An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study [version 1; referees: 2 approved]

by Zichen Wang, Avi Ma'ayan
Published 2016-07-01

Predicting opioid dependence from electronic health records with machine learning

by Randall J. Ellis, Zichen Wang, Nicholas Genes, Avi Ma’ayan
Published 2019-01-01

Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition.

by Simon Koplev, Katie Lin, Anders B Dohlman, Avi Ma'ayan
Published 2018-01-01

Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells.

by Huilei Xu, Yen-Sin Ang, Ana Sevilla, Ihor R Lemischka, Avi Ma'ayan
Published 2014-08-01

Endothelial cells instruct liver specification of embryonic stem cell-derived endoderm through endothelial VEGFR2 signaling and endoderm epigenetic modifications

by Songyan Han, Christopher Tan, Junjun Ding, Jianlong Wang, Avi Ma'ayan, Valerie Gouon-Evans
Published 2018-07-01

Massive mining of publicly available RNA-seq data from human and mouse

by Alexander Lachmann, Denis Torre, Alexandra B. Keenan, Kathleen M. Jagodnik, Hoyjin J. Lee, Lily Wang, Moshe C. Silverstein, Avi Ma’ayan
Published 2018-04-01

Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis.

by Noura S Abul-Husn, Suresh P Annangudi, Avi Ma'ayan, Dinah L Ramos-Ortolaza, Steven D Stockton, Ivone Gomes, Jonathan V Sweedler, Lakshmi A Devi
Published 2011-01-01

Transcriptome analysis of human dermal fibroblasts following red light phototherapy

by Evan Austin, Eugene Koo, Alexander Merleev, Denis Torre, Alina Marusina, Guillaume Luxardi, Andrew Mamalis, Roslyn Rivkah Isseroff, Avi Ma’ayan, Emanual Maverakis, Jared Jagdeo
Published 2021-04-01

Far away from the lamppost.

by Tudor I Oprea, Lily Jan, Gary L Johnson, Bryan L Roth, Avi Ma'ayan, Stephan Schürer, Brian K Shoichet, Larry A Sklar, Michael T McManus
Published 2018-12-01

Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles

by Amélie Rezza, Zichen Wang, Rachel Sennett, Wenlian Qiao, Dongmei Wang, Nicholas Heitman, Ka Wai Mok, Carlos Clavel, Rui Yi, Peter Zandstra, Avi Ma’ayan, Michael Rendl
Published 2016-03-01

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

by Claudia Scheckel, Elodie Drapeau, Maria A Frias, Christopher Y Park, John Fak, Ilana Zucker-Scharff, Yan Kou, Vahram Haroutunian, Avi Ma'ayan, Joseph D Buxbaum, Robert B Darnell
Published 2016-02-01

Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons.

by Raphael Rozenfeld, Ittai Bushlin, Ivone Gomes, Nikos Tzavaras, Achla Gupta, Susana Neves, Lorenzo Battini, G Luca Gusella, Alexander Lachmann, Avi Ma'ayan, Robert D Blitzer, Lakshmi A Devi
Published 2012-01-01

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling

by Mario Niepel, Marc Hafner, Qiaonan Duan, Zichen Wang, Evan O. Paull, Mirra Chung, Xiaodong Lu, Joshua M. Stuart, Todd R. Golub, Aravind Subramanian, Avi Ma’ayan, Peter K. Sorger
Published 2017-10-01

Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.

by Amin R Mazloom, Ruth Dannenfelser, Neil R Clark, Arsen V Grigoryan, Kathryn M Linder, Timothy J Cardozo, Julia C Bond, Aislyn D W Boran, Ravi Iyengar, Anna Malovannaya, Rainer B Lanz, Avi Ma'ayan
Published 2011-12-01

The COVID-19 Drug and Gene Set Library

by Maxim V. Kuleshov, Daniel J. Stein, Daniel J.B. Clarke, Eryk Kropiwnicki, Kathleen M. Jagodnik, Alon Bartal, John E. Evangelista, Jason Hom, Minxuan Cheng, Allison Bailey, Abigail Zhou, Laura B. Ferguson, Alexander Lachmann, Avi Ma'ayan
Published 2020-09-01

Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming

by Andreia M. Gomes, Ilia Kurochkin, Betty Chang, Michael Daniel, Kenneth Law, Namita Satija, Alexander Lachmann, Zichen Wang, Lino Ferreira, Avi Ma’ayan, Benjamin K. Chen, Dmitri Papatsenko, Ihor R. Lemischka, Kateri A. Moore, Carlos-Filipe Pereira
Published 2018-12-01

SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling

by Thomas Strub, Flavia G. Ghiraldini, Saul Carcamo, Man Li, Aleksandra Wroblewska, Rajendra Singh, Matthew S. Goldberg, Dan Hasson, Zichen Wang, Stuart J. Gallagher, Peter Hersey, Avi Ma’ayan, Georgina V. Long, Richard A. Scolyer, Brian Brown, Bin Zheng, Emily Bernstein
Published 2018-08-01

Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte.

by Thomas Hays, Avi Ma'ayan, Neil R Clark, Christopher M Tan, Avelino Teixeira, Angela Teixeira, Jae W Choi, Nora Burdis, Sung Yun Jung, Amol O Bajaj, Bert W O'Malley, John C He, Deborah P Hyink, Paul E Klotman
Published 2014-01-01

A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis.

by Raymond Liang, Genís Campreciós, Yan Kou, Kathleen McGrath, Roberta Nowak, Seana Catherman, Carolina L Bigarella, Pauline Rimmelé, Xin Zhang, Merlin Nithya Gnanapragasam, James J Bieker, Dmitri Papatsenko, Avi Ma'ayan, Emery Bresnick, Velia Fowler, James Palis, Saghi Ghaffari
Published 2015-10-01

Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing

by Daniel J. B. Clarke, Alison W. Rebman, Allison Bailey, Megan L. Wojciechowicz, Sherry L. Jenkins, John E. Evangelista, Matteo Danieletto, Jinshui Fan, Mark W. Eshoo, Michael R. Mosel, William Robinson, Nitya Ramadoss, Jason Bobe, Mark J. Soloski, John N. Aucott, Avi Ma'ayan
Published 2021-03-01