Garber Lab Publications
This collection showcases journal articles and other publications authored by researchers in the Garber Lab. The Garber Lab at the University of Massachusetts Medical School was established in 2012, in the Program in Bioinformatics and Integrative Biology.
Publications from 2020
The Tec kinase ITK differentially optimizes NFAT, NF-κB, and MAPK signaling during early T cell activation to regulate graded gene induction [preprint], Michael P. Gallagher, James M. Conley, Pranitha Vangala, Andrea Reboldi, Manuel Garber, and Leslie J. Berg
A comparative genomics multitool for scientific discovery and conservation, Zoonomia Consortium, Diane P. Genereux, Manuel Garber, Kerstin Lindblad-Toh, and Elinor K. Karlsson
An atlas of cell types in the mouse epididymis and vas deferens, Vera D. Rinaldi, Elisa Donnard, Kyle Gellatly, Morten Rasmussen, Alper Kucukural, Onur Yukselen, Manuel Garber, Upasna Sharma, and Oliver J. Rando
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues, Carly G. K. Ziegler, Yuming Cao, Zhiru Guo, Jennifer P. Wang, Robert W. Finberg, Manuel Garber, Alex K. Shalek, Jose Ordovas-Montanes, and HCA Lung Biological Network
DolphinNext: a distributed data processing platform for high throughput genomics, Onur Yukselen, Osman Turkyilmaz, Ahmet R. Ozturk, Manuel Garber, and Alper Kucukural
HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cells, Yetao Wang, Lawrence M. Lifshitz, Kyle Gellatly, Sean M. McCauley, Pranitha Vangala, Kyusik Kim, Alan G. Derr, Smita Jaiswal, Alper Kucukural, Patrick McDonel, Thomas C. Greenough, JeanMarie Houghton, Manuel Garber, and Jeremy Luban
Single Cell Transcriptomics Reveals Dysregulated Cellular and Molecular Networks in a Fragile X Syndrome model [preprint], Elisa Donnard, Huan Shu, and Manuel Garber
An atlas of cell types in the mammalian epididymis and vas deferens [preprint], Vera D. Rinaldi, Elisa Donnard, Kyle Gellatly, Morten Rasmussen, Alper Kucukural, Onur Yukselen, Manuel Garber, Upasna Sharma, and Oliver J. Rando
Recovery of viable endocrine-specific cells and transcriptomes from human pancreatic islet-engrafted mice, Sambra D. Redick, Linda Leehy, Ann R. Rittenhouse, David M. Blodgett, Alan G. Derr, Alper Kucukural, Manuel Garber, Leonard D. Shultz, Dale L. Greiner, Jennifer P. Wang, David M. Harlan, Rita Bortell, and Agata Jurczyk
Publications from 2019
Frequent Loss of IRF2 in Cancers Leads to Immune Evasion through Decreased MHC Class I Antigen Presentation and Increased PD-L1 Expression, Barry Kriegsman, Pranitha Vangala, Benjamin J. Chen, Paul Meraner, Abraham L. Brass, Manuel Garber, and Kenneth L. Rock
Diverse repertoire of human adipocyte subtypes develops from transcriptionally distinct mesenchymal progenitor cells, So Yun Min, Anand Desai, Zinger Yang, Agastya Sharma, Tiffany DeSouza, Ryan Genga, Alper Kucukural, Lawrence M. Lifshitz, Soren Nielsen, Camilla Scheele, Rene Maehr, Manuel Garber, and Silvia Corvera
HLA Class II Antigen Processing and Presentation Pathway Components Demonstrated by Transcriptome and Protein Analyses of Islet beta-Cells From Donors With Type 1 Diabetes, Mark A. Russell, Sambra D. Redick, David Blodgett, Jenny Aurielle B. Babon, Chaoxing Yang, Sally C. Kent, Alan G. Derr, Alper Kucukural, Manuel Garber, and David M. Harlan
DEBrowser: interactive differential expression analysis and visualization tool for count data, Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, and Manuel Garber
Publications from 2018
Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus, Sofia A. Quinodoz, Barbara Tabak, Patrick McDonel, Manuel Garber, and Mitchell Guttman
Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon, Elisa Donnard, Pranitha Vangala, Shaked Afik, Sean M. McCauley, Anetta Nowosielska, Alper Kucukural, Barbara Tabak, Xiaopeng Zhu, William E. Diehl, Patrick McDonel, Nir Yosef, Jeremy Luban, and Manuel Garber
HIV-1 unmasks the plasticity of innate lymphoid cells [preprint], Yetao Wang, Kyle Gellatly, Alan G. Derr, Smita Jaiswal, Alper Kucukural, Patrick McDonel, Thomas C. Greenough, JeanMarie Houghton, Manuel Garber, and Jeremy Luban
Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection, Eric R. Weiss, Susanna L. Lamers, Jennifer L. Henderson, Alexandre Melnikov, Mohan Somasundaran, Manuel Garber, Liisa K. Selin, Chad Nusbaum, and Katherine Luzuriaga
Publications from 2017
Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation, Hsin-Jung Chou, Elisa Donnard, H. Tobias Gustafsson, Manuel Garber, and Oliver J. Rando
GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases, Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Herve Pages, Alper Kucukural, Manuel Garber, and Scot A. Wolfe
Defining the 5 and 3 landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq, Shaked Afik, Osnat Bartok, Maxim N. Artyomov, Alexander A. Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, and Sebastian Kadener
Publications from 2016
