome proliferator-activated receptor γ in smooth muscle enhances myogenic tone in the cerebrovasculature via A Rho kinase-dependent mechanism. (De Silva TM, Ketsawatsomkron P, Pelham C, Sigmund CD, Faraci FM) Hypertension 2015 Feb;65(2):345-51 21 Citations |
| 1 | Estrogen receptor expression is high but is of lower intensity in tubular carcinoma than in well-differentiated invasive ductal carcinoma. (Jorns JM, Thomas DG, Healy PN, Daignault S, Vickery TL, Snider JE, Mardis ER, Davies SR, Ellis MJ, Visscher DW) Arch Pathol Lab Med 2014 Nov;138(11):1507-13 5 Citations |
| 1 | Unique molecular landscapes in cancer: implications for individualized, curated drug combinations. (Wheler J, Lee JJ, Kurzrock R) Cancer Res 2014 Dec 15;74(24):7181-4 58 Citations |
| 2 | RNA expression profiling of human iPSC-derived cardiomyocytes in a cardiac hypertrophy model. (Aggarwal P, Turner A, Matter A, Kattman SJ, Stoddard A, Lorier R, Swanson BJ, Arnett DK, Broeckel U) PLoS One 2014;9(9):e108051 45 Citations |
| 1 | Study familial hypertrophic cardiomyopathy using patient-specific induced pluripotent stem cells. (Han L, Li Y, Tchao J, Kaplan AD, Lin B, Li Y, Mich-Basso J, Lis A, Hassan N, London B, Bett GC, Tobita K, Rasmusson RL, Yang L) Cardiovasc Res 2014 Nov 01;104(2):258-69 165 Citations |
| 1 | A quest for miRNA bio-marker: a track back approach from gingivo buccal cancer to two different types of precancers. (De Sarkar N, Roy R, Mitra JK, Ghose S, Chakraborty A, Paul RR, Mukhopadhyay I, Roy B) PLoS One 2014;9(8):e104839 32 Citations |
| 1 | Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. (Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA) J Clin Invest 2014 Aug;124(8):3617-33 423 Citations |
| 1 | Intermittent cold exposure enhances fat accumulation in mice. (Yoo HS, Qiao L, Bosco C, Leong LH, Lytle N, Feng GS, Chi NW, Shao J) PLoS One 2014;9(5):e96432 34 Citations |
| 1 | Outcomes in patients with relapsed or refractory multiple myeloma in a phase I study of everolimus in combination with lenalidomide. (Yee AJ, Hari P, Marcheselli R, Mahindra AK, Cirstea DD, Scullen TA, Burke JN, Rodig SJ, Hideshima T, Laubach JP, Ghobrial IM, Schlossman RL, Munshi NC, Anderson KC, Weller EA, Richardson PG, Raje NS) Br J Haematol 2014 Aug;166(3):401-9 41 Citations |
| 3 | Characterization of biological pathways associated with a 1.37 Mbp genomic region protective of hypertension in Dahl S rats. (Cowley AW Jr, Moreno C, Jacob HJ, Peterson CB, Stingo FC, Ahn KW, Liu P, Vannucci M, Laud PW, Reddy P, Lazar J, Evans L, Yang C, Kurth T, Liang M) Physiol Genomics 2014 Jun 01;46(11):398-410 18 Citations |
| 1 | A conserved BDNF, glutamate- and GABA-enriched gene module related to human depression identified by coexpression meta-analysis and DNA variant genome-wide association studies. (Chang LC, Jamain S, Lin CW, Rujescu D, Tseng GC, Sibille E) PLoS One 2014;9(3):e90980 86 Citations |
| 1 | A critical evaluation of microRNA biomarkers in non-neoplastic disease. (Haider BA, Baras AS, McCall MN, Hertel JA, Cornish TC, Halushka MK) PLoS One 2014;9(2):e89565 143 Citations |
| 1 | Characterization of Toll-like receptors 1-10 in spotted hyenas. (Flies AS, Maksimoski MT, Mansfield LS, Weldele ML, Holekamp KE) Vet Res Commun 2014 Jun;38(2):165-70 8 Citations |
| 1 | Diubiquitin (Ubd) is a susceptibility gene for virus-triggered autoimmune diabetes in rats. (Cort L, Habib M, Eberwine RA, Hessner MJ, Mordes JP, Blankenhorn EP) Genes Immun 2014;15(3):168-75 14 Citations |
| 1 | Expression profiling of the RPE in zebrafish smarca4 mutant revealed altered signals that potentially affect RPE and retinal differentiation. (Zhang L, Ma P, Collery R, Trowbridge S, Zhang M, Zhong W, Leung YF) Mol Vis 2014;20:56-72 5 Citations |
| 1 | Integrated metagenomic and metatranscriptomic analyses of microbial communities in the meso- and bathypelagic realm of north pacific ocean. (Wu J, Gao W, Johnson RH, Zhang W, Meldrum DR) Mar Drugs 2013 Oct 11;11(10):3777-801 41 Citations |
| 1 | Identification of candidate B-lymphoma genes by cross-species gene expression profiling. (Tompkins VS, Han SS, Olivier A, Syrbu S, Bair T, Button A, Jacobus L, Wang Z, Lifton S, Raychaudhuri P, Morse HC 3rd, Weiner G, Link B, Smith BJ, Janz S) PLoS One 2013;8(10):e76889 11 Citations |
| 2 | Mmp17b is essential for proper neural crest cell migration in vivo. (Leigh NR, Schupp MO, Li K, Padmanabhan V, Gastonguay A, Wang L, Chun CZ, Wilkinson GA, Ramchandran R) PLoS One 2013;8(10):e76484 37 Citations |
| 1 | Characteristics of microRNAs enriched in specific cell types and primary tissue types in solid organs. (Kriegel AJ, Liu Y, Liu P, Baker MA, Hodges MR, Hua X, Liang M) Physiol Genomics 2013 Dec 01;45(23):1144-56 29 Citations |
| 1 | The Cancer Genome Atlas Pan-Cancer analysis project. (Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM) Nat Genet 2013 Oct;45(10):1113-20 6367 Citations |
| 1 | A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation. (Boccuto L, Aoki K, Flanagan-Steet H, Chen CF, Fan X, Bartel F, Petukh M, Pittman A, Saul R, Chaubey A, Alexov E, Tiemeyer M, Steet R, Schwartz CE) Hum Mol Genet 2014 Jan 15;23(2):418-33 150 Citations |
| 1 | Comparison of breast and abdominal adipose tissue mesenchymal stromal/stem cells in support of proliferation of breast cancer cells. (Kim J, Escalante LE, Dollar BA, Hanson SE, Hematti P) Cancer Invest 2013 Oct;31(8):550-4 22 Citations |
| 1 | Ets2 in tumor fibroblasts promotes angiogenesis in breast cancer. (Wallace JA, Li F, Balakrishnan S, Cantemir-Stone CZ, Pecot T, Martin C, Kladney RD, Sharma SM, Trimboli AJ, Fernandez SA, Yu L, Rosol TJ, Stromberg PC, Lesurf R, Hallett M, Park M, Leone G, Ostrowski MC) PLoS One 2013;8(8):e71533 35 Citations |
| 1 | MicroRNA-31 predicts the presence of lymph node metastases and survival in patients with lung adenocarcinoma. (Meng W, Ye Z, Cui R, Perry J, Dedousi-Huebner V, Huebner A, Wang Y, Li B, Volinia S, Nakanishi H, Kim T, Suh SS, Ayers LW, Ross P, Croce CM, Chakravarti A, Jin VX, Lautenschlaeger T) Clin Cancer Res 2013 Oct 01;19(19):5423-33 101 Citations |
