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Items: 11


Improving the value of public RNA-seq expression data by phenotype prediction.

Ellis SE, Collado-Torres L, Jaffe A, Leek JT.

Nucleic Acids Res. 2018 Mar 5. doi: 10.1093/nar/gky102. [Epub ahead of print]


recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor.

Collado-Torres L, Nellore A, Jaffe AE.

F1000Res. 2017 Aug 24;6:1558. doi: 10.12688/f1000research.12223.1. eCollection 2017.


Altered expression of histamine signaling genes in autism spectrum disorder.

Wright C, Shin JH, Rajpurohit A, Deep-Soboslay A, Collado-Torres L, Brandon NJ, Hyde TM, Kleinman JE, Jaffe AE, Cross AJ, Weinberger DR.

Transl Psychiatry. 2017 May 9;7(5):e1126. doi: 10.1038/tp.2017.87.


Reproducible RNA-seq analysis using recount2.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT.

Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. No abstract available.


Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA III, Karbhari N, Hansen KD, Langmead B, Leek JT.

Genome Biol. 2016 Dec 30;17(1):266. doi: 10.1186/s13059-016-1118-6.


Flexible expressed region analysis for RNA-seq with derfinder.

Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE.

Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29.


Rail-RNA: scalable analysis of RNA-seq splicing and coverage.

Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B.

Bioinformatics. 2017 Dec 15;33(24):4033-4040. doi: 10.1093/bioinformatics/btw575.


regionReport: Interactive reports for region-level and feature-level genomic analyses.

Collado-Torres L, Jaffe AE, Leek JT.

Version 2. F1000Res. 2015 May 1 [revised 2016 Jan 1];4:105. doi: 10.12688/f1000research.6379.2. eCollection 2015.


Developmental regulation of human cortex transcription and its clinical relevance at single base resolution.

Jaffe AE, Shin J, Collado-Torres L, Leek JT, Tao R, Li C, Gao Y, Jia Y, Maher BJ, Hyde TM, Kleinman JE, Weinberger DR.

Nat Neurosci. 2015 Jan;18(1):154-161. doi: 10.1038/nn.3898. Epub 2014 Dec 15.


Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus.

Shank EA, Klepac-Ceraj V, Collado-Torres L, Powers GE, Losick R, Kolter R.

Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):E1236-43. doi: 10.1073/pnas.1103630108. Epub 2011 Nov 10.


RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D98-105. doi: 10.1093/nar/gkq1110. Epub 2010 Nov 4.

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