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For: Frazee AC, Jaffe AE, Langmead B, Leek JT. Polyester: simulating RNA-seq datasets with differential transcript expression. Bioinformatics 2015;31:2778-84. [PMID: 25926345 DOI: 10.1093/bioinformatics/btv272] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 04/18/2015] [Indexed: 12/26/2022]  Open
Number Cited by Other Article(s)
1
Aquino J, Witoslawski D, Park S, Holder J, Amei A, Han MV. A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection. Brief Bioinform 2025;26:bbaf204. [PMID: 40341920 PMCID: PMC12062524 DOI: 10.1093/bib/bbaf204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 11/24/2024] [Accepted: 04/07/2025] [Indexed: 05/11/2025]  Open
2
Singlan N, Abou Choucha F, Pasquier C. A new Similarity Based Adapted Louvain Algorithm (SIMBA) for active module identification in p-value attributed biological networks. Sci Rep 2025;15:11360. [PMID: 40175439 PMCID: PMC11965526 DOI: 10.1038/s41598-025-95749-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2025] [Accepted: 03/24/2025] [Indexed: 04/04/2025]  Open
3
Mabin JW, Vock IW, Machyna M, Haque N, Thakran P, Zhang A, Rai G, Leibler INM, Inglese J, Simon MD, Hogg JR. Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.12.642874. [PMID: 40161772 PMCID: PMC11952489 DOI: 10.1101/2025.03.12.642874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
4
Prigozhin DM, Sutherland CA, Rangavajjhala S, Krasileva KV. Majority of the Highly Variable NLRs in Maize Share Genomic Location and Contain Additional Target-Binding Domains. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2025;38:275-284. [PMID: 39013614 DOI: 10.1094/mpmi-05-24-0047-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
5
Singh NP, Wu EY, Fan J, Love MI, Patro R. Tree-based differential testing using inferential uncertainty for RNA-Seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.12.25.573288. [PMID: 38234739 PMCID: PMC10793400 DOI: 10.1101/2023.12.25.573288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
6
Kubota N, Chen L, Zheng S. Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms. Nucleic Acids Res 2025;53:gkaf098. [PMID: 39997221 PMCID: PMC11851117 DOI: 10.1093/nar/gkaf098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 02/04/2025] [Indexed: 02/26/2025]  Open
7
Van Hecke M, Beerenwinkel N, Lootens T, Fostier J, Raedt R, Marchal K. ELLIPSIS: robust quantification of splicing in scRNA-seq. Bioinformatics 2025;41:btaf028. [PMID: 39936571 PMCID: PMC11878791 DOI: 10.1093/bioinformatics/btaf028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 12/09/2024] [Accepted: 02/10/2025] [Indexed: 02/13/2025]  Open
8
Guo W, Schreiber M, Marosi VB, Bagnaresi P, Jørgensen ME, Braune KB, Chalmers K, Chapman B, Dang V, Dockter C, Fiebig A, Fincher GB, Fricano A, Fuller J, Haaning A, Haberer G, Himmelbach A, Jayakodi M, Jia Y, Kamal N, Langridge P, Li C, Lu Q, Lux T, Mascher M, Mayer KFX, McCallum N, Milne L, Muehlbauer GJ, Nielsen MTS, Padmarasu S, Pedas PR, Pillen K, Pozniak C, Rasmussen MW, Sato K, Schmutzer T, Scholz U, Schüler D, Šimková H, Skadhauge B, Stein N, Thomsen NW, Voss C, Wang P, Wonneberger R, Zhang XQ, Zhang G, Cattivelli L, Spannagl M, Bayer M, Simpson C, Zhang R, Waugh R. A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity. Nat Genet 2025;57:441-450. [PMID: 39901014 PMCID: PMC11821519 DOI: 10.1038/s41588-024-02069-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 12/20/2024] [Indexed: 02/05/2025]
9
Kubota N, Chen L, Zheng S. Shiba: A versatile computational method for systematic identification of differential RNA splicing across platforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.05.30.596331. [PMID: 38895326 PMCID: PMC11185541 DOI: 10.1101/2024.05.30.596331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
10
Zhang Y, Tang L, Zhi S, Hu B, Zuo Z, Ren J, Xie Y, Luo X. M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications. Gigascience 2025;14:giaf040. [PMID: 40388309 PMCID: PMC12087454 DOI: 10.1093/gigascience/giaf040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 01/05/2025] [Accepted: 03/07/2025] [Indexed: 05/21/2025]  Open
11