| 1 | Overexpression of microRNA-1 promotes cardiomyocyte commitment from human cardiovascular progenitors via suppressing WNT and FGF signaling pathways. (Lu TY, Lin B, Li Y, Arora A, Han L, Cui C, Coronnello C, Sheng Y, Benos PV, Yang L) J Mol Cell Cardiol 2013 Oct;63:146-54 63 Citations |
| 1 | Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. (Hou P, Li Y, Zhang X, Liu C, Guan J, Li H, Zhao T, Ye J, Yang W, Liu K, Ge J, Xu J, Zhang Q, Zhao Y, Deng H) Science 2013 Aug 09;341(6146):651-4 1193 Citations |
| 1 | Antagonistic regulation by the transcription factors C/EBPα and MITF specifies basophil and mast cell fates. (Qi X, Hong J, Chaves L, Zhuang Y, Chen Y, Wang D, Chabon J, Graham B, Ohmori K, Li Y, Huang H) Immunity 2013 Jul 25;39(1):97-110 121 Citations |
| 1 | Molecular profiling and the reclassification of cancer: divide and conquer. (Munoz J, Swanton C, Kurzrock R) Am Soc Clin Oncol Educ Book 2013:127-34 29 Citations |
| 1 | Genome-wide microRNA expression profiling in idiopathic non-obstructive azoospermia: significant up-regulation of miR-141, miR-429 and miR-7-1-3p. (Wu W, Qin Y, Li Z, Dong J, Dai J, Lu C, Guo X, Zhao Y, Zhu Y, Zhang W, Hang B, Sha J, Shen H, Xia Y, Hu Z, Wang X) Hum Reprod 2013 Jul;28(7):1827-36 129 Citations |
| 1 | A new method for stranded whole transcriptome RNA-seq. (Miller DF, Yan PS, Buechlein A, Rodriguez BA, Yilmaz AS, Goel S, Lin H, Collins-Burow B, Rhodes LV, Braun C, Pradeep S, Rupaimoole R, Dalkilic M, Sood AK, Burow ME, Tang H, Huang TH, Liu Y, Rusch DB, Nephew KP) Methods 2013 Sep 15;63(2):126-34 40 Citations |
| 1 | Profiling bortezomib resistance identifies secondary therapies in a mouse myeloma model. (Stessman HA, Baughn LB, Sarver A, Xia T, Deshpande R, Mansoor A, Walsh SA, Sunderland JJ, Dolloff NG, Linden MA, Zhan F, Janz S, Myers CL, Van Ness BG) Mol Cancer Ther 2013 Jun;12(6):1140-50 63 Citations |
| 1 | RAS/MEK-independent gene expression reveals BMP2-related malignant phenotypes in the Nf1-deficient MPNST. (Sun D, Haddad R, Kraniak JM, Horne SD, Tainsky MA) Mol Cancer Res 2013 Jun;11(6):616-27 12 Citations |
| 1 | QTL-based association analyses reveal novel genes influencing pleiotropy of metabolic syndrome (MetS). (Zhang Y, Kent JW Jr, Olivier M, Ali O, Broeckel U, Abdou RM, Dyer TD, Comuzzie A, Curran JE, Carless MA, Rainwater DL, Göring HH, Blangero J, Kissebah AH) Obesity (Silver Spring) 2013 Oct;21(10):2099-111 14 Citations |
| 1 | Gene expression-based classifiers identify Staphylococcus aureus infection in mice and humans. (Ahn SH, Tsalik EL, Cyr DD, Zhang Y, van Velkinburgh JC, Langley RJ, Glickman SW, Cairns CB, Zaas AK, Rivers EP, Otero RM, Veldman T, Kingsmore SF, Lucas J, Woods CW, Ginsburg GS, Fowler VG Jr) PLoS One 2013;8(1):e48979 51 Citations |
| 1 | Evolution of the Stx2-encoding prophage in persistent bovine Escherichia coli O157:H7 strains. (Park D, Stanton E, Ciezki K, Parrell D, Bozile M, Pike D, Forst SA, Jeong KC, Ivanek R, Döpfer D, Kaspar CW) Appl Environ Microbiol 2013 Mar;79(5):1563-72 21 Citations |
| 1 | Human induced pluripotent stem cell-derived models to investigate human cytomegalovirus infection in neural cells. (D'Aiuto L, Di Maio R, Heath B, Raimondi G, Milosevic J, Watson AM, Bamne M, Parks WT, Yang L, Lin B, Miki T, Mich-Basso JD, Arav-Boger R, Sibille E, Sabunciyan S, Yolken R, Nimgaonkar V) PLoS One 2012;7(11):e49700 63 Citations |
| 1 | Molecular control of axon growth: insights from comparative gene profiling and high-throughput screening. (Blackmore MG) Int Rev Neurobiol 2012;105:39-70 32 Citations |
| 1 | Increased dietary intake of vitamin A promotes aortic valve calcification in vivo. (Huk DJ, Hammond HL, Kegechika H, Lincoln J) Arterioscler Thromb Vasc Biol 2013 Feb;33(2):285-93 30 Citations |
| 4 | Increased proliferative cells in the medullary thick ascending limb of the loop of Henle in the Dahl salt-sensitive rat. (Yang C, Stingo FC, Ahn KW, Liu P, Vannucci M, Laud PW, Skelton M, O'Connor P, Kurth T, Ryan RP, Moreno C, Tsaih SW, Patone G, Hummel O, Jacob HJ, Liang M, Cowley AW Jr) Hypertension 2013 Jan;61(1):208-15 18 Citations |
| 1 | Metabolomics of cerebrospinal fluid from humans treated for rabies. (O'Sullivan A, Willoughby RE, Mishchuk D, Alcarraz B, Cabezas-Sanchez C, Condori RE, David D, Encarnacion R, Fatteh N, Fernandez J, Franka R, Hedderwick S, McCaughey C, Ondrush J, Paez-Martinez A, Rupprecht C, Velasco-Villa A, Slupsky CM) J Proteome Res 2013 Jan 04;12(1):481-90 51 Citations |
| 1 | Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes. (Tang B, Hsu HK, Hsu PY, Bonneville R, Chen SS, Huang TH, Jin VX) Sci Rep 2012;2:875 25 Citations |
| 1 | TRPA1 is functionally expressed primarily by IB4-binding, non-peptidergic mouse and rat sensory neurons. (Barabas ME, Kossyreva EA, Stucky CL) PLoS One 2012;7(10):e47988 92 Citations |
| 2 | Biobreeding rat islets exhibit reduced antioxidative defense and N-acetyl cysteine treatment delays type 1 diabetes. (Bogdani M, Henschel AM, Kansra S, Fuller JM, Geoffrey R, Jia S, Kaldunski ML, Pavletich S, Prosser S, Chen YG, Lernmark A, Hessner MJ) J Endocrinol 2013 Feb;216(2):111-23 25 Citations |
| 1 | Regulation of glycan structures in murine embryonic stem cells: combined transcript profiling of glycan-related genes and glycan structural analysis. (Nairn AV, Aoki K, dela Rosa M, Porterfield M, Lim JM, Kulik M, Pierce JM, Wells L, Dalton S, Tiemeyer M, Moremen KW) J Biol Chem 2012 Nov 02;287(45):37835-56 89 Citations |
| 1 | Genetic variants in Arhgef11 are associated with kidney injury in the Dahl salt-sensitive rat. (Williams JM, Johnson AC, Stelloh C, Dreisbach AW, Franceschini N, Regner KR, Townsend RR, Roman RJ, Garrett MR) Hypertension 2012 Nov;60(5):1157-68 31 Citations |
| 1 | Transcriptional signatures as a disease-specific and predictive inflammatory biomarker for type 1 diabetes. (Levy H, Wang X, Kaldunski M, Jia S, Kramer J, Pavletich SJ, Reske M, Gessel T, Yassai M, Quasney MW, Dahmer MK, Gorski J, Hessner MJ) Genes Immun 2012 Dec;13(8):593-604 60 Citations |