High Epstein-Barr Virus Load and Genomic Diversity Are Associated with Generation of gp350-Specific Neutralizing Antibodies following Acute Infectious Mononucleosis, Eric R. Weiss, Galit Alter, Javier Gordon Ogembo, Jennifer L. Henderson, Barbara Tabak, Yasin Bakis, Mohan Somasundaran, Manuel Garber, Liisa K. Selin, and Katherine Luzuriaga
Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic, William E. Diehl, Kyusik Kim, Pyae Phyo Kyawe, Sean M. McCauley, Elisa Donnard, Alper Kucukural, Patrick E. McDonel, Manuel Garber, and Jeremy Luban
End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David M. Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim N. Artyomov, and Manuel Garber
Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs, Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Mitchell Guttman, Jacob H. Hanna, Aviv Regev, and Manuel Garber
Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals, Upasna Sharma, Colin C. Conine, Jeremy Shea, Ana Boskovic, Alan G. Derr, Xin Y. Bing, Clemence Belleannee, Alper Kucukural, Ryan W. Serra, Fengyun Sun, Lina Song, Benjamin R. Carone, Emiliano P. Ricci, Xin Z. Li, Lucas Fauquier, Melissa J. Moore, Robert Sullivan, Craig C. Mello, Manuel Garber, and Oliver J. Rando
Publications from 2015
Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome, Jeremy Shea, Ryan W. Serra, Benjamin R. Carone, Hennady P. Shulha, Alper Kucukural, Michael Ziller, Markus Vallaster, Hongcang Gu, Andrew R. Tapper, Paul D. Gardner, Alexander Meissner, Manuel Garber, and Oliver J. Rando
DNA-binding-domain fusions enhance the targeting range and precision of Cas9, Mehmet Fatih Bolukbasi, Ankit Gupta, Sarah Oikemus, Alan G. Derr, Manuel Garber, Michael H. Brodsky, Lihua Julie Zhu, and Scot A. Wolfe
Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs [preprint], Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Jacob H. Hanna, Aviv Regev, and Manuel Garber
Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets, David M. Blodgett, Anetta Nowosielska, Shaked Afik, Susanne Pechhold, Anthony J. Cura, Norman J. Kennedy, Soyoung Kim, Alper Kucukural, Roger J. Davis, Sally C. Kent, Dale L. Greiner, Manuel Garber, David M. Harlan, and Philip J. diLorio Jr.
Functional annotation of native enhancers with a Cas9-histone demethylase fusion, Nicola A. Kearns, Hannah Pham, Barbara Tabak, Ryan M. J. Genga, Noah J. Silverstein, Manuel Garber, and Rene Maehr
Simultaneous generation of many RNA-seq libraries in a single reaction, Alexander A. Shishkin, Georgia Giannoukos, Alper Kucukural, Dawn Ciulla, Michele Busby, Christine Surka, Jenny Chen, Roby P. Bhattacharyya, Robert F. Rudy, Milesh M. Patel, Nathaniel Novod, Deborah T. Hung, Andreas Gnirke, Manuel Garber, Mitchell Guttman, and Jonathan Livny
Publications from 2014
A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States, Chamutal Bornstein, Deborah Winter, Zohar Barnett-Itzhaki, Eyal David, Sabah Kadri, Manuel Garber, and Ido Amit
HIV type 1 (HIV-1) proviral reservoirs decay continuously under sustained virologic control in HIV-1-infected children who received early treatment, Katherine Luzuriaga, Barbara Tabak, Manuel Garber, Ya Hui Chen, Carrie Ziemniak, Margaret M. McManus, Danielle Murray, Matthew Strain, Douglas Richman, Tae-Wook Chun, Coleen K. Cunningham, and Deborah Persaud
The PPARalpha-FGF21 hormone axis contributes to metabolic regulation by the hepatic JNK signaling pathway, Santiago Vernia, Julie Cavanagh, Luisa Garcia-Haro, Guadalupe Sabio, Tamera Barrett, Dae Young Jung, Jason K. Kim, Jia Xu, Hennady P. Shulha, Manuel Garber, Guangping Gao, and Roger J. Davis
Epstein-barr virus latent membrane protein 1 genetic variability in peripheral blood B cells and oropharyngeal fluids, Nicholas Renzette, Mohan Somasundaran, Frank E. Brewster, James Coderre, Eric R. Weiss, Margaret M. McManus, Thomas C. Greenough, Barbara Tabak, Manuel Garber, Timothy F. Kowalik, and Katherine Ruiz De Luzuriaga
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals, Stefan Washietl, Manolis Kellis, and Manuel Garber
Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells, Nicola A. Kearns, Ryan M. J. Genga, Metewo Selase Enuameh, Manuel Garber, Scot A. Wolfe, and Rene Maehr
Publications from 2013
Genome-wide assessment of post-transcriptional control in the fly brain, Shaul Mezan, Reut Ashwal-Fluss, Rom Shenhav, Manuel Garber, and Sebastian Kadener
Semiconductor-based DNA sequencing of histone modification states, Christine S. Cheng, Manuel Garber, Lynda Chin, Aviv Regev, and Ido Amit
Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis, Gal Haimovich, Daniel A. Medina, Sebastien Z. Causse, Manuel Garber, Gonzalo Millan-Zambrano, Oren Barkai, Sebastian Chavez, Jose E. Perez-Ortin, Xavier Darzacq, and Mordechai Choder
Publications from 2012
The Bioinformatics Core and The Garber Lab, Manuel Garber
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals, Manuel Garber and Ido Amit