Li X, Peng L, Wang YP, Zhang W. Open challenges and opportunities in federated foundation models towards biomedical healthcare. BioData Min 2025;18:2. [PMID: 39755653 DOI: 10.1186/s13040-024-00414-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 12/09/2024] [Indexed: 01/06/2025]  Open
12
Ou J, Liu H, Park S, Green MR, Zhu LJ. InPAS: An R/Bioconductor Package for Identifying Novel Polyadenylation Sites and Alternative Polyadenylation from Bulk RNA-seq Data. Front Biosci (Schol Ed) 2024;16:21. [PMID: 39736014 DOI: 10.31083/j.fbs1604021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 09/20/2024] [Accepted: 10/10/2024] [Indexed: 12/31/2024]
13
Zhang X. Highly effective batch effect correction method for RNA-seq count data. Comput Struct Biotechnol J 2024;27:58-64. [PMID: 39802213 PMCID: PMC11718288 DOI: 10.1016/j.csbj.2024.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 12/13/2024] [Accepted: 12/14/2024] [Indexed: 01/16/2025]  Open
14
Simon NM, Kim Y, Gribnau J, Bautista DM, Dutton JR, Brem RB. Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes. Heredity (Edinb) 2024;133:308-316. [PMID: 39164520 PMCID: PMC11527988 DOI: 10.1038/s41437-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 08/22/2024]  Open
15
Santiago KCL, Shrestha AMS. DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms. BMC Bioinformatics 2024;25:335. [PMID: 39448913 PMCID: PMC11515663 DOI: 10.1186/s12859-024-05924-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 09/05/2024] [Indexed: 10/26/2024]  Open
16
Wang R, Zheng Y, Zhang Z, Song K, Wu E, Zhu X, Wu TP, Ding J. MATES: a deep learning-based model for locus-specific quantification of transposable elements in single cell. Nat Commun 2024;15:8798. [PMID: 39394211 PMCID: PMC11470080 DOI: 10.1038/s41467-024-53114-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 09/24/2024] [Indexed: 10/13/2024]  Open
17
Ueda MT, Inamo J, Miya F, Shimada M, Yamaguchi K, Kochi Y. Functional and dynamic profiling of transcript isoforms reveals essential roles of alternative splicing in interferon response. CELL GENOMICS 2024;4:100654. [PMID: 39288763 PMCID: PMC11602592 DOI: 10.1016/j.xgen.2024.100654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 04/04/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024]
18
Garbulowski M, Hillerton T, Morgan D, Seçilmiş D, Sonnhammer L, Tjärnberg A, Nordling TEM, Sonnhammer ELL. GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data. NAR Genom Bioinform 2024;6:lqae121. [PMID: 39296931 PMCID: PMC11409065 DOI: 10.1093/nargab/lqae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/20/2024] [Accepted: 09/02/2024] [Indexed: 09/21/2024]  Open
19
Ritter AJ, Wallace A, Ronaghi N, Sanford J. junctionCounts: comprehensive alternative splicing analysis and prediction of isoform-level impacts to the coding sequence. NAR Genom Bioinform 2024;6:lqae093. [PMID: 39131822 PMCID: PMC11310779 DOI: 10.1093/nargab/lqae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 08/13/2024]  Open
20
Zang XC, Li X, Metcalfe K, Ben-Yehezkel T, Kelley R, Shao M. Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads. LIPICS : LEIBNIZ INTERNATIONAL PROCEEDINGS IN INFORMATICS 2024;312:22. [PMID: 39764549 PMCID: PMC11702288 DOI: 10.4230/lipics.wabi.2024.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
21
Paiva I, Seguin J, Grgurina I, Singh AK, Cosquer B, Plassard D, Tzeplaeff L, Le Gras S, Cotellessa L, Decraene C, Gambi J, Alcala-Vida R, Eswaramoorthy M, Buée L, Cassel JC, Giacobini P, Blum D, Merienne K, Kundu TK, Boutillier AL. Dysregulated expression of cholesterol biosynthetic genes in Alzheimer's disease alters epigenomic signatures of hippocampal neurons. Neurobiol Dis 2024;198:106538. [PMID: 38789057 DOI: 10.1016/j.nbd.2024.106538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]  Open
22
Zhao Z, Chen Y, Zou X, Lin L, Zhou X, Cheng X, Yang G, Xu Q, Gong L, Li L, Ni T. Pan-cancer transcriptome analysis reveals widespread regulation through alternative tandem transcription initiation. SCIENCE ADVANCES 2024;10:eadl5606. [PMID: 38985880 PMCID: PMC11235174 DOI: 10.1126/sciadv.adl5606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 06/05/2024] [Indexed: 07/12/2024]
23