| 2 | PPARγ regulates resistance vessel tone through a mechanism involving RGS5-mediated control of protein kinase C and BKCa channel activity. (Ketsawatsomkron P, Lorca RA, Keen HL, Weatherford ET, Liu X, Pelham CJ, Grobe JL, Faraci FM, England SK, Sigmund CD) Circ Res 2012 Nov 09;111(11):1446-58 54 Citations |
| 1 | Coex-Rank: An approach incorporating co-expression information for combined analysis of microarray data. (Cai J, Keen HL, Sigmund CD, Casavant TL) J Integr Bioinform 2012 Jul 30;9(1):208 3 Citations |
| 1 | The feed-forward loop between YB-1 and MYC is essential for multiple myeloma cell survival. (Bommert KS, Effenberger M, Leich E, Küspert M, Murphy D, Langer C, Moll R, Janz S, Mottok A, Weissbach S, Rosenwald A, Bargou R, Bommert K) Leukemia 2013 Feb;27(2):441-50 46 Citations |
| 1 | The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum. (Feagin JE, Harrell MI, Lee JC, Coe KJ, Sands BH, Cannone JJ, Tami G, Schnare MN, Gutell RR) PLoS One 2012;7(6):e38320 100 Citations |
| 1 | Profiling of residual breast cancers after neoadjuvant chemotherapy identifies DUSP4 deficiency as a mechanism of drug resistance. (Balko JM, Cook RS, Vaught DB, Kuba MG, Miller TW, Bhola NE, Sanders ME, Granja-Ingram NM, Smith JJ, Meszoely IM, Salter J, Dowsett M, Stemke-Hale K, González-Angulo AM, Mills GB, Pinto JA, Gómez HL, Arteaga CL) Nat Med 2012 Jul;18(7):1052-9 230 Citations |
| 3 | Role of genetic modifiers in an orthologous rat model of ARPKD. (O'Meara CC, Hoffman M, Sweeney WE Jr, Tsaih SW, Xiao B, Jacob HJ, Avner ED, Moreno C) Physiol Genomics 2012 Aug 01;44(15):741-53 23 Citations |
| 3 | Requirements for growth and IL-10 expression of highly purified human T regulatory cells. (Bonacci B, Edwards B, Jia S, Williams CB, Hessner MJ, Gauld SB, Verbsky JW) J Clin Immunol 2012 Oct;32(5):1118-28 11 Citations |
| 1 | Collaborative Ocular Oncology Group report number 1: prospective validation of a multi-gene prognostic assay in uveal melanoma. (Onken MD, Worley LA, Char DH, Augsburger JJ, Correa ZM, Nudleman E, Aaberg TM Jr, Altaweel MM, Bardenstein DS, Finger PT, Gallie BL, Harocopos GJ, Hovland PG, McGowan HD, Milman T, Mruthyunjaya P, Simpson ER, Smith ME, Wilson DJ, Wirostko WJ, Harbour JW) Ophthalmology 2012 Aug;119(8):1596-603 435 Citations |
| 2 | Atypical E2F repressors and activators coordinate placental development. (Ouseph MM, Li J, Chen HZ, Pécot T, Wenzel P, Thompson JC, Comstock G, Chokshi V, Byrne M, Forde B, Chong JL, Huang K, Machiraju R, de Bruin A, Leone G) Dev Cell 2012 Apr 17;22(4):849-62 84 Citations |
| 2 | Intestinal microbiota as novel biomarkers of prior radiation exposure. (Lam V, Moulder JE, Salzman NH, Dubinsky EA, Andersen GL, Baker JE) Radiat Res 2012 May;177(5):573-83 69 Citations |
| 1 | Identification of vascular and hematopoietic genes downstream of etsrp by deep sequencing in zebrafish. (Gomez G, Lee JH, Veldman MB, Lu J, Xiao X, Lin S) PLoS One 2012;7(3):e31658 25 Citations |
| 1 | Obesity-insulin targeted genes in the 3p26-25 region in human studies and LG/J and SM/J mice. (Kraja AT, Lawson HA, Arnett DK, Borecki IB, Broeckel U, de las Fuentes L, Hunt SC, Province MA, Cheverud J, Rao DC) Metabolism 2012 Aug;61(8):1129-41 11 Citations |
| 1 | Identification of prostate-enriched proteins by in-depth proteomic analyses of expressed prostatic secretions in urine. (Principe S, Kim Y, Fontana S, Ignatchenko V, Nyalwidhe JO, Lance RS, Troyer DA, Alessandro R, Semmes OJ, Kislinger T, Drake RR, Medin JA) J Proteome Res 2012 Apr 06;11(4):2386-96 68 Citations |
| 5 | Human gene copy number spectra analysis in congenital heart malformations. (Tomita-Mitchell A, Mahnke DK, Struble CA, Tuffnell ME, Stamm KD, Hidestrand M, Harris SE, Goetsch MA, Simpson PM, Bick DP, Broeckel U, Pelech AN, Tweddell JS, Mitchell ME) Physiol Genomics 2012 May 01;44(9):518-41 91 Citations |
| 1 | Myocardial alternative RNA splicing and gene expression profiling in early stage hypoplastic left heart syndrome. (Ricci M, Xu Y, Hammond HL, Willoughby DA, Nathanson L, Rodriguez MM, Vatta M, Lipshultz SE, Lincoln J) PLoS One 2012;7(1):e29784 27 Citations |
| 1 | Pathway-specific analysis of gene expression data identifies the PI3K/Akt pathway as a novel therapeutic target in cervical cancer. (Schwarz JK, Payton JE, Rashmi R, Xiang T, Jia Y, Huettner P, Rogers BE, Yang Q, Watson M, Rader JS, Grigsby PW) Clin Cancer Res 2012 Mar 01;18(5):1464-71 98 Citations |
| 1 | Differential expression--the next generation and beyond. (Auer PL, Srivastava S, Doerge RW) Brief Funct Genomics 2012 Jan;11(1):57-62 25 Citations |
| 2 | Reprogramming of the tumour microenvironment by stromal PTEN-regulated miR-320. (Bronisz A, Godlewski J, Wallace JA, Merchant AS, Nowicki MO, Mathsyaraja H, Srinivasan R, Trimboli AJ, Martin CK, Li F, Yu L, Fernandez SA, Pécot T, Rosol TJ, Cory S, Hallett M, Park M, Piper MG, Marsh CB, Yee LD, Jimenez RE, Nuovo G, Lawler SE, Chiocca EA, Leone G, Ostrowski MC) Nat Cell Biol 2011 Dec 18;14(2):159-67 251 Citations |
| 1 | S100A7 enhances mammary tumorigenesis through upregulation of inflammatory pathways. (Nasser MW, Qamri Z, Deol YS, Ravi J, Powell CA, Trikha P, Schwendener RA, Bai XF, Shilo K, Zou X, Leone G, Wolf R, Yuspa SH, Ganju RK) Cancer Res 2012 Feb 01;72(3):604-15 108 Citations |
| 1 | Global gene expression profiling in mouse plasma cell tumor precursor and bystander cells reveals potential intervention targets for plasma cell neoplasia. (LeGrand J, Park ES, Wang H, Gupta S, Owens JD Jr, Nelson PJ, DuBois W, Bair T, Janz S, Mushinski JF) Blood 2012 Jan 26;119(4):1018-28 6 Citations |
| 1 | Microdeletions and microduplications in patients with congenital heart disease and multiple congenital anomalies. (Goldmuntz E, Paluru P, Glessner J, Hakonarson H, Biegel JA, White PS, Gai X, Shaikh TH) Congenit Heart Dis 2011;6(6):592-602 92 Citations |
| 2 | Mechanochemical control of mesenchymal condensation and embryonic tooth organ formation. (Mammoto T, Mammoto A, Torisawa YS, Tat T, Gibbs A, Derda R, Mannix R, de Bruijn M, Yung CW, Huh D, Ingber DE) Dev Cell 2011 Oct 18;21(4):758-69 175 Citations |
