Medical College of Wisconsin
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Publications indexed to the term Sequence Analysis, RNA

FacultyTitle
1Large-Scale Multi-omic Analysis of COVID-19 Severity. (Overmyer KA, Shishkova E, Miller IJ, Balnis J, Bernstein MN, Peters-Clarke TM, Meyer JG, Quan Q, Muehlbauer LK, Trujillo EA, He Y, Chopra A, Chieng HC, Tiwari A, Judson MA, Paulson B, Brademan DR, Zhu Y, Serrano LR, Linke V, Drake LA, Adam AP, Schwartz BS, Singer HA, Swanson S, Mosher DF, Stewart R, Coon JJ, Jaitovich A) Cell Syst 2021 01 20;12(1):23-40.e7       17 Citations
1Cell 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 09 24;10(1):15716       2 Citations
5RNA Sequencing Reveals Cancer-Associated Changes in Laryngeal Cells Exposed to Non-Acid Pepsin. (Samuels TL, Zimmermann MT, Zeighami A, Demos W, Southwood JE, Blumin JH, Bock JM, Johnston N) Laryngoscope 2021 01;131(1):121-129       2 Citations
1Prediction of survival of HPV16-negative, p16-negative oral cavity cancer patients using a 13-gene signature: A multicenter study using FFPE samples. (Chen C, Lohavanichbutr P, Zhang Y, Houck JR, Upton MP, Abedi-Ardekani B, Agudo A, Ahrens W, Alemany L, Anantharaman D, Conway DI, Futran ND, Holcatova I, Günther K, Hansen BT, Healy CM, Itani D, Kjaerheim K, Monroe MM, Thomson PJ, Witt BL, Nakoneshny S, Peterson LA, Schwartz SM, Zarins KR, Hashibe M, Brennan P, Rozek LS, Wolf G, Dort JC, Wang P) Oral Oncol 2020 01;100:104487       1 Citation
1Regionally 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 07 08;146(13)       15 Citations
1Characterization of a KLK2-FGFR2 fusion gene in two cases of metastatic prostate cancer. (Krook MA, Barker H, Chen HZ, Reeser JW, Wing MR, Martin D, Smith AM, Dao T, Bonneville R, Samorodnitsky E, Miya J, Freud AG, Monk JP, Clinton SK, Roychowdhury S) Prostate Cancer Prostatic Dis 2019 12;22(4):624-632       3 Citations
2GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display. (Stamm K, Tomita-Mitchell A, Bozdag S) BMC Bioinformatics 2019 Mar 06;20(1):115       1 Citation
1Ulcerative 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 01 03;10(1):38       41 Citations
1De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. (Qi H, Yu L, Zhou X, Wynn J, Zhao H, Guo Y, Zhu N, Kitaygorodsky A, Hernan R, Aspelund G, Lim FY, Crombleholme T, Cusick R, Azarow K, Danko ME, Chung D, Warner BW, Mychaliska GB, Potoka D, Wagner AJ, ElFiky M, Wilson JM, Nickerson D, Bamshad M, High FA, Longoni M, Donahoe PK, Chung WK, Shen Y) PLoS Genet 2018 12;14(12):e1007822       22 Citations
3Single-cell RNA sequencing unveils an IL-10-producing helper subset that sustains humoral immunity during persistent infection. (Xin G, Zander R, Schauder DM, Chen Y, Weinstein JS, Drobyski WR, Tarakanova V, Craft J, Cui W) Nat Commun 2018 11 28;9(1):5037       30 Citations
3Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. (Lomberk G, Blum Y, Nicolle R, Nair A, Gaonkar KS, Marisa L, Mathison A, Sun Z, Yan H, Elarouci N, Armenoult L, Ayadi M, Ordog T, Lee JH, Oliver G, Klee E, Moutardier V, Gayet O, Bian B, Duconseil P, Gilabert M, Bigonnet M, Garcia S, Turrini O, Delpero JR, Giovannini M, Grandval P, Gasmi M, Secq V, De Reyniès A, Dusetti N, Iovanna J, Urrutia R) Nat Commun 2018 05 17;9(1):1978       66 Citations
1Clinical 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 06;154(8):2097-2110       25 Citations
1Targeted 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 11 25;14(1):327       11 Citations
1Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukaemia. (Gu Z, Churchman M, Roberts K, Li Y, Liu Y, Harvey RC, McCastlain K, Reshmi SC, Payne-Turner D, Iacobucci I, Shao Y, Chen IM, Valentine M, Pei D, Mungall KL, Mungall AJ, Ma Y, Moore R, Marra M, Stonerock E, Gastier-Foster JM, Devidas M, Dai Y, Wood B, Borowitz M, Larsen EE, Maloney K, Mattano LA Jr, Angiolillo A, Salzer WL, Burke MJ, Gianni F, Spinelli O, Radich JP, Minden MD, Moorman AV, Patel B, Fielding AK, Rowe JM, Luger SM, Bhatia R, Aldoss I, Forman SJ, Kohlschmidt J, Mrózek K, Marcucci G, Bloomfield CD, Stock W, Kornblau S, Kantarjian HM, Konopleva M, Paietta E, Willman CL, Loh ML, Hunger SP, Mullighan CG) Nat Commun 2016 11 08;7:13331       91 Citations
1Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing. (Blinka S, Reimer MH Jr, Pulakanti K, Pinello L, Yuan GC, Rao S) Methods Mol Biol 2017;1468:91-109       6 Citations
