167 related articles for article (PubMed ID: 25717192)
1. Guidance for RNA-seq co-expression network construction and analysis: safety in numbers.
Ballouz S; Verleyen W; Gillis J
Bioinformatics; 2015 Jul; 31(13):2123-30. PubMed ID: 25717192
[TBL] [Abstract][Full Text] [Related]
2. Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.
Li W; Jiang T
Bioinformatics; 2012 Nov; 28(22):2914-21. PubMed ID: 23060617
[TBL] [Abstract][Full Text] [Related]
3. Seq-ing improved gene expression estimates from microarrays using machine learning.
Korir PK; Geeleher P; Seoighe C
BMC Bioinformatics; 2015 Sep; 16():286. PubMed ID: 26338512
[TBL] [Abstract][Full Text] [Related]
4. Covariate-dependent negative binomial factor analysis of RNA sequencing data.
Zamani Dadaneh S; Zhou M; Qian X
Bioinformatics; 2018 Jul; 34(13):i61-i69. PubMed ID: 29949981
[TBL] [Abstract][Full Text] [Related]
5. Genes, behavior and next-generation RNA sequencing.
Hitzemann R; Bottomly D; Darakjian P; Walter N; Iancu O; Searles R; Wilmot B; McWeeney S
Genes Brain Behav; 2013 Feb; 12(1):1-12. PubMed ID: 23194347
[TBL] [Abstract][Full Text] [Related]
6. LSTrAP: efficiently combining RNA sequencing data into co-expression networks.
Proost S; Krawczyk A; Mutwil M
BMC Bioinformatics; 2017 Oct; 18(1):444. PubMed ID: 29017446
[TBL] [Abstract][Full Text] [Related]
7. From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data.
Li J; Hou J; Sun L; Wilkins JM; Lu Y; Niederhuth CE; Merideth BR; Mawhinney TP; Mossine VV; Greenlief CM; Walker JC; Folk WR; Hannink M; Lubahn DB; Birchler JA; Cheng J
PLoS One; 2015; 10(4):e0125000. PubMed ID: 25902288
[TBL] [Abstract][Full Text] [Related]
8. Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data.
Johnson KA; Krishnan A
Genome Biol; 2022 Jan; 23(1):1. PubMed ID: 34980209
[TBL] [Abstract][Full Text] [Related]
9. Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data.
Huang J; Vendramin S; Shi L; McGinnis KM
Plant Physiol; 2017 Sep; 175(1):568-583. PubMed ID: 28768814
[TBL] [Abstract][Full Text] [Related]
10. Empirical Bayes conditional independence graphs for regulatory network recovery.
Mahdi R; Madduri AS; Wang G; Strulovici-Barel Y; Salit J; Hackett NR; Crystal RG; Mezey JG
Bioinformatics; 2012 Aug; 28(15):2029-36. PubMed ID: 22685074
[TBL] [Abstract][Full Text] [Related]
11. RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.
Warren AS; Aurrecoechea C; Brunk B; Desai P; Emrich S; Giraldo-Calderón GI; Harb O; Hix D; Lawson D; Machi D; Mao C; McClelland M; Nordberg E; Shukla M; Vosshall LB; Wattam AR; Will R; Yoo HS; Sobral B
Bioinformatics; 2015 May; 31(9):1496-8. PubMed ID: 25573919
[TBL] [Abstract][Full Text] [Related]
12. An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era.
Su Z; Fang H; Hong H; Shi L; Zhang W; Zhang W; Zhang Y; Dong Z; Lancashire LJ; Bessarabova M; Yang X; Ning B; Gong B; Meehan J; Xu J; Ge W; Perkins R; Fischer M; Tong W
Genome Biol; 2014 Dec; 15(12):523. PubMed ID: 25633159
[TBL] [Abstract][Full Text] [Related]
13. Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference.
Singh V; Kirtipal N; Song B; Lee S
Brief Bioinform; 2024 Mar; 25(3):. PubMed ID: 38770720
[TBL] [Abstract][Full Text] [Related]
14. A Poisson Log-Normal Model for Constructing Gene Covariation Network Using RNA-seq Data.
Choi Y; Coram M; Peng J; Tang H
J Comput Biol; 2017 Jul; 24(7):721-731. PubMed ID: 28557607
[TBL] [Abstract][Full Text] [Related]
15. Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data.
Zhang J; Zhu W; Wang Q; Gu J; Huang LF; Sun X
PLoS Comput Biol; 2019 Nov; 15(11):e1007435. PubMed ID: 31682596
[TBL] [Abstract][Full Text] [Related]
16. CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model.
Wang J; Wan YW; Al-Ouran R; Huang M; Liu Z
Brief Bioinform; 2023 Nov; 25(1):. PubMed ID: 38113079
[TBL] [Abstract][Full Text] [Related]
17. Ambiguous genes due to aligners and their impact on RNA-seq data analysis.
Szabelska-Beresewicz A; Zyprych-Walczak J; Siatkowski I; Okoniewski M
Sci Rep; 2023 Dec; 13(1):21770. PubMed ID: 38066001
[TBL] [Abstract][Full Text] [Related]
18. Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain.
Harris BD; Crow M; Fischer S; Gillis J
Cell Syst; 2021 Jul; 12(7):748-756.e3. PubMed ID: 34015329
[TBL] [Abstract][Full Text] [Related]
19. A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets.
Izadi F; Zarrini HN; Kiani G; Jelodar NB
Bioinformation; 2016; 12(6):340-346. PubMed ID: 28293077
[TBL] [Abstract][Full Text] [Related]
20. A global [Formula: see text] gene co-expression network constructed from hundreds of experimental conditions with missing values.
Kuang J; Buchon N; Michel K; Scoglio C
BMC Bioinformatics; 2022 May; 23(1):170. PubMed ID: 35534830
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]