| 1 | Defining the nature of human pluripotent stem cell progeny. (Patterson M, Chan DN, Ha I, Case D, Cui Y, Van Handel B, Mikkola HK, Lowry WE) Cell Res 2012 Jan;22(1):178-93 117 Citations |
| 1 | Integrated genomic analyses of ovarian carcinoma. (Cancer Genome Atlas Research Network) Nature 2011 Jun 29;474(7353):609-15 6460 Citations |
| 1 | Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice. (Leduc MS, Hageman RS, Verdugo RA, Tsaih SW, Walsh K, Churchill GA, Paigen B) J Lipid Res 2011 Sep;52(9):1672-82 22 Citations |
| 1 | The Borrelia burgdorferi integrin ligand P66 affects gene expression by human cells in culture. (LaFrance ME, Pierce JV, Antonara S, Coburn J) Infect Immun 2011 Aug;79(8):3249-61 18 Citations |
| 1 | Use of transcriptional signatures induced in lymphoid and myeloid cell lines as an inflammatory biomarker in Type 1 diabetes. (Jia S, Kaldunski M, Jailwala P, Geoffrey R, Kramer J, Wang X, Hessner MJ) Physiol Genomics 2011 Jun 15;43(11):697-709 12 Citations |
| 1 | The YaaA protein of the Escherichia coli OxyR regulon lessens hydrogen peroxide toxicity by diminishing the amount of intracellular unincorporated iron. (Liu Y, Bauer SC, Imlay JA) J Bacteriol 2011 May;193(9):2186-96 66 Citations |
| 1 | A gene expression signature from human breast cancer cells with acquired hormone independence identifies MYC as a mediator of antiestrogen resistance. (Miller TW, Balko JM, Ghazoui Z, Dunbier A, Anderson H, Dowsett M, González-Angulo AM, Mills GB, Miller WR, Wu H, Shyr Y, Arteaga CL) Clin Cancer Res 2011 Apr 01;17(7):2024-34 88 Citations |
| 1 | synMuv B proteins antagonize germline fate in the intestine and ensure C. elegans survival. (Petrella LN, Wang W, Spike CA, Rechtsteiner A, Reinke V, Strome S) Development 2011 Mar;138(6):1069-79 72 Citations |
| 1 | Responses of human endothelial cells to pathogenic and non-pathogenic Leptospira species. (Martinez-Lopez DG, Fahey M, Coburn J) PLoS Negl Trop Dis 2010 Dec 14;4(12):e918 47 Citations |
| 1 | Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data. (Gu F, Hsu HK, Hsu PY, Wu J, Ma Y, Parvin J, Huang TH, Jin VX) BMC Syst Biol 2010 Dec 17;4:170 42 Citations |
| 1 | Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling. (Gao S, Hartman JL 4th, Carter JL, Hessner MJ, Wang X) BMC Syst Biol 2010 Dec 03;4:167 8 Citations |
| 1 | Generation of iPSCs from mouse fibroblasts with a single gene, Oct4, and small molecules. (Li Y, Zhang Q, Yin X, Yang W, Du Y, Hou P, Ge J, Liu C, Zhang W, Zhang X, Wu Y, Li H, Liu K, Wu C, Song Z, Zhao Y, Shi Y, Deng H) Cell Res 2011 Jan;21(1):196-204 305 Citations |
| 1 | Characterization of soy-based changes in Wnt-frizzled signaling in prostate cancer. (Liss MA, Schlicht M, Kahler A, Fitzgerald R, Thomassi T, Degueme A, Hessner M, Datta MW) Cancer Genomics Proteomics 2010;7(5):245-52 |
| 1 | Geno-transcriptomic dissection of proteinuria in the uninephrectomized rat uncovers a molecular complexity with sexual dimorphism. (Yagil Y, Hessner M, Schulz H, Gosele C, Lebedev L, Barkalifa R, Sapojnikov M, Hubner N, Yagil C) Physiol Genomics 2010 Nov 29;42A(4):301-16 7 Citations |
| 1 | Gene and noncoding RNA regulation underlying photoreceptor protection: microarray study of dietary antioxidant saffron and photobiomodulation in rat retina. (Natoli R, Zhu Y, Valter K, Bisti S, Eells J, Stone J) Mol Vis 2010 Sep 03;16:1801-22 117 Citations |
| 1 | Tumor antigen analysis in neuroblastoma by serological interrogation of bioinformatic data. (Kohler ME, Johnson BD, Palen K, Chen QR, Khan J, Orentas RJ) Cancer Sci 2010 Nov;101(11):2316-24 6 Citations |
| 1 | Early expression of stem cell-associated genes within the CD8 compartment after treatment with a tumor vaccine. (Kohler ME, Hallett WH, Chen QR, Khan J, Johnson BD, Orentas RJ) Cell Immunol 2010;265(1):65-73 5 Citations |
| 1 | Diagnosis of partial body radiation exposure in mice using peripheral blood gene expression profiles. (Meadows SK, Dressman HK, Daher P, Himburg H, Russell JL, Doan P, Chao NJ, Lucas J, Nevins JR, Chute JP) PLoS One 2010 Jul 12;5(7):e11535 52 Citations |
| 1 | Early differential expression of oncostatin M in obstructive nephropathy. (Elbjeirami WM, Truong LD, Tawil A, Wang W, Dawson S, Lan HY, Zhang P, Garcia GE, Wayne Smith C) J Interferon Cytokine Res 2010 Jul;30(7):513-23 16 Citations |
| 1 | Use of cross species genomic profiling identifies pathways and genes differentially regulated in prostate cancer cells treated with soy protein isolates or purified genistein. (Liss MA, Schlicht M, Degueme A, Hessner M, Datta MW) Cancer Genomics Proteomics 2010;7(3):111-28 5 Citations |
| 1 | Ectopic expression of wild-type FGFR3 cooperates with MYC to accelerate development of B-cell lineage neoplasms. (Zingone A, Cultraro CM, Shin DM, Bean CM, Morse HC 3rd, Janz S, Kuehl WM) Leukemia 2010 Jun;24(6):1171-8 21 Citations |
| 1 | Elevated PIN1 expression by C/EBPalpha-p30 blocks C/EBPalpha-induced granulocytic differentiation through c-Jun in AML. (Pulikkan JA, Dengler V, Peer Zada AA, Kawasaki A, Geletu M, Pasalic Z, Bohlander SK, Ryo A, Tenen DG, Behre G) Leukemia 2010 May;24(5):914-23 47 Citations |
| 1 | Emerging regulatory paradigms for control of gene expression by 1,25-dihydroxyvitamin D3. (Pike JW, Meyer MB, Martowicz ML, Bishop KA, Lee SM, Nerenz RD, Goetsch PD) J Steroid Biochem Mol Biol 2010 Jul;121(1-2):130-5 51 Citations |
| 1 | Renal medullary microRNAs in Dahl salt-sensitive rats: miR-29b regulates several collagens and related genes. (Liu Y, Taylor NE, Lu L, Usa K, Cowley AW Jr, Ferreri NR, Yeo NC, Liang M) Hypertension 2010 Apr;55(4):974-82 227 Citations |
| 1 | An ets2-driven transcriptional program in tumor-associated macrophages promotes tumor metastasis. (Zabuawala T, Taffany DA, Sharma SM, Merchant A, Adair B, Srinivasan R, Rosol TJ, Fernandez S, Huang K, Leone G, Ostrowski MC) Cancer Res 2010 Feb 15;70(4):1323-33 110 Citations |
| 1 | A microRNA expression signature for cervical cancer prognosis. (Hu X, Schwarz JK, Lewis JS Jr, Huettner PC, Rader JS, Deasy JO, Grigsby PW, Wang X) Cancer Res 2010 Feb 15;70(4):1441-8 281 Citations |
