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For: Li Y, Ge X, Peng F, Li W, Li JJ. Exaggerated false positives by popular differential expression methods when analyzing human population samples. Genome Biol 2022;23:79. [PMID: 35292087 PMCID: PMC8922736 DOI: 10.1186/s13059-022-02648-4] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/07/2022] [Indexed: 12/05/2022]  Open
Number Cited by Other Article(s)
1
Chen Y, You Y, Xie Y, Li X, Zhu Z, Li W, Du X, Yan Z. ZBP1 synchronized with periodontopathogenesis as the essential pattern recognition receptor. Microb Pathog 2025;205:107678. [PMID: 40349992 DOI: 10.1016/j.micpath.2025.107678] [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: 07/22/2024] [Revised: 05/03/2025] [Accepted: 05/05/2025] [Indexed: 05/14/2025]
2
Huang X, Yu W, Tian J, Zhang Y, Wei A, Li Y, Chen S. Identification and analysis of extracellular matrix and epithelial-mesenchymal transition-related genes in idiopathic pulmonary fibrosis by bioinformatics analysis and experimental validation. Gene 2025;956:149464. [PMID: 40187620 DOI: 10.1016/j.gene.2025.149464] [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: 11/22/2024] [Revised: 03/27/2025] [Accepted: 03/31/2025] [Indexed: 04/07/2025]
3
Zhang H, Li X, Song D, Yukselen O, Nanda S, Kucukural A, Li JJ, Garber M, Walhout AJM. Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq. Nat Commun 2025;16:4785. [PMID: 40404656 PMCID: PMC12098853 DOI: 10.1038/s41467-025-60154-0] [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: 05/14/2024] [Accepted: 05/15/2025] [Indexed: 05/24/2025]  Open
4
Qi X, Ji H, Bianchi E, Hall SJ, Avellino G, Berg W, Bearelly P, Sigman M, Wu Z, Spade DJ. Downregulation of spermatogenesis-associated transcripts in the spermatozoa of idiopathic infertile men. Andrology 2025. [PMID: 40346865 DOI: 10.1111/andr.70060] [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: 01/17/2025] [Revised: 04/11/2025] [Accepted: 04/28/2025] [Indexed: 05/12/2025]
5
Wang Y, Zheng L, Liu J, Zhang M, Kan Y, Wang W, Yang J. Prognostic role and tumor-suppressive effects of CADM family members and the potential molecular mechanisms of CADM1 in neuroblastoma. Discov Oncol 2025;16:648. [PMID: 40310517 PMCID: PMC12045911 DOI: 10.1007/s12672-025-02350-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Accepted: 04/09/2025] [Indexed: 05/02/2025]  Open
6
Degen PM, Medo M. Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes. PLoS Comput Biol 2025;21:e1011630. [PMID: 40324149 PMCID: PMC12077797 DOI: 10.1371/journal.pcbi.1011630] [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: 10/24/2023] [Revised: 05/14/2025] [Accepted: 04/07/2025] [Indexed: 05/07/2025]  Open
7
Corachea AJM, Ferrer RJE, Ty LPB, Aquino LAC, Morta MT, Macalindong SS, Uy GLB, Odoño EG, Llames JHS, Tablizo FA, Cutiongco-Dela Paz EMC, Dofitas RB, Velarde MC. Lymphovascular Invasion Is Associated With Doxorubicin Resistance in Breast Cancer. J Transl Med 2025;105:104115. [PMID: 39978641 DOI: 10.1016/j.labinv.2025.104115] [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: 08/07/2024] [Revised: 01/30/2025] [Accepted: 02/08/2025] [Indexed: 02/22/2025]  Open
8
M A Basher AR, Hallinan C, Lee K. Heterogeneity-preserving discriminative feature selection for disease-specific subtype discovery. Nat Commun 2025;16:3593. [PMID: 40234411 PMCID: PMC12000357 DOI: 10.1038/s41467-025-58718-1] [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: 02/16/2024] [Accepted: 03/26/2025] [Indexed: 04/17/2025]  Open
9
Matyasovska N, Valkova N, Gala M, Bendikova S, Abdulhamed A, Palicka V, Renwick N, Čekan P, Paul E. Deep sequencing reveals distinct microRNA-mRNA signatures that differentiate pancreatic neuroendocrine tumor from non-diseased pancreas tissue. BMC Cancer 2025;25:669. [PMID: 40217502 PMCID: PMC11987397 DOI: 10.1186/s12885-025-14043-w] [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: 10/14/2024] [Accepted: 03/31/2025] [Indexed: 04/14/2025]  Open
10
