A
Alexandra B Keenan
Researcher at Icahn School of Medicine at Mount Sinai
Publications - 11
Citations - 1887
Alexandra B Keenan is an academic researcher from Icahn School of Medicine at Mount Sinai. The author has contributed to research in topics: Gene & Gene expression. The author has an hindex of 10, co-authored 11 publications receiving 1004 citations.
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Journal ArticleDOI
Massive mining of publicly available RNA-seq data from human and mouse.
Alexander Lachmann,Denis Torre,Alexandra B Keenan,Kathleen M. Jagodnik,Hoyjin J. Lee,Lily Wang,Moshe C. Silverstein,Avi Ma'ayan +7 more
TL;DR: A high-throughput processing infrastructure and search database (ARCHS4) that provides processed RNA-seq data for 187,946 publicly available mouse and human samples to support exploration and reuse is developed.
Journal ArticleDOI
ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Alexandra B Keenan,Denis Torre,Alexander Lachmann,Ariel K Leong,Megan L. Wojciechowicz,Vivian Utti,Kathleen M. Jagodnik,Eryk Kropiwnicki,Zichen Wang,Avi Ma'ayan +9 more
TL;DR: The ChEA3 background database contains a collection of gene set libraries generated from multiple sources including TF–gene co-expression from RNA-seq studies, TF–target associations from ChIP-seq experiments, and TF-gree co-occurrence computed from crowd-submitted gene lists, which illuminate general transcription factor properties such as whether the TF behaves as an activator or a repressor.
Journal ArticleDOI
The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations
Alexandra B Keenan,Sherry L. Jenkins,Kathleen M. Jagodnik,Simon Koplev,Edward He,Denis Torre,Zichen Wang,Anders B. Dohlman,Moshe C. Silverstein,Alexander Lachmann,Maxim V. Kuleshov,Avi Ma'ayan,Vasileios Stathias,Raymond Terryn,Daniel J. Cooper,Michele Forlin,Amar Koleti,Dusica Vidovic,Caty Chung,Stephan C. Schürer,Jouzas Vasiliauskas,Marcin Pilarczyk,Behrouz Shamsaei,Mehdi Fazel,Yan Ren,Wen Niu,Nicholas A. Clark,Shana White,Naim Al Mahi,Lixia Zhang,Michal Kouril,John F. Reichard,Siva Sivaganesan,Mario Medvedovic,Jaroslaw Meller,Rick J. Koch,Marc R. Birtwistle,Ravi Iyengar,Eric A. Sobie,Evren U. Azeloglu,Julia A. Kaye,Jeannette Osterloh,Kelly Haston,Jaslin Kalra,Steve Finkbiener,Jonathan Z. Li,Pamela Milani,Miriam Adam,Renan Escalante-Chong,Karen Sachs,Alexander LeNail,Divya Ramamoorthy,Ernest Fraenkel,Gavin Daigle,Uzma Hussain,Alyssa Coye,Jeffrey D. Rothstein,Dhruv Sareen,Loren Ornelas,Maria G. Banuelos,Berhan Mandefro,Ritchie Ho,Clive N. Svendsen,Ryan G. Lim,Jennifer Stocksdale,Malcolm Casale,Terri G. Thompson,Jie Wu,Leslie M. Thompson,Victoria Dardov,Vidya Venkatraman,Andrea Matlock,Jennifer E. Van Eyk,Jacob D. Jaffe,Malvina Papanastasiou,Aravind Subramanian,Todd R. Golub,Sean D. Erickson,Mohammad Fallahi-Sichani,Marc Hafner,Nathanael S. Gray,Jia-Ren Lin,Caitlin E. Mills,Jeremy L. Muhlich,Mario Niepel,Caroline E. Shamu,Elizabeth H. Williams,David Wrobel,Peter K. Sorger,Laura M. Heiser,Joe W. Gray,James E. Korkola,Gordon B. Mills,Mark A. LaBarge,Mark A. LaBarge,Heidi S. Feiler,Mark A. Dane,Elmar Bucher,Michel Nederlof,Damir Sudar,Sean M. Gross,David Kilburn,Rebecca Smith,Kaylyn Devlin,Ron Margolis,Leslie Derr,Albert Lee,Ajay Pillai +107 more
TL;DR: The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders.
Journal ArticleDOI
Brain Cell Type Specific Gene Expression and Co-expression Network Architectures
Andrew M. McKenzie,Minghui Wang,Mads E. Hauberg,John F. Fullard,Alexey Kozlenkov,Alexandra B Keenan,Yasmin L. Hurd,Stella Dracheva,Patrizia Casaccia,Panos Roussos,Bin Zhang +10 more
TL;DR: A set of novel brain cell consensus signatures and robust networks from the integration of multiple datasets are identified and therefore transcend limitations related to technical issues characteristic of each individual study.
Posted ContentDOI
Massive Mining of Publicly Available RNA-seq Data from Human and Mouse
Alexander Lachmann,Denis Torre,Alexandra B Keenan,Kathleen M. Jagodnik,Hoyjin J. Lee,Moshe C. Silverstein,Lily Wang,Avi Ma'ayan +7 more
TL;DR: ARCHS4, a web resource that makes the majority of previously published RNA-seq data from human and mouse freely available at the gene count level, outperforms co-expression data created from other major gene expression data repositories such as GTEx and CCLE.