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Publications indexed to the term Sequence Analysis, RNA

FacultyTitle
3A 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    
1Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations. (Zhou Y, Li T, Choppavarapu L, Fang K, Lin S, Jin VX) Nat Commun 2024 Sep 27;15(1):8310       1 Citation
8Enhancing prognostic power in multiple myeloma using a plasma cell signature derived from single-cell RNA sequencing. (Li JR, Arsang-Jang S, Cheng Y, Sun F, D'Souza A, Dhakal B, Hari P, Huang Q, Auer P, Li Y, Urrutia R, Zhan F, Shaughnessy JD Jr, Janz S, Dong J, Cheng C) Blood Cancer J 2024 Mar 06;14(1):38       3 Citations
3Robustness 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       4 Citations
1Tgfβ1-Cthrc1 Signaling Plays an Important Role in the Short-Term Reparative Response to Heart Valve Endothelial Injury. (Nordquist EM, Dutta P, Kodigepalli KM, Mattern C, McDermott MR, Trask AJ, LaHaye S, Lindner V, Lincoln J) Arterioscler Thromb Vasc Biol 2021 Dec;41(12):2923-2942       6 Citations
1Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level. (Kannan S, Farid M, Lin BL, Miyamoto M, Kwon C) PLoS Comput Biol 2021 Sep;17(9):e1009305       28 Citations
1Induced Pluripotent Stem Cells From Subjects With Primary Sclerosing Cholangitis Develop a Senescence Phenotype Following Biliary Differentiation. (Jalan-Sakrikar N, De Assuncao TM, Navarro-Corcuera A, Hamdan FH, Loarca L, Kirkeby LA, Resch ZT, O'Hara SP, Juran BD, Lazaridis KN, Rosen CB, Heimbach JK, Taner T, Shah VH, LaRusso NF, Huebert RC) Hepatol Commun 2022 Feb;6(2):345-360       16 Citations
1Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. (Shen L, Bard JD, Triche TJ, Judkins AR, Biegel JA, Gai X) Emerg Microbes Infect 2021 Dec;10(1):1293-1299       16 Citations
1Single cell RNA-seq analysis of the flexor digitorum brevis mouse myofibers. (Verma RX, Kannan S, Lin BL, Fomchenko KM, Nieuwenhuis TO, Patil AH, Lukban C, Yang X, Fox-Talbot K, McCall MN, Kwon C, Kass DA, Rosenberg AZ, Halushka MK) Skelet Muscle 2021 May 17;11(1):13       3 Citations
1Increased viral variants in children and young adults with impaired humoral immunity and persistent SARS-CoV-2 infection: A consecutive case series. (Truong TT, Ryutov A, Pandey U, Yee R, Goldberg L, Bhojwani D, Aguayo-Hiraldo P, Pinsky BA, Pekosz A, Shen L, Boyd SD, Wirz OF, Röltgen K, Bootwalla M, Maglinte DT, Ostrow D, Ruble D, Han JH, Biegel JA, Li M, Huang C, Sahoo MK, Pannaraj PS, O'Gorman M, Judkins AR, Gai X, Dien Bard J) EBioMedicine 2021 May;67:103355       109 Citations
1Single-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)       27 Citations
1E2A-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
1Chromosome 2 Fragment Substitutions in Dahl Salt-Sensitive Rats and RNA Sequencing Identified Enpep and Hs2st1 as Vascular Inflammatory Modulators. (Berillo O, Ouerd S, Idris-Khodja N, Rehman A, Richer C, Sinnett D, Kwitek AE, Paradis P, Schiffrin EL) Hypertension 2021 Jan;77(1):178-189       5 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 Sep 24;10(1):15716       13 Citations
5Single-Nucleus RNA Sequencing of the Hypothalamic Arcuate Nucleus of C57BL/6J Mice After Prolonged Diet-Induced Obesity. (Deng G, Morselli LL, Wagner VA, Balapattabi K, Sapouckey SA, Knudtson KL, Rahmouni K, Cui H, Sigmund CD, Kwitek AE, Grobe JL) Hypertension 2020 Aug;76(2):589-597       23 Citations
1Hepatic stellate cell autophagy inhibits extracellular vesicle release to attenuate liver fibrosis. (Gao J, Wei B, de Assuncao TM, Liu Z, Hu X, Ibrahim S, Cooper SA, Cao S, Shah VH, Kostallari E) J Hepatol 2020 Nov;73(5):1144-1154       240 Citations
4RNA 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 Jan;131(1):121-129       31 Citations
1RNA 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       19 Citations
2Comprehensive molecular characterization of mitochondrial genomes in human cancers. (Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, PCAWG Consortium) Nat Genet 2020 Mar;52(3):342-352       282 Citations
2Integrative 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       138 Citations
1Large Particle Fluorescence-Activated Cell Sorting Enables High-Quality Single-Cell RNA Sequencing and Functional Analysis of Adult Cardiomyocytes. (Kannan S, Miyamoto M, Lin BL, Zhu R, Murphy S, Kass DA, Andersen P, Kwon C) Circ Res 2019 Aug 16;125(5):567-569       34 Citations