Shi Q, Zhang Q, Shao M. Accurate assembly of multiple RNA-seq samples with Aletsch. Bioinformatics 2024;40:i307-i317. [PMID: 38940157 PMCID: PMC11211816 DOI: 10.1093/bioinformatics/btae215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]  Open
24
Popitsch N, Neumann T, von Haeseler A, Ameres SL. Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework. Genome Biol 2024;25:166. [PMID: 38918865 PMCID: PMC11514792 DOI: 10.1186/s13059-024-03313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024]  Open
25
Gonzalez Gomez C, Rosa-Calatrava M, Fouret J. Optimizing in silico drug discovery: simulation of connected differential expression signatures and applications to benchmarking. Brief Bioinform 2024;25:bbae299. [PMID: 38935068 PMCID: PMC11210109 DOI: 10.1093/bib/bbae299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/19/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]  Open
26
Zhang X. Highly Effective Batch Effect Correction Method for RNA-seq Count Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592266. [PMID: 38746101 PMCID: PMC11092589 DOI: 10.1101/2024.05.02.592266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
27
Brooks TG, Lahens NF, Mrčela A, Grant GR. Challenges and best practices in omics benchmarking. Nat Rev Genet 2024;25:326-339. [PMID: 38216661 DOI: 10.1038/s41576-023-00679-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 01/14/2024]
28
Ng JCF, Montamat Garcia G, Stewart AT, Blair P, Mauri C, Dunn-Walters DK, Fraternali F. sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data. Nat Methods 2024;21:823-834. [PMID: 37932398 PMCID: PMC11093741 DOI: 10.1038/s41592-023-02060-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/02/2023] [Indexed: 11/08/2023]
29
Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features. EMBO Rep 2024;25:2306-2322. [PMID: 38528170 PMCID: PMC11093987 DOI: 10.1038/s44319-024-00122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024]  Open
30
Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. PLoS Comput Biol 2024;20:e1011408. [PMID: 38768228 PMCID: PMC11104602 DOI: 10.1371/journal.pcbi.1011408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024]  Open
31
Liu Z, Ouyang T, Yang Y, Sheng Y, Shi H, Liu Q, Bai Y, Ge Q. The Impact of Blood Sample Processing on Ribonucleic Acid (RNA) Sequencing. Genes (Basel) 2024;15:502. [PMID: 38674435 PMCID: PMC11050547 DOI: 10.3390/genes15040502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024]  Open
32
Li H, Khang TF. SIEVE: One-stop differential expression, variability, and skewness analyses using RNA-Seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588804. [PMID: 38645120 PMCID: PMC11030344 DOI: 10.1101/2024.04.09.588804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
33
Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. Brief Bioinform 2024;25:bbae164. [PMID: 38605641 PMCID: PMC11009461 DOI: 10.1093/bib/bbae164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]  Open
34
Barra J, Taverna F, Bong F, Ahmed I, Karakach TK. Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression. Brief Bioinform 2024;25:bbae233. [PMID: 38770716 PMCID: PMC11106635 DOI: 10.1093/bib/bbae233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 05/22/2024]  Open
35
Liu X, Chen H, Li Z, Yang X, Jin W, Wang Y, Zheng J, Li L, Xuan C, Yuan J, Yang Y. InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data. Nat Commun 2024;15:2583. [PMID: 38519498 PMCID: PMC10960005 DOI: 10.1038/s41467-024-46875-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024]  Open
36
Coxe T, Burks DJ, Singh U, Mittler R, Azad RK. Benchmarking RNA-Seq Aligners at Base-Level and Junction Base-Level Resolution Using the Arabidopsis thaliana Genome. PLANTS (BASEL, SWITZERLAND) 2024;13:582. [PMID: 38475429 DOI: 10.3390/plants13050582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
37
Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.03.551759. [PMID: 37577548 PMCID: PMC10418283 DOI: 10.1101/2023.08.03.551759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
38
Zayakin P. sRNAflow: A Tool for the Analysis of Small RNA-Seq Data. Noncoding RNA 2024;10:6. [PMID: 38250806 PMCID: PMC10801628 DOI: 10.3390/ncrna10010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/29/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024]  Open
