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

by Helena Kuri-Magaña, Helena Kuri-Magaña, Leonardo Collado-Torres, Leonardo Collado-Torres, Andrew E. Jaffe, Andrew E. Jaffe, Andrew E. Jaffe, Andrew E. Jaffe, Humberto Valdovinos-Torres, Marbella Ovilla-Muñoz, Juan Téllez-Sosa, Laura C. Bonifaz, Jesús Martínez-Barnetche
Published 2018-11-01

regionReport: Interactive reports for region-level and feature-level genomic analyses [version 2; referees: 2 approved, 1 approved with reservations]

by Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek
Published 2016-06-01

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]

by Leonardo Collado-Torres, Abhinav Nellore, Andrew E. Jaffe
Published 2017-08-01

Addressing confounding artifacts in reconstruction of gene co-expression networks

by Princy Parsana, Claire Ruberman, Andrew E. Jaffe, Michael C. Schatz, Alexis Battle, Jeffrey T. Leek
Published 2019-05-01

DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epige...

by Alexey Kozlenkov, Andrew E. Jaffe, Alisa Timashpolsky, Pasha Apontes, Sergei Rudchenko, Mihaela Barbu, William Byne, Yasmin L. Hurd, Steve Horvath, Stella Dracheva
Published 2017-05-01

BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior

by Kristen R Maynard, John W Hobbs, BaDoi N Phan, Amolika Gupta, Sumita Rajpurohit, Courtney Williams, Anandita Rajpurohit, Joo Heon Shin, Andrew E Jaffe, Keri Martinowich
Published 2018-09-01

Use of postmortem human dura mater and scalp for deriving human fibroblast cultures.

by Lindsay A Bliss, Malik R Sams, Amy Deep-Soboslay, Renee Ren-Patterson, Andrew E Jaffe, Josh G Chenoweth, Amritha Jaishankar, Joel E Kleinman, Thomas M Hyde
Published 2012-01-01

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

by Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger, Joo Heon Shin
Published 2019-06-01

Cerebral cortex and blood transcriptome changes in mouse neonates prenatally exposed to air pollution particulate matter

by Amin Haghani, Jason I. Feinberg, Kristy C. Lewis, Christine Ladd-Acosta, Richard G. Johnson, Andrew E. Jaffe, Constantinos Sioutas, Caleb E. Finch, Daniel B. Campbell, Todd E. Morgan, Heather E. Volk
Published 2021-08-01

African-American and Caucasian participation in postmortem human brain donation for neuropsychiatric research.

by Amy Deep-Soboslay, Michelle I Mighdoll, Andrew E Jaffe, Stephen B Thomas, Mary M Herman, Jonathan Sirovatka, Jewell P King, David R Fowler, Dawn Zulauf, Constance DiAngelo, Thomas M Hyde, Joel E Kleinman
Published 2019-01-01

Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age.

by Nikolay A Ivanov, Ran Tao, Joshua G Chenoweth, Anna Brandtjen, Michelle I Mighdoll, John D Genova, Ronald D McKay, Yankai Jia, Daniel R Weinberger, Joel E Kleinman, Thomas M Hyde, Andrew E Jaffe
Published 2016-02-01

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation

by Amanda J. Price, Leonardo Collado-Torres, Nikolay A. Ivanov, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Published 2019-09-01

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

by Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe, Leonardo Collado-Torres
Published 2021-05-01

Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses

by Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe, Leonardo Collado-Torres
Published 2021-07-01

Comparison of quantitative trait loci methods: Total expression and allelic imbalance method in brain RNA-seq.

by Jesper R Gådin, Alfonso Buil, Carlo Colantuoni, Andrew E Jaffe, Jacob Nielsen, Joo-Heon Shin, Thomas M Hyde, Joel E Kleinman, BrainSeq Consortium, Niels Plath, Per Eriksson, Søren Brunak, Michael Didriksen, Daniel R Weinberger, Lasse Folkersen
Published 2019-01-01

Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk

by Kira A. Perzel Mandell, Nicholas J. Eagles, Richard Wilton, Amanda J. Price, Stephen A. Semick, Leonardo Collado-Torres, William S. Ulrich, Ran Tao, Shizhong Han, Alexander S. Szalay, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Published 2021-09-01

Hypomethylation of the IL17RC Promoter in Peripheral Blood Leukocytes Is Not A Hallmark of Age-Related Macular Degeneration

by Verity F. Oliver, Maria Franchina, Andrew E. Jaffe, Kari E. Branham, Mohammad Othman, John R. Heckenlively, Anand Swaroop, Betsy Campochiaro, Brendan J. Vote, Jamie E. Craig, Richard Saffery, David A. Mackey, Jiang Qian, Donald J. Zack, Alex W. Hewitt, Shannath L. Merbs
Published 2013-12-01

Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

by Emily E. Burke, Joshua G. Chenoweth, Joo Heon Shin, Leonardo Collado-Torres, Suel-Kee Kim, Nicola Micali, Yanhong Wang, Carlo Colantuoni, Richard E. Straub, Daniel J. Hoeppner, Huei-Ying Chen, Alana Sellers, Kamel Shibbani, Gregory R. Hamersky, Marcelo Diaz Bustamante, BaDoi N. Phan, William S. Ulrich, Cristian Valencia, Amritha Jaishankar, Amanda J. Price, Anandita Rajpurohit, Stephen A. Semick, Roland W. Bürli, James C. Barrow, Daniel J. Hiler, Stephanie C. Page, Keri Martinowich, Thomas M. Hyde, Joel E. Kleinman, Karen F. Berman, Jose A. Apud, Alan J. Cross, Nicholas J. Brandon, Daniel R. Weinberger, Brady J. Maher, Ronald D. G. McKay, Andrew E. Jaffe
Published 2020-01-01