Golas MM, Gunawan B, Gutenberg A, Danner BC, Gerdes JS, Stadelmann C, Füzesi L, Liersch T, Sander B. Cytogenetic signatures favoring metastatic organotropism in colorectal cancer. Nat Commun 2025;16:3261. [PMID: 40188208 PMCID: PMC11972295 DOI: 10.1038/s41467-025-58413-1] [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: 12/28/2022] [Accepted: 03/21/2025] [Indexed: 04/07/2025]  Open
11
Yang J, Shen L, Cai Y, Wu J, Chen K, Xu D, Lei Y, Chai S, Xiong N. The Role of Coagulation-Related Genes in Glioblastoma: A Comprehensive Analysis of the Tumor Microenvironment, Prognosis, and Treatment. Biochem Genet 2025:10.1007/s10528-025-11086-3. [PMID: 40113719 DOI: 10.1007/s10528-025-11086-3] [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: 10/10/2024] [Accepted: 03/10/2025] [Indexed: 03/22/2025]
12
Zhou F, Aw AJ, Erdmann-Pham DD, Fischer J, Song YS. Robust and Adaptive Non-Parametric Tests for Detecting General Distributional Shifts in Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.06.641952. [PMID: 40161649 PMCID: PMC11952341 DOI: 10.1101/2025.03.06.641952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
13
Bhattacharya A, Fon EA, Dagher A, Iturria-Medina Y, Stratton JA, Savignac C, Stanley J, Hodgson L, Hammou BA, Bennett DA, Bzdok D. Cell type transcriptomics reveal shared genetic mechanisms in Alzheimer's and Parkinson's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.17.638647. [PMID: 40027681 PMCID: PMC11870532 DOI: 10.1101/2025.02.17.638647] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
14
Pacheco NL, Hooten NN, Wu SF, Mensah-Bonsu M, Zhang Y, Chitrala KN, De S, Mode NA, Ezike N, Moody DLB, Zonderman AB, Evans MK. Genome-wide transcriptome differences associated with perceived discrimination in an urban, community-dwelling middle-aged cohort. FASEB J 2025;39:e70366. [PMID: 39887814 PMCID: PMC11874777 DOI: 10.1096/fj.202402000r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 01/09/2025] [Accepted: 01/21/2025] [Indexed: 02/01/2025]
15
Yu X, Xu H, Xing Y, Sun D, Li D, Shi J, Sui G, Li G. Identifying Essential Hub Genes and circRNA-Regulated ceRNA Networks in Hepatocellular Carcinoma. Int J Mol Sci 2025;26:1408. [PMID: 40003874 PMCID: PMC11855757 DOI: 10.3390/ijms26041408] [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: 01/05/2025] [Revised: 02/05/2025] [Accepted: 02/05/2025] [Indexed: 02/27/2025]  Open
16
Zhang H, Li X, Song D, Yukselen O, Nanda S, Kucukural A, Li JJ, Garber M, Walhout AJ. Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.02.636107. [PMID: 39975282 PMCID: PMC11838469 DOI: 10.1101/2025.02.02.636107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
17
Zhang Y, Chen F, Cao Y, Zhang H, Zhao L, Xu Y. Identifying diagnostic markers and establishing prognostic model for lung cancer based on lung cancer-derived exosomal genes. Cancer Biomark 2025;42:18758592251317400. [PMID: 40179422 DOI: 10.1177/18758592251317400] [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] [Indexed: 04/05/2025]
18
Yan G, Hua SH, Li JJ. Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data. Nat Commun 2025;16:1141. [PMID: 39880807 PMCID: PMC11779979 DOI: 10.1038/s41467-025-56080-w] [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: 05/28/2024] [Accepted: 01/06/2025] [Indexed: 01/31/2025]  Open
19
Dollinger E, Hernandez-Davies J, Felgner J, Jain A, Hwang M, Strahsburger E, Nakajima R, Jasinskas A, Nie Q, Pone EJ, Othy S, Davies DH. Combination adjuvant improves influenza virus immunity by downregulation of immune homeostasis genes in lymphocytes. Immunohorizons 2025;9:vlae007. [PMID: 39849993 PMCID: PMC11841980 DOI: 10.1093/immhor/vlae007] [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: 10/23/2024] [Accepted: 10/23/2024] [Indexed: 01/30/2025]  Open
20
Gui Y, Zhou G, Cui S, Li H, Lu H, Zhao H. The left amygdala is genetically sexually-dimorphic: multi-omics analysis of structural MRI volumes. Transl Psychiatry 2025;15:17. [PMID: 39843917 PMCID: PMC11754786 DOI: 10.1038/s41398-025-03223-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 12/03/2024] [Accepted: 01/07/2025] [Indexed: 01/24/2025]  Open