| 1 | PepD participates in the mycobacterial stress response mediated through MprAB and SigE. (White MJ, He H, Penoske RM, Twining SS, Zahrt TC) J Bacteriol 2010 Mar;192(6):1498-510 56 Citations |
| 2 | Bioinformatic analysis of gene sets regulated by ligand-activated and dominant-negative peroxisome proliferator-activated receptor gamma in mouse aorta. (Keen HL, Halabi CM, Beyer AM, de Lange WJ, Liu X, Maeda N, Faraci FM, Casavant TL, Sigmund CD) Arterioscler Thromb Vasc Biol 2010 Mar;30(3):518-25 23 Citations |
| 1 | IL-6 and MYC collaborate in plasma cell tumor formation in mice. (Rutsch S, Neppalli VT, Shin DM, DuBois W, Morse HC 3rd, Goldschmidt H, Janz S) Blood 2010 Mar 04;115(9):1746-54 45 Citations |
| 1 | Dynamic convergence and divergence of renal genomic and biological pathways in protection from Dahl salt-sensitive hypertension. (Lu L, Li P, Yang C, Kurth T, Misale M, Skelton M, Moreno C, Roman RJ, Greene AS, Jacob HJ, Lazar J, Liang M, Cowley AW Jr) Physiol Genomics 2010 Mar 03;41(1):63-70 27 Citations |
| 1 | Erk1 and Erk2 regulate endothelial cell proliferation and migration during mouse embryonic angiogenesis. (Srinivasan R, Zabuawala T, Huang H, Zhang J, Gulati P, Fernandez S, Karlo JC, Landreth GE, Leone G, Ostrowski MC) PLoS One 2009 Dec 14;4(12):e8283 149 Citations |
| 1 | Brucella melitensis, B. neotomae and B. ovis elicit common and distinctive macrophage defense transcriptional responses. (Covert J, Mathison AJ, Eskra L, Banai M, Splitter G) Exp Biol Med (Maywood) 2009 Dec;234(12):1450-67 33 Citations |
| 3 | A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo. (Li K, Blum Y, Verma A, Liu Z, Pramanik K, Leigh NR, Chun CZ, Samant GV, Zhao B, Garnaas MK, Horswill MA, Stanhope SA, North PE, Miao RQ, Wilkinson GA, Affolter M, Ramchandran R) Blood 2010 Jan 07;115(1):133-9 140 Citations |
| 1 | Genetic analysis of xenocoumacin antibiotic production in the mutualistic bacterium Xenorhabdus nematophila. (Park D, Ciezki K, van der Hoeven R, Singh S, Reimer D, Bode HB, Forst S) Mol Microbiol 2009 Sep;73(5):938-49 75 Citations |
| 2 | Apoptosis of CD4+ CD25(high) T cells in type 1 diabetes may be partially mediated by IL-2 deprivation. (Jailwala P, Waukau J, Glisic S, Jana S, Ehlenbach S, Hessner M, Alemzadeh R, Matsuyama S, Laud P, Wang X, Ghosh S) PLoS One 2009 Aug 05;4(8):e6527 74 Citations |
| 1 | OpnS, an outer membrane porin of Xenorhabdus nematophila, confers a competitive advantage for growth in the insect host. (van der Hoeven R, Forst S) J Bacteriol 2009 Sep;191(17):5471-9 8 Citations |
| 1 | Identification of migR, a regulatory element of the Francisella tularensis live vaccine strain iglABCD virulence operon required for normal replication and trafficking in macrophages. (Buchan BW, McCaffrey RL, Lindemann SR, Allen LA, Jones BD) Infect Immun 2009 Jun;77(6):2517-29 58 Citations |
| 1 | Intramucosal distribution of WNT signaling components in human esophagus. (Ali I, Rafiee P, Zheng Y, Johnson C, Banerjee B, Haasler G, Jacob H, Shaker R) J Clin Gastroenterol 2009 Apr;43(4):327-37 11 Citations |
| 1 | Discovery and characterization of novel vascular and hematopoietic genes downstream of etsrp in zebrafish. (Gomez GA, Veldman MB, Zhao Y, Burgess S, Lin S) PLoS One 2009;4(3):e4994 41 Citations |
| 1 | Functional genomics of Enterococcus faecalis: multiple novel genetic determinants for biofilm formation in the core genome. (Ballering KS, Kristich CJ, Grindle SM, Oromendia A, Beattie DT, Dunny GM) J Bacteriol 2009 Apr;191(8):2806-14 52 Citations |
| 1 | Sequence mining and transcript profiling to explore cyst nematode parasitism. (Elling AA, Mitreva M, Gai X, Martin J, Recknor J, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ) BMC Genomics 2009 Jan 30;10:58 38 Citations |
| 1 | Chemical genomics of cancer chemopreventive dithiolethiones. (Tran QT, Xu L, Phan V, Goodwin SB, Rahman M, Jin VX, Sutter CH, Roebuck BD, Kensler TW, George EO, Sutter TR) Carcinogenesis 2009 Mar;30(3):480-6 22 Citations |
| 1 | Quorum sensing primes the oxidative stress response in the insect endosymbiont, Sodalis glossinidius. (Pontes MH, Babst M, Lochhead R, Oakeson K, Smith K, Dale C) PLoS One 2008;3(10):e3541 38 Citations |
| 1 | Identification of cold-shock protein RBM3 as a possible regulator of skeletal muscle size through expression profiling. (Dupont-Versteegden EE, Nagarajan R, Beggs ML, Bearden ED, Simpson PM, Peterson CA) Am J Physiol Regul Integr Comp Physiol 2008 Oct;295(4):R1263-73 31 Citations |
| 1 | Zebrafish as a developmental model organism for pediatric research. (Veldman MB, Lin S) Pediatr Res 2008 Nov;64(5):470-6 167 Citations |
| 1 | Global expression profiling identifies a novel biosignature for protein aggregation R120GCryAB cardiomyopathy in mice. (Rajasekaran NS, Firpo MA, Milash BA, Weiss RB, Benjamin IJ) Physiol Genomics 2008 Oct 08;35(2):165-72 26 Citations |
| 1 | Aberrant expression of oncogenic and tumor-suppressive microRNAs in cervical cancer is required for cancer cell growth. (Wang X, Tang S, Le SY, Lu R, Rader JS, Meyers C, Zheng ZM) PLoS One 2008 Jul 02;3(7):e2557 658 Citations |
| 1 | Differential display identifies overexpression of the USP36 gene, encoding a deubiquitinating enzyme, in ovarian cancer. (Li J, Olson LM, Zhang Z, Li L, Bidder M, Nguyen L, Pfeifer J, Rader JS) Int J Med Sci 2008 Jun 06;5(3):133-42 25 Citations |
| 2 | Molecular networks in Dahl salt-sensitive hypertension based on transcriptome analysis of a panel of consomic rats. (Liang M, Lee NH, Wang H, Greene AS, Kwitek AE, Kaldunski ML, Luu TV, Frank BC, Bugenhagen S, Jacob HJ, Cowley AW Jr) Physiol Genomics 2008 Jun 12;34(1):54-64 43 Citations |
| 1 | High perfusion pressure accelerates renal injury in salt-sensitive hypertension. (Mori T, Polichnowski A, Glocka P, Kaldunski M, Ohsaki Y, Liang M, Cowley AW Jr) J Am Soc Nephrol 2008 Aug;19(8):1472-82 94 Citations |
| 1 | Genetic analysis of congenital cystic adenomatoid malformation reveals a novel pulmonary gene: fatty acid binding protein-7 (brain type). (Wagner AJ, Stumbaugh A, Tigue Z, Edmondson J, Paquet AC, Farmer DL, Hawgood S) Pediatr Res 2008 Jul;64(1):11-6 42 Citations |
