list of publications from Garber Lab

Simultaneous profiling of multiple chromatin proteins in the same cells

Thursday, November 18, 2021

Author(s): Sneha Gopalan, Yuqing Wang, Nicholas W. Harper, Manuel Garber, Thomas G. Fazzio

Source: Molecular cell

scRNA-seq of human vitiligo reveals complex networks of subclinical immune activation and a role for CCR5 in Treg function

Wednesday, September 08, 2021

Author(s): Kyle Gellatly, James P. Strassner, Kingsley I. Essien, Maggi Ahmed Refat, Rachel L. Murphy, Anthony Coffin-Schmitt, Michael L. Frisoli, Xueli Fan, Evangeline E. Kim, Zainab Abbas, Patrick McDonel, Man...

Source: Science translational medicine

Hierarchy of signaling thresholds downstream of the T cell receptor and the Tec kinase ITK

Tuesday, August 31, 2021

Author(s): Michael P. Gallagher, James M. Conley, Pranitha Vangala, Manuel Garber, Andrea Reboldi, Leslie J. Berg

Source: Proceedings of the National Academy of Sciences of the United States of America

Simultaneous profiling of multiple chromatin proteins in the same cells [preprint]

Wednesday, April 28, 2021

Author(s): Sneha Gopalan, Yuqing Wang, Nicholas W. Harper, Manuel Garber, Thomas G. Fazzio

Source: bioRxiv; The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 Internationa...

Gaining Insight into Vitiligo Genetics through the Lens of a Large Epidemiologic Study

Thursday, April 01, 2021

Author(s): Ken Okamura, Manuel Garber, John E. Harris

Source: The Journal of investigative dermatology

The Tec kinase ITK differentially optimizes NFAT, NF-κB, and MAPK signaling during early T cell activation to regulate graded gene induction [preprint]

Saturday, November 14, 2020

Author(s): Michael P. Gallagher, James M. Conley, Pranitha Vangala, Andrea Reboldi, Manuel Garber, Leslie J. Berg

Source: bioRxiv; The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International lice...

A comparative genomics multitool for scientific discovery and conservation

Wednesday, November 11, 2020

Author(s): Zoonomia Consortium, Diane P. Genereux, Manuel Garber, Kerstin Lindblad-Toh, Elinor K. Karlsson

Source: Nature; © The Author(s) 2020. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproductio...

An atlas of cell types in the mouse epididymis and vas deferens

Thursday, July 30, 2020

Author(s): Vera D. Rinaldi, Elisa Donnard, Kyle Gellatly, Morten Rasmussen, Alper Kucukural, Onur Yukselen, Manuel Garber, Upasna Sharma, Oliver J. Rando

Source: eLife; Copyright Rinaldi et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original au...

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

Monday, April 27, 2020

Author(s): Carly G. K. Ziegler, Yuming Cao, Zhiru Guo, Jennifer P. Wang, Robert W. Finberg, Manuel Garber, Alex K. Shalek, Jose Ordovas-Montanes, HCA Lung Biological Network

DolphinNext: a distributed data processing platform for high throughput genomics

Sunday, April 19, 2020

Author(s): Onur Yukselen, Osman Turkyilmaz, Ahmet R. Ozturk, Manuel Garber, Alper Kucukural

Source: BMC genomics; © The Author(s). 2020 Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and repro...

HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cells

Sunday, March 01, 2020

Author(s): 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,...

Source: Nature immunology

Single Cell Transcriptomics Reveals Dysregulated Cellular and Molecular Networks in a Fragile X Syndrome model [preprint]

Thursday, February 13, 2020

Author(s): Elisa Donnard, Huan Shu, Manuel Garber

Source: bioRxiv; The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-ND 4.0 International license.

An atlas of cell types in the mammalian epididymis and vas deferens [preprint]

Friday, January 24, 2020

Author(s): Vera D. Rinaldi, Elisa Donnard, Kyle Gellatly, Morten Rasmussen, Alper Kucukural, Onur Yukselen, Manuel Garber, Upasna Sharma, Oliver J. Rando

Source: bioRxiv; The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY 4.0 International license.

Recovery of viable endocrine-specific cells and transcriptomes from human pancreatic islet-engrafted mice

Wednesday, January 01, 2020

Author(s): 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,...

Source: FASEB journal : official publication of the Federation of