21
Bennett AR, Lundstrøm J, Chatterjee S, Thaysen-Andersen M, Bojar D. Compositional data analysis enables statistical rigor in comparative glycomics. Nat Commun 2025;16:795. [PMID: 39824855 PMCID: PMC11748655 DOI: 10.1038/s41467-025-56249-3] [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: 06/10/2024] [Accepted: 01/13/2025] [Indexed: 01/20/2025]  Open
22
Liu C, Li H, Hu X, Yan M, Fu Z, Zhang H, Wang Y, Du N. Spermine Synthase : A Potential Prognostic Marker for Lower-Grade Gliomas. J Korean Neurosurg Soc 2025;68:75-96. [PMID: 39492653 PMCID: PMC11725456 DOI: 10.3340/jkns.2024.0080] [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: 04/08/2024] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 11/05/2024]  Open
23
Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2025;68:5-102. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [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: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
24
Ahmad P, Escalante-Herrera A, Marin LM, Siqueira WL. Progression from healthy periodontium to gingivitis and periodontitis: Insights from bioinformatics-driven proteomics - A systematic review with meta-analysis. J Periodontal Res 2025;60:8-29. [PMID: 38873831 DOI: 10.1111/jre.13313] [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: 10/02/2023] [Revised: 05/23/2024] [Accepted: 05/26/2024] [Indexed: 06/15/2024]
25
Bhat GS, Shaik Mohammad AF. Mechanistic Modeling the Role of MicroRNAs and Transcription Factors in Disease Progression. Methods Mol Biol 2025;2883:195-230. [PMID: 39702710 DOI: 10.1007/978-1-0716-4290-0_9] [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] [Indexed: 12/21/2024]
26
Zhou J, Li M, Chen Y, Wang S, Wang D, Suo C, Chen X. Attenuated sex-related DNA methylation differences in cancer highlight the magnitude bias mediating existing disparities. Biol Sex Differ 2024;15:106. [PMID: 39716176 DOI: 10.1186/s13293-024-00682-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Accepted: 12/08/2024] [Indexed: 12/25/2024]  Open
27
Agrawal P, Hannenhalli S. Protocol for identifying key genes using network-based approach as an alternative to differential expression analysis. STAR Protoc 2024;5:103472. [PMID: 39636731 DOI: 10.1016/j.xpro.2024.103472] [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: 08/14/2024] [Revised: 09/23/2024] [Accepted: 10/30/2024] [Indexed: 12/07/2024]  Open
28
Grønvold L, van Dalum MJ, Striberny A, Manousi D, Ytrestøyl T, Mørkøre T, Boison S, Gjerde B, Jørgensen E, Sandve SR, Hazlerigg DG. Transcriptomic profiling of gill biopsies to define predictive markers for seawater survival in farmed Atlantic salmon. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39681120 DOI: 10.1111/jfb.16025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 11/20/2024] [Accepted: 11/25/2024] [Indexed: 12/18/2024]
29
Kim SC, Song JH, Kong NY. Personalized Game-Based Content and Performance: A Pilot Study on a Digital Intervention for Children with ADHD. Bioengineering (Basel) 2024;11:1277. [PMID: 39768095 PMCID: PMC11673005 DOI: 10.3390/bioengineering11121277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 12/10/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025]  Open
30
Wang J, Tian L, Yan L. Statistical methods for comparing two independent exponential-gamma means with application to single cell protein data. PLoS One 2024;19:e0314705. [PMID: 39671382 PMCID: PMC11643000 DOI: 10.1371/journal.pone.0314705] [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: 05/15/2024] [Accepted: 11/14/2024] [Indexed: 12/15/2024]  Open
31
Yang X, Chatterjee D, Couetil JL, Liu Z, Ardon VD, Chen C, Zhang J, Huang K, Johnson TS. Gradient boosting reveals spatially diverse cholesterol gene signatures in colon cancer. Front Genet 2024;15:1410353. [PMID: 39678375 PMCID: PMC11638177 DOI: 10.3389/fgene.2024.1410353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 11/08/2024] [Indexed: 12/17/2024]  Open