| 1 | Gene expression signatures of radiation response are specific, durable and accurate in mice and humans. (Meadows SK, Dressman HK, Muramoto GG, Himburg H, Salter A, Wei Z, Ginsburg GS, Chao NJ, Nevins JR, Chute JP) PLoS One 2008 Apr 02;3(4):e1912 104 Citations |
| 1 | Curcumin (diferuloylmethane) alters the expression profiles of microRNAs in human pancreatic cancer cells. (Sun M, Estrov Z, Ji Y, Coombes KR, Harris DH, Kurzrock R) Mol Cancer Ther 2008 Mar;7(3):464-73 415 Citations |
| 1 | Identification of differentially regulated francisella tularensis genes by use of a newly developed Tn5-based transposon delivery system. (Buchan BW, McLendon MK, Jones BD) Appl Environ Microbiol 2008 May;74(9):2637-45 29 Citations |
| 2 | Interference with PPARgamma signaling causes cerebral vascular dysfunction, hypertrophy, and remodeling. (Beyer AM, Baumbach GL, Halabi CM, Modrick ML, Lynch CM, Gerhold TD, Ghoneim SM, de Lange WJ, Keen HL, Tsai YS, Maeda N, Sigmund CD, Faraci FM) Hypertension 2008 Apr;51(4):867-71 105 Citations |
| 1 | Differential display of DNA-binding proteins reveals heat-shock factor 1 as a circadian transcription factor. (Reinke H, Saini C, Fleury-Olela F, Dibner C, Benjamin IJ, Schibler U) Genes Dev 2008 Feb 01;22(3):331-45 195 Citations |
| 1 | Identification of a molecular signature in human type 1 diabetes mellitus using serum and functional genomics. (Wang X, Jia S, Geoffrey R, Alemzadeh R, Ghosh S, Hessner MJ) J Immunol 2008 Feb 01;180(3):1929-37 99 Citations |
| 1 | Aging alters gene expression of growth and remodeling factors in human skeletal muscle both at rest and in response to acute resistance exercise. (Dennis RA, Przybyla B, Gurley C, Kortebein PM, Simpson P, Sullivan DH, Peterson CA) Physiol Genomics 2008 Feb 19;32(3):393-400 89 Citations |
| 1 | The role of nitric oxide and the unfolded protein response in cytokine-induced beta-cell death. (Chambers KT, Unverferth JA, Weber SM, Wek RC, Urano F, Corbett JA) Diabetes 2008 Jan;57(1):124-32 72 Citations |
| 1 | Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. (Elling AA, Mitreva M, Recknor J, Gai X, Martin J, Maier TR, McDermott JP, Hewezi T, McK Bird D, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ) Genome Biol 2007;8(10):R211 43 Citations |
| 1 | Microarray analysis reveals distinctive signaling between the bed nucleus of the stria terminalis, nucleus accumbens, and dorsal striatum. (Olsen CM, Huang Y, Goodwin S, Ciobanu DC, Lu L, Sutter TR, Winder DG) Physiol Genomics 2008 Feb 19;32(3):283-98 18 Citations |
| 2 | Molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: insights into TCDD-induced endocrine disruption and reproductive toxicity. (Heiden TC, Struble CA, Rise ML, Hessner MJ, Hutz RJ, Carvan MJ 3rd) Reprod Toxicol 2008 Jan;25(1):47-57 56 Citations |
| 1 | Genetic analysis of albuminuria in a cross between C57BL/6J and DBA/2J mice. (Sheehan S, Tsaih SW, King BL, Stanton C, Churchill GA, Paigen B, DiPetrillo K) Am J Physiol Renal Physiol 2007 Nov;293(5):F1649-56 37 Citations |
| 1 | Gene expression profiling reveals different pathways related to Abl and other genes that cooperate with c-Myc in a model of plasma cell neoplasia. (Park ES, Shaughnessy JD Jr, Gupta S, Wang H, Lee JS, Woo HG, Zhan F, Owens JD Jr, Potter M, Janz S, Mushinski JF) BMC Genomics 2007 Aug 31;8:302 19 Citations |
| 1 | Profiling microdissected epithelium and stroma to model genomic signatures for cervical carcinogenesis accommodating for covariates. (Gius D, Funk MC, Chuang EY, Feng S, Huettner PC, Nguyen L, Bradbury CM, Mishra M, Gao S, Buttin BM, Cohn DE, Powell MA, Horowitz NS, Whitcomb BP, Rader JS) Cancer Res 2007 Aug 01;67(15):7113-23 79 Citations |
| 2 | Distinct profiles of endothelial gene expression in hyperpermeable regions of the porcine aortic arch and thoracic aorta. (LaMack JA, Himburg HA, Friedman MH) Atherosclerosis 2007 Dec;195(2):e35-41 11 Citations |
| 1 | Fluorescence activated cell sorting (FACS) using RNAlater to minimize RNA degradation and perturbation of mRNA expression from cells involved in initial host microbe interactions. (Nishimoto KP, Newkirk D, Hou S, Fruehauf J, Nelson EL) J Microbiol Methods 2007 Jul;70(1):205-8 21 Citations |
| 1 | A transgenic mouse model of plasma cell malignancy shows phenotypic, cytogenetic, and gene expression heterogeneity similar to human multiple myeloma. (Boylan KL, Gosse MA, Staggs SE, Janz S, Grindle S, Kansas GS, Van Ness BG) Cancer Res 2007 May 01;67(9):4069-78 38 Citations |
| 1 | Anaplastic, plasmablastic, and plasmacytic plasmacytomas of mice: relationships to human plasma cell neoplasms and late-stage differentiation of normal B cells. (Qi CF, Zhou JX, Lee CH, Naghashfar Z, Xiang S, Kovalchuk AL, Fredrickson TN, Hartley JW, Roopenian DC, Davidson WF, Janz S, Morse HC 3rd) Cancer Res 2007 Mar 15;67(6):2439-47 24 Citations |
| 1 | Gene expression analysis of gallium-resistant and gallium-sensitive lymphoma cells reveals a role for metal-responsive transcription factor-1, metallothionein-2A, and zinc transporter-1 in modulating the antineoplastic activity of gallium nitrate. (Yang M, Kroft SH, Chitambar CR) Mol Cancer Ther 2007 Feb;6(2):633-43 36 Citations |
| 1 | Regulatory T cell development in the absence of functional Foxp3. (Lin W, Haribhai D, Relland LM, Truong N, Carlson MR, Williams CB, Chatila TA) Nat Immunol 2007 Apr;8(4):359-68 418 Citations |
| 1 | ADME transcriptome in Hispanic versus White donor livers: evidence of a globally enhanced NR1I3 (CAR, constitutive androstane receptor) gene signature in Hispanics. (Finkelstein D, Lamba V, Assem M, Rengelshausen J, Yasuda K, Strom S, Schuetz E) Xenobiotica 2006;36(10-11):989-1012 12 Citations |
| 2 | Evidence of a functional role for mast cells in the development of type 1 diabetes mellitus in the BioBreeding rat. (Geoffrey R, Jia S, Kwitek AE, Woodliff J, Ghosh S, Lernmark A, Wang X, Hessner MJ) J Immunol 2006 Nov 15;177(10):7275-86 66 Citations |
| 1 | The genetic dissection of essential hypertension. (Cowley AW Jr) Nat Rev Genet 2006 Nov;7(11):829-40 243 Citations |