1Rat Genome Assemblies, Annotation, and Variant Repository. (Tutaj M, Smith JR, Bolton ER) Methods Mol Biol 2019;2018:43-70       6 Citations
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 Jul 08;146(13)       52 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 Dec;22(4):624-632       7 Citations
1GSEPD: 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       4 Citations
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 Jan 03;10(1):38       241 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 Dec;14(12):e1007822       81 Citations
2Single-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 Nov 28;9(1):5037       68 Citations
1GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts. (Walker MA, Pedamallu CS, Ojesina AI, Bullman S, Sharpe T, Whelan CW, Meyerson M) Bioinformatics 2018 Dec 15;34(24):4287-4289       77 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 May 17;9(1):1978       192 Citations
1Cytokine-Producing B Cells Promote Immune-Mediated Bile Duct Injury in Murine Biliary Atresia. (Bednarek J, Traxinger B, Brigham D, Roach J, Orlicky D, Wang D, Pelanda R, Mack CL) Hepatology 2018 Nov;68(5):1890-1904       34 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 Jun;154(8):2097-2110       73 Citations
1The 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
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 Nov 25;14(1):327       22 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 Nov 08;7:13331       237 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       16 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 Aug 01;126(8):2955-69       77 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 Jun 24;6:28294       57 Citations
2Comprehensive 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       73 Citations
1miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy. (Baras AS, Mitchell CJ, Myers JR, Gupta S, Weng LC, Ashton JM, Cornish TC, Pandey A, Halushka MK) PLoS One 2015;10(11):e0143066       71 Citations
1deGPS 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
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       71 Citations
1Modeling and study of the mechanism of dilated cardiomyopathy using induced pluripotent stem cells derived from individuals with Duchenne muscular dystrophy. (Lin B, Li Y, Han L, Kaplan AD, Ao Y, Kalra S, Bett GC, Rasmusson RL, Denning C, Yang L) Dis Model Mech 2015 May;8(5):457-66       95 Citations
1A 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       16 Citations
1Activin-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       30 Citations
1Characteristics 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       50 Citations
2RNA 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
1Whole exome sequence analysis of Peters anomaly. (Weh E, Reis LM, Happ HC, Levin AV, Wheeler PG, David KL, Carney E, Angle B, Hauser N, Semina EV) Hum Genet 2014 Dec;133(12):1497-511       62 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       10 Citations
1Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. (Ye Z, Chen Z, Lan X, Hara S, Sunkel B, Huang TH, Elnitski L, Wang Q, Jin VX) Nucleic Acids Res 2014 Mar;42(5):2856-69       24 Citations
1Drosophila life span and physiology are modulated by sexual perception and reward. (Gendron CM, Kuo TH, Harvanek ZM, Chung BY, Yew JY, Dierick HA, Pletcher SD) Science 2014 Jan 31;343(6170):544-8       118 Citations
1Small RNA profiling of influenza A virus-infected cells identifies miR-449b as a regulator of histone deacetylase 1 and interferon beta. (Buggele WA, Krause KE, Horvath CM) PLoS One 2013;8(9):e76560       37 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       40 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       41 Citations
1An integrated encyclopedia of DNA elements in the human genome. (ENCODE Project Consortium) Nature 2012 Sep 06;489(7414):57-74       13181 Citations
1Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. (Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX) Nucleic Acids Res 2012 Sep;40(16):7690-704       85 Citations
1PathSeq: software to identify or discover microbes by deep sequencing of human tissue. (Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, Meyerson M) Nat Biotechnol 2011 May;29(5):393-6       253 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       11 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       18 Citations