32
Baldazzi D, Doni M, Valenti B, Ciuffetti ME, Pezzella S, Maestro R. DElite: a tool for integrated differential expression analysis. Front Genet 2024;15:1440994. [PMID: 39634274 PMCID: PMC11614847 DOI: 10.3389/fgene.2024.1440994] [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: 05/30/2024] [Accepted: 11/05/2024] [Indexed: 12/07/2024]  Open
33
Okamoto F, Chitre AS, Missfeldt Sanches T, Chen D, Munro D, Aron AT, Beeson A, Bimschleger HV, Eid M, Garcia Martinez AG, Han W, Holl K, Jackson T, Johnson BB, King CP, Kuhn BN, Lamparelli AC, Netzley AH, Nguyen KMH, Peng BF, Tripi JA, Wang T, Ziegler KS, Adams DJ, Baud A, Carrette LLG, Chen H, de Guglielmo G, Dorrestein P, George O, Ishiwari K, Jablonski MM, Jhou TC, Kallupi M, Knight R, Meyer PJ, Solberg Woods LC, Polesskaya O, Palmer AA. Y and mitochondrial chromosomes in the heterogeneous stock rat population. G3 (BETHESDA, MD.) 2024;14:jkae213. [PMID: 39250761 PMCID: PMC11540319 DOI: 10.1093/g3journal/jkae213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 07/18/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024]
34
Huang AY, Burke KP, Porter R, Meiger L, Fatouros P, Yang J, Robitschek E, Vokes N, Ricker C, Rosado V, Tarantino G, Chen J, Aprati TJ, Glettig MC, He Y, Wang C, Fu D, Ho LL, Galani K, Freeman GJ, Buchbinder EI, Stephen Hodi F, Kellis M, Boland GM, Sharpe AH, Liu D. Stratified analysis identifies HIF-2α as a therapeutic target for highly immune-infiltrated melanomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.29.620300. [PMID: 39554029 PMCID: PMC11565796 DOI: 10.1101/2024.10.29.620300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
35
Yang L, Zhang X, Chen J. Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples. Genome Biol 2024;25:282. [PMID: 39478636 PMCID: PMC11523781 DOI: 10.1186/s13059-024-03230-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 03/28/2024] [Indexed: 11/02/2024]  Open
36
Hejblum BP, Ba K, Thiébaut R, Agniel D. Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives. Genome Biol 2024;25:281. [PMID: 39478633 PMCID: PMC11523660 DOI: 10.1186/s13059-024-03231-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 03/28/2024] [Indexed: 11/02/2024]  Open
37
Ge X, Li Y, Li W, Li JJ. Response to "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" and "Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples". Genome Biol 2024;25:283. [PMID: 39478544 PMCID: PMC11526515 DOI: 10.1186/s13059-024-03232-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/28/2024] [Indexed: 11/02/2024]  Open
38
Spottiswoode N, Tsitsiklis A, Chu VT, Phan HV, DeVoe C, Love C, Ghale R, Bloomstein J, Zha BS, Maguire CP, Glascock A, Sarma A, Mourani PM, Kalantar KL, Detweiler A, Neff N, Haller SC, COMET Consortium, DeRisi JL, Erle DJ, Hendrickson CM, Kangelaris KN, Krummel MF, Matthay MA, Woodruff PG, Calfee CS, Langelier CR. Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia. Nat Commun 2024;15:9339. [PMID: 39472555 PMCID: PMC11522429 DOI: 10.1038/s41467-024-53566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Collaborators] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 10/16/2024] [Indexed: 11/02/2024]  Open
39
Pan Y, Chiu TP, Zhou L, Chan P, Kuo TT, Battaglin F, Soni S, Jayachandran P, Li JJ, Lenz HJ, Mumenthaler SM, Rohs R, Torres ER, Kay SA. Targeting circadian transcriptional programs through a cis-regulatory mechanism in triple negative breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.590360. [PMID: 38746115 PMCID: PMC11092448 DOI: 10.1101/2024.04.26.590360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
40
Yan G, Hua SH, Li JJ. Categorization of 33 computational methods to detect spatially variable genes from spatially resolved transcriptomics data. ARXIV 2024:arXiv:2405.18779v4. [PMID: 38855546 PMCID: PMC11160866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
41