| 1 | Proteomic analysis of acute promyelocytic leukemia: PML-RARalpha leads to decreased phosphorylation of OP18 at serine 63. (Zada AA, Geletu MH, Pulikkan JA, Müller-Tidow C, Reddy VA, Christopeit M, Hiddemann WD, Behre HM, Tenen DG, Behre G) Proteomics 2006 Nov;6(21):5705-19 14 Citations |
| 1 | Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays. (Wang X, Jia S, Meyer L, Xiang B, Chen LY, Jiang N, Moreno C, Jacob HJ, Ghosh S, Hessner MJ) BMC Bioinformatics 2006 Aug 14;7:378 9 Citations |
| 1 | Microarray analysis of differentially expressed genes in mouse bone marrow tissues after ionizing radiation. (Dai JM, Sun DC, Lin RX, Yang J, Lou S, Wang SQ) Int J Radiat Biol 2006 Jul;82(7):511-21 19 Citations |
| 1 | Dickkopf homologs in squamous mucosa of esophagitis patients are overexpressed compared with Barrett's patients and healthy controls. (Ali I, Rafiee P, Hogan WJ, Jacob HJ, Komorowski RA, Haasler GB, Shaker R) Am J Gastroenterol 2006 Jul;101(7):1437-48 19 Citations |
| 1 | Gene expression patterns in advanced human cervical cancer. (Grigsby PW, Watson M, Powell MA, Zhang Z, Rader JS) Int J Gynecol Cancer 2006;16(2):562-7 28 Citations |
| 1 | The mitogen-activated protein kinases and Akt are developmentally regulated in the chronically anemic fetal sheep heart. (Olson AK, Protheroe KN, Scholz TD, Segar JL) J Soc Gynecol Investig 2006 Apr;13(3):157-65 11 Citations |
| 1 | Stem cell factor receptor induces progenitor and natural killer cell-mediated cardiac survival and repair after myocardial infarction. (Ayach BB, Yoshimitsu M, Dawood F, Sun M, Arab S, Chen M, Higuchi K, Siatskas C, Lee P, Lim H, Zhang J, Cukerman E, Stanford WL, Medin JA, Liu PP) Proc Natl Acad Sci U S A 2006 Feb 14;103(7):2304-9 110 Citations |
| 1 | Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. (Cheng AS, Jin VX, Fan M, Smith LT, Liyanarachchi S, Yan PS, Leu YW, Chan MW, Plass C, Nephew KP, Davuluri RV, Huang TH) Mol Cell 2006 Feb 03;21(3):393-404 159 Citations |
| 1 | Physiogenomic resources for rat models of heart, lung and blood disorders. (Malek RL, Wang HY, Kwitek AE, Greene AS, Bhagabati N, Borchardt G, Cahill L, Currier T, Frank B, Fu X, Hasinoff M, Howe E, Letwin N, Luu TV, Saeed A, Sajadi H, Salzberg SL, Sultana R, Thiagarajan M, Tsai J, Veratti K, White J, Quackenbush J, Jacob HJ, Lee NH) Nat Genet 2006 Feb;38(2):234-9 45 Citations |
| 1 | Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms. (Hessner MJ, Xiang B, Jia S, Geoffrey R, Holmes S, Meyer L, Muheisen S, Wang X) Physiol Genomics 2006 Mar 13;25(1):166-78 6 Citations |
| 2 | Fetomaternal cross talk in the placental vascular bed: control of coagulation by trophoblast cells. (Sood R, Kalloway S, Mast AE, Hillard CJ, Weiler H) Blood 2006 Apr 15;107(8):3173-80 89 Citations |
| 1 | Molecular and cytological features of the mouse B-cell lymphoma line iMycEmu-1. (Han SS, Shaffer AL, Peng L, Chung ST, Lim JH, Maeng S, Kim JS, McNeil N, Ried T, Staudt LM, Janz S) Mol Cancer 2005 Nov 09;4:40 6 Citations |
| 1 | Expression of matrix metalloproteinases subsequent to urogenital Chlamydia muridarum infection of mice. (Ramsey KH, Sigar IM, Schripsema JH, Shaba N, Cohoon KP) Infect Immun 2005 Oct;73(10):6962-73 58 Citations |
| 1 | Tools and strategies for physiological genomics: the Rat Genome Database. (Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, Jacob HJ) Physiol Genomics 2005 Oct 17;23(2):246-56 22 Citations |
| 1 | Overexpression of neuropilin-1 promotes constitutive MAPK signalling and chemoresistance in pancreatic cancer cells. (Wey JS, Gray MJ, Fan F, Belcheva A, McCarty MF, Stoeltzing O, Somcio R, Liu W, Evans DB, Klagsbrun M, Gallick GE, Ellis LM) Br J Cancer 2005 Jul 25;93(2):233-41 109 Citations |
| 1 | Changes in gene expression following high-temperature adaptation in experimentally evolved populations of E. coli. (Riehle MM, Bennett AF, Long AD) Physiol Biochem Zool 2005;78(3):299-315 21 Citations |
| 2 | Transcriptome analysis and kidney research: toward systems biology. (Liang M, Cowley AW Jr, Hessner MJ, Lazar J, Basile DP, Pietrusz JL) Kidney Int 2005 Jun;67(6):2114-22 23 Citations |
| 2 | Cell-free protein production and labeling protocol for NMR-based structural proteomics. (Vinarov DA, Lytle BL, Peterson FC, Tyler EM, Volkman BF, Markley JL) Nat Methods 2004 Nov;1(2):149-53 122 Citations |
| 1 | Defective expression of Tamm-Horsfall protein/uromodulin in COX-2-deficient mice increases their susceptibility to urinary tract infections. (Dou W, Thompson-Jaeger S, Laulederkind SJ, Becker JW, Montgomery J, Ruiz-Bustos E, Hasty DL, Ballou LR, Eastman PS, Srichai B, Breyer MD, Raghow R) Am J Physiol Renal Physiol 2005 Jul;289(1):F49-60 29 Citations |
| 1 | Overexpression of tropomysin-related kinase B in metastatic human pancreatic cancer cells. (Sclabas GM, Fujioka S, Schmidt C, Li Z, Frederick WA, Yang W, Yokoi K, Evans DB, Abbruzzese JL, Hess KR, Zhang W, Fidler IJ, Chiao PJ) Clin Cancer Res 2005 Jan 15;11(2 Pt 1):440-9 124 Citations |
| 1 | Identification of persistently altered gene expression in the kidney after functional recovery from ischemic acute renal failure. (Basile DP, Fredrich K, Alausa M, Vio CP, Liang M, Rieder MR, Greene AS, Cowley AW Jr) Am J Physiol Renal Physiol 2005 May;288(5):F953-63 89 Citations |
| 1 | Involvement of eotaxin, eosinophils, and pancreatic predisposition in development of type 1 diabetes mellitus in the BioBreeding rat. (Hessner MJ, Wang X, Meyer L, Geoffrey R, Jia S, Fuller J, Lernmark A, Ghosh S) J Immunol 2004 Dec 01;173(11):6993-7002 53 Citations |
| 1 | A novel approach for high-quality microarray processing using third-dye array visualization technology. (Wang X, Jiang N, Feng X, Xie Y, Tonellato PJ, Ghosh S, Hessner MJ) IEEE Trans Nanobioscience 2003 Dec;2(4):193-201 15 Citations |
| 1 | Cross-species global and subset gene expression profiling identifies genes involved in prostate cancer response to selenium. (Schlicht M, Matysiak B, Brodzeller T, Wen X, Liu H, Zhou G, Dhir R, Hessner MJ, Tonellato P, Suckow M, Pollard M, Datta MW) BMC Genomics 2004 Aug 20;5(1):58 28 Citations |
