Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 18

1.

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods.

Wright C, Rajpurohit A, Burke EE, Williams C, Collado-Torres L, Kimos M, Brandon NJ, Cross AJ, Jaffe AE, Weinberger DR, Shin JH.

BMC Genomics. 2019 Jun 21;20(1):513. doi: 10.1186/s12864-019-5870-3.

2.

Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia.

Collado-Torres L, Burke EE, Peterson A, Shin J, Straub RE, Rajpurohit A, Semick SA, Ulrich WS; BrainSeq Consortium, Price AJ, Valencia C, Tao R, Deep-Soboslay A, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE.

Neuron. 2019 Jul 17;103(2):203-216.e8. doi: 10.1016/j.neuron.2019.05.013. Epub 2019 Jun 4.

PMID:
31174959
3.

Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells.

Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado-Torres L, Halushka MK, Kim MS, Pandey A.

Proteomics. 2019 Aug;19(15):e1800315. doi: 10.1002/pmic.201800315. Epub 2019 Jun 26.

PMID:
30983154
4.

Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer's disease.

Semick SA, Bharadwaj RA, Collado-Torres L, Tao R, Shin JH, Deep-Soboslay A, Weiss JR, Weinberger DR, Hyde TM, Kleinman JE, Jaffe AE, Mattay VS.

Acta Neuropathol. 2019 Apr;137(4):557-569. doi: 10.1007/s00401-019-01966-5. Epub 2019 Feb 2.

PMID:
30712078
5.

Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses.

Kuri-Magaña H, Collado-Torres L, Jaffe AE, Valdovinos-Torres H, Ovilla-Muñoz M, Téllez-Sosa J, Bonifaz LC, Martínez-Barnetche J.

Front Immunol. 2018 Nov 21;9:2679. doi: 10.3389/fimmu.2018.02679. eCollection 2018.

6.

Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome.

Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A, Tao R, Huestis MA, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberger DR, Hancock DB, Kleinman JE, Jaffe AE.

Mol Psychiatry. 2018 Aug 21. doi: 10.1038/s41380-018-0223-1. [Epub ahead of print]

7.

Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis.

Jaffe AE, Straub RE, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-Soboslay A; BrainSeq Consortium, Cross AJ, Brandon NJ, Leek JT, Hyde TM, Kleinman JE, Weinberger DR.

Nat Neurosci. 2018 Aug;21(8):1117-1125. doi: 10.1038/s41593-018-0197-y. Epub 2018 Jul 26.

8.

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 May 18;46(9):e54. doi: 10.1093/nar/gky102.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

Supplemental Content

Loading ...
Support Center