Redmond EJ, Ronald J, Davis SJ, Ezer D. Single-plant-omics reveals the cascade of transcriptional changes during the vegetative-to-reproductive transition. THE PLANT CELL 2024;36:4594-4606. [PMID: 39121073 PMCID: PMC11449079 DOI: 10.1093/plcell/koae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 06/26/2024] [Accepted: 08/02/2024] [Indexed: 08/11/2024]
42
He MY, Tong KI, Liu T, Whittaker Hawkins R, Shelton V, Zeng Y, Bakhtiari M, Xiao Y, Zheng G, Sakhdari A, Yang L, Xu W, Brooks DG, Laister RC, He HH, Kridel R. GNAS knockout potentiates HDAC3 inhibition through viral mimicry-related interferon responses in lymphoma. Leukemia 2024;38:2210-2224. [PMID: 39117798 PMCID: PMC11436380 DOI: 10.1038/s41375-024-02325-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 08/10/2024]
43
He C, Zhang J, Bai X, Lu C, Zhang K. Lysine lactylation-based insight to understanding the characterization of cervical cancer. Biochim Biophys Acta Mol Basis Dis 2024;1870:167356. [PMID: 39025375 DOI: 10.1016/j.bbadis.2024.167356] [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: 11/09/2023] [Revised: 06/28/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024]
44
Chen B, Wang D, Xu Y, Guo Q, Pan J, Yu S, Fang Y, Xiao S, Ruan Y, Yang S, Lin M, Hong J, Zhan Z, Lin S. 5-Hydroxymethylcytosines in circulating cell-free DNA as a diagnostic biomarker for nasopharyngeal carcinoma. Eur J Cancer 2024;210:114294. [PMID: 39213787 DOI: 10.1016/j.ejca.2024.114294] [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: 04/24/2024] [Revised: 07/07/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
45
Pelayo R, Gutiérrez-Gil B, Marina H, Fonseca PAS, Alonso-García M, Arranz JJ, Suárez-Vega A. Unraveling Dynamic Transcriptomic Changes in Sheep's Lactating Mammary Gland Following Escherichia coli Lipopolysaccharide Exposure. J Dairy Sci 2024:S0022-0302(24)01149-4. [PMID: 39343208 DOI: 10.3168/jds.2024-25009] [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: 04/04/2024] [Accepted: 08/16/2024] [Indexed: 10/01/2024]
46
von der Heyde S, Raman N, Gabelia N, Matias-Guiu X, Yoshino T, Tsukada Y, Melino G, Marshall JL, Wellstein A, Juhl H, Landgrebe J. Tumor specimen cold ischemia time impacts molecular cancer drug target discovery. Cell Death Dis 2024;15:691. [PMID: 39327466 PMCID: PMC11427669 DOI: 10.1038/s41419-024-07090-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 09/12/2024] [Accepted: 09/17/2024] [Indexed: 09/28/2024]
47
Chen S, Wang P, Guo H, Zhang Y. Deciphering gene expression patterns using large-scale transcriptomic data and its applications. Brief Bioinform 2024;25:bbae590. [PMID: 39541191 PMCID: PMC11562847 DOI: 10.1093/bib/bbae590] [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: 08/02/2024] [Revised: 10/07/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024]  Open
48
Yu A, Yesilkanal A, Thakur A, Wang F, Yang Y, Phillips W, Wu X, Muir A, He X, Spitz F, Yang L. HYENA detects oncogenes activated by distal enhancers in cancer. Nucleic Acids Res 2024;52:e77. [PMID: 39051548 PMCID: PMC11381332 DOI: 10.1093/nar/gkae646] [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: 04/04/2024] [Revised: 06/07/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024]  Open
49
McCrimmon CM, Toker D, Pahos M, Lozano K, Lin JJ, Parent J, Tidball A, Zheng J, Molnár L, Mody I, Novitch BG, Samarasinghe RA. Modeling Cortical Versus Hippocampal Network Dysfunction in a Human Brain Assembloid Model of Epilepsy and Intellectual Disability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.07.611739. [PMID: 39282353 PMCID: PMC11398483 DOI: 10.1101/2024.09.07.611739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
50
Wang D, Gazzara MR, Jewell S, Wales-McGrath B, Brown CD, Choi PS, Barash Y. A Deep Dive into Statistical Modeling of RNA Splicing QTLs Reveals New Variants that Explain Neurodegenerative Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.01.610696. [PMID: 39282456 PMCID: PMC11398334 DOI: 10.1101/2024.09.01.610696] [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: 09/22/2024]
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