| 1 | Statistical modeling for selecting housekeeper genes. (Szabo A, Perou CM, Karaca M, Perreard L, Palais R, Quackenbush JF, Bernard PS) Genome Biol 2004;5(8):R59 164 Citations |
| 1 | Expression of constitutive androstane receptor splice variants in human tissues and their functional consequences. (Lamba JK, Lamba V, Yasuda K, Lin YS, Assem M, Thompson E, Strom S, Schuetz E) J Pharmacol Exp Ther 2004 Nov;311(2):811-21 94 Citations |
| 1 | Gene expression profiling of potential PPARgamma target genes in mouse aorta. (Keen HL, Ryan MJ, Beyer A, Mathur S, Scheetz TE, Gackle BD, Faraci FM, Casavant TL, Sigmund CD) Physiol Genomics 2004 Jun 17;18(1):33-42 45 Citations |
| 1 | Effect of high glucose on gene expression in mesangial cells: upregulation of the thiol pathway is an adaptational response. (Morrison J, Knoll K, Hessner MJ, Liang M) Physiol Genomics 2004 May 19;17(3):271-82 42 Citations |
| 1 | Utilization of a labeled tracking oligonucleotide for visualization and quality control of spotted 70-mer arrays. (Hessner MJ, Singh VK, Wang X, Khan S, Tschannen MR, Zahrt TC) BMC Genomics 2004 Feb 09;5(1):12 33 Citations |
| 1 | A multiplex microsphere bead assay for comparative RNA expression analysis using flow cytometry. (Fuja T, Hou S, Bryant P) J Biotechnol 2004 Mar 18;108(3):193-205 24 Citations |
| 1 | Difference in gene expression profiles between human CD4+CD25+ and CD4+CD25- T cells. (Pati N, Ghosh S, Hessner MJ, Khoo HJ, Wang X) Ann N Y Acad Sci 2003 Nov;1005:279-83 6 Citations |
| 1 | Multivariate exploratory tools for microarray data analysis. (Szabo A, Boucher K, Jones D, Tsodikov AD, Klebanov LB, Yakovlev AY) Biostatistics 2003 Oct;4(4):555-67 35 Citations |
| 1 | Serial analysis of gene expression. (el-Meanawy MA, Barathan S, Hayden PS, Iyengar SK, Schelling JR, Sedor JR) Methods Mol Med 2003;86:257-74 3 Citations |
| 1 | Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction. (Wang X, Hessner MJ, Wu Y, Pati N, Ghosh S) Bioinformatics 2003 Jul 22;19(11):1341-7 69 Citations |
| 1 | DNA expression analysis: serial analysis of gene expression, microarrays and kidney disease. (Hayden PS, El-Meanawy A, Schelling JR, Sedor JR) Curr Opin Nephrol Hypertens 2003 Jul;12(4):407-14 15 Citations |
| 1 | Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. (Hessner MJ, Wang X, Khan S, Meyer L, Schlicht M, Tackes J, Datta MW, Jacob HJ, Ghosh S) Nucleic Acids Res 2003 Jun 01;31(11):e60 43 Citations |
| 1 | Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature. (Riehle MM, Bennett AF, Lenski RE, Long AD) Physiol Genomics 2003 Jun 24;14(1):47-58 79 Citations |
| 1 | Genomics and homeostasis. (Cowley AW Jr) Am J Physiol Regul Integr Comp Physiol 2003 Mar;284(3):R611-27 47 Citations |
| 1 | Characterization of the common fragile site FRA9E and its potential role in ovarian cancer. (Callahan G, Denison SR, Phillips LA, Shridhar V, Smith DI) Oncogene 2003 Jan 30;22(4):590-601 64 Citations |
| 1 | Identification of gene expression profiles that segregate patients with childhood leukemia. (Moos PJ, Raetz EA, Carlson MA, Szabo A, Smith FE, Willman C, Wei Q, Hunger SP, Carroll WL) Clin Cancer Res 2002 Oct;8(10):3118-30 85 Citations |
| 1 | Meeting report: Physiological Genomics of Cardiovascular Disease: from Technology to Physiology. (Glueck SB, Sigmund CD) Physiol Genomics 2002;9(3):135-6 1 Citation |
| 1 | Generation of kidney transcriptomes using serial analysis of gene expression. (Schelling JR, El-Meanawy MA, Barathan S, Dodig T, Iyengar SK, Sedor JR) Exp Nephrol 2002;10(2):82-92 11 Citations |
| 1 | PKHD1, the polycystic kidney and hepatic disease 1 gene, encodes a novel large protein containing multiple immunoglobulin-like plexin-transcription-factor domains and parallel beta-helix 1 repeats. (Onuchic LF, Furu L, Nagasawa Y, Hou X, Eggermann T, Ren Z, Bergmann C, Senderek J, Esquivel E, Zeltner R, Rudnik-Schöneborn S, Mrug M, Sweeney W, Avner ED, Zerres K, Guay-Woodford LM, Somlo S, Germino GG) Am J Hum Genet 2002 May;70(5):1305-17 443 Citations |
| 1 | Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization. (Fernandes J, Brendel V, Gai X, Lal S, Chandler VL, Elumalai RP, Galbraith DW, Pierson EA, Walbot V) Plant Physiol 2002 Mar;128(3):896-910 89 Citations |
| 1 | Renal medullary genes in salt-sensitive hypertension: a chromosomal substitution and cDNA microarray study. (Liang M, Yuan B, Rute E, Greene AS, Zou AP, Soares P, MCQuestion GD, Slocum GR, Jacob HJ, Cowley AW Jr) Physiol Genomics 2002 Feb 28;8(2):139-49 47 Citations |
| 1 | Variable selection and pattern recognition with gene expression data generated by the microarray technology. (Szabo A, Boucher K, Carroll WL, Klebanov LB, Tsodikov AD, Yakovlev AY) Math Biosci 2002 Mar;176(1):71-98 58 Citations |
| 1 | Multivariate approach for selecting sets of differentially expressed genes. (Chilingaryan A, Gevorgyan N, Vardanyan A, Jones D, Szabo A) Math Biosci 2002 Mar;176(1):59-69 35 Citations |
| 1 | Adjustments and measures of differential expression for microarray data. (Tsodikov A, Szabo A, Jones D) Bioinformatics 2002 Feb;18(2):251-60 54 Citations |
| 1 | Gene expression profiling. Methods and clinical applications in oncology. (Raetz EA, Moos PJ, Szabo A, Carroll WL) Hematol Oncol Clin North Am 2001 Oct;15(5):911-30, ix |
| 1 | Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. (Ishida S, Huang E, Zuzan H, Spang R, Leone G, West M, Nevins JR) Mol Cell Biol 2001 Jul;21(14):4684-99 516 Citations |
| 1 | Expression of chick Tbx-2, Tbx-3, and Tbx-5 genes during early heart development: evidence for BMP2 induction of Tbx2. (Yamada M, Revelli JP, Eichele G, Barron M, Schwartz RJ) Dev Biol 2000 Dec 01;228(1):95-105 186 Citations |
| 1 | Genetically defined risk of salt sensitivity in an intercross of Brown Norway and Dahl S rats. (Cowley AW Jr, Stoll M, Greene AS, Kaldunski ML, Roman RJ, Tonellato PJ, Schork NJ, Dumas P, Jacob HJ) Physiol Genomics 2000 Apr 27;2(3):107-15 70 Citations |
| 1 | Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. (Arfin SM, Long AD, Ito ET, Tolleri L, Riehle MM, Paegle ES, Hatfield GW) J Biol Chem 2000 Sep 22;275(38):29672-84 228 Citations |