39
Li G, Mahajan S, Ma S, Jeffery ED, Zhang X, Bhattacharjee A, Venkatasubramanian M, Weirauch MT, Miraldi ER, Grimes HL, Sheynkman GM, Tilburgs T, Salomonis N. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Sci Transl Med 2024;16:eade2886. [PMID: 38232136 PMCID: PMC11517820 DOI: 10.1126/scitranslmed.ade2886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
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Mestre-Tomás J, Liu T, Pardo-Palacios F, Conesa A. SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark. Genome Biol 2023;24:286. [PMID: 38082294 PMCID: PMC10712166 DOI: 10.1186/s13059-023-03127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023]  Open
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Bendik J, Kalavacherla S, Webster N, Califano J, Fertig EJ, Ochs MF, Carter H, Guo T. OutSplice: A Novel Tool for the Identification of Tumor-Specific Alternative Splicing Events. BIOMEDINFORMATICS 2023;3:853-868. [PMID: 40236985 PMCID: PMC11997874 DOI: 10.3390/biomedinformatics3040053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
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Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with distinct genomic and epigenomic features. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523861. [PMID: 36711945 PMCID: PMC9882162 DOI: 10.1101/2023.01.12.523861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Li H, Khang TF. clrDV: a differential variability test for RNA-Seq data based on the skew-normal distribution. PeerJ 2023;11:e16126. [PMID: 37790621 PMCID: PMC10544356 DOI: 10.7717/peerj.16126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/27/2023] [Indexed: 10/05/2023]  Open
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Zhang J, Zhang H, Ju Z, Peng Y, Pan Y, Xi W, Wei Y. JCcirc: circRNA full-length sequence assembly through integrated junction contigs. Brief Bioinform 2023;24:bbad363. [PMID: 37833842 DOI: 10.1093/bib/bbad363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]  Open
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Mestre-Tomás J, Liu T, Pardo-Palacios F, Conesa A. SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554392. [PMID: 37662216 PMCID: PMC10473693 DOI: 10.1101/2023.08.23.554392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
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Wu EY, Singh NP, Choi K, Zakeri M, Vincent M, Churchill GA, Ackert-Bicknell CL, Patro R, Love MI. SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty. Genome Biol 2023;24:165. [PMID: 37438847 PMCID: PMC10337143 DOI: 10.1186/s13059-023-03003-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023]  Open
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Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth PA, Hennighausen L, List M. circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. BIOINFORMATICS ADVANCES 2023;3:vbad093. [PMID: 37485422 PMCID: PMC10359604 DOI: 10.1093/bioadv/vbad093] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
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Singh NP, Love MI, Patro R. TreeTerminus -creating transcript trees using inferential replicate counts. iScience 2023;26:106961. [PMID: 37378336 PMCID: PMC10291472 DOI: 10.1016/j.isci.2023.106961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023]  Open
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Wajnberg G, Allain EP, Roy JW, Srivastava S, Saucier D, Morin P, Marrero A, O’Connell C, Ghosh A, Lewis SM, Ouellette RJ, Crapoulet N. Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy. FRONTIERS IN BIOINFORMATICS 2023;3:1127661. [PMID: 37252342 PMCID: PMC10213969 DOI: 10.3389/fbinf.2023.1127661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/17/2023] [Indexed: 05/31/2023]  Open
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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537847. [PMID: 37162982 PMCID: PMC10168222 DOI: 10.1101/2023.04.21.537847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
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