2E2f8 mediates tumor suppression in postnatal liver development. (Kent LN, Rakijas JB, Pandit SK, Westendorp B, Chen HZ, Huntington JT, Tang X, Bae S, Srivastava A, Senapati S, Koivisto C, Martin CK, Cuitino MC, Perez M, Clouse JM, Chokshi V, Shinde N, Kladney R, Sun D, Perez-Castro A, Matondo RB, Nantasanti S, Mokry M, Huang K, Machiraju R, Fernandez S, Rosol TJ, Coppola V, Pohar KS, Pipas JM, Schmidt CR, de Bruin A, Leone G) J Clin Invest 2016 08 01;126(8):2955-69       32 Citations
1Divergent viral presentation among human tumors and adjacent normal tissues. (Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R 3rd, Johnson KJ, Gay H, Chen K, Rader JS, Dipersio JF, Chen F, Ding L) Sci Rep 2016 06 24;6:28294       30 Citations
1Comprehensive 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       39 Citations
3deGPS 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;16:455       10 Citations
1CNTF Gene Therapy Confers Lifelong Neuroprotection in a Mouse Model of Human Retinitis Pigmentosa. (Lipinski DM, Barnard AR, Singh MS, Martin C, Lee EJ, Davies WIL, MacLaren RE) Mol Ther 2015 Aug;23(8):1308-1319       43 Citations
2Activin-A and Bmp4 levels modulate cell type specification during CHIR-induced cardiomyogenesis. (Kim MS, Horst A, Blinka S, Stamm K, Mahnke D, Schuman J, Gundry R, Tomita-Mitchell A, Lough J) PLoS One 2015;10(2):e0118670       13 Citations
4Characteristics of long non-coding RNAs in the Brown Norway rat and alterations in the Dahl salt-sensitive rat. (Wang F, Li L, Xu H, Liu Y, Yang C, Cowley AW Jr, Wang N, Liu P, Liang M) Sci Rep 2014 Nov 21;4:7146       39 Citations
1RNA 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       35 Citations
1Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis. (Singh RK, Xia Z, Bland CS, Kalsotra A, Scavuzzo MA, Curk T, Ule J, Li W, Cooper TA) Mol Cell 2014 Aug 21;55(4):592-603       61 Citations
1RNA-seq analysis to identify novel roles of scleraxis during embryonic mouse heart valve remodeling. (Barnette DN, VandeKopple M, Wu Y, Willoughby DA, Lincoln J) PLoS One 2014;9(7):e101425       7 Citations
1Identification of the transforming STRN-ALK fusion as a potential therapeutic target in the aggressive forms of thyroid cancer. (Kelly LM, Barila G, Liu P, Evdokimova VN, Trivedi S, Panebianco F, Gandhi M, Carty SE, Hodak SP, Luo J, Dacic S, Yu YP, Nikiforova MN, Ferris RL, Altschuler DL, Nikiforov YE) Proc Natl Acad Sci U S A 2014 Mar 18;111(11):4233-8       152 Citations
1ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer. (Leeman-Neill RJ, Kelly LM, Liu P, Brenner AV, Little MP, Bogdanova TI, Evdokimova VN, Hatch M, Zurnadzy LY, Nikiforova MN, Yue NJ, Zhang M, Mabuchi K, Tronko MD, Nikiforov YE) Cancer 2014 Mar 15;120(6):799-807       155 Citations
1RNA sequencing identifies multiple fusion transcripts, differentially expressed genes, and reduced expression of immune function genes in BRAF (V600E) mutant vs BRAF wild-type papillary thyroid carcinoma. (Smallridge RC, Chindris AM, Asmann YW, Casler JD, Serie DJ, Reddi HV, Cradic KW, Rivera M, Grebe SK, Necela BM, Eberhardt NL, Carr JM, McIver B, Copland JA, Thompson EA) J Clin Endocrinol Metab 2014 Feb;99(2):E338-47       35 Citations
2Characterization of human plasma-derived exosomal RNAs by deep sequencing. (Huang X, Yuan T, Tschannen M, Sun Z, Jacob H, Du M, Liang M, Dittmar RL, Liu Y, Liang M, Kohli M, Thibodeau SN, Boardman L, Wang L) BMC Genomics 2013 May 10;14:319       525 Citations
1A 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       32 Citations
1COPI transport complexes bind to specific RNAs in neuronal cells. (Todd AG, Lin H, Ebert AD, Liu Y, Androphy EJ) Hum Mol Genet 2013 Feb 15;22(4):729-36       32 Citations
1Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. (Ramsköld D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, Daniels GA, Khrebtukova I, Loring JF, Laurent LC, Schroth GP, Sandberg R) Nat Biotechnol 2012 Aug;30(8):777-82       789 Citations
1Selection of antisense oligonucleotides based on multiple predicted target mRNA structures. (Bo X, Lou S, Sun D, Shu W, Yang J, Wang S) BMC Bioinformatics 2006 Mar 09;7:122       9 Citations
1Antigenic structure, function, and evolution of the hemagglutinin-neuraminidase protein of human parainfluenza virus type 1. (Henrickson KJ, Savatski LL) J Infect Dis 1997 Oct;176(4):867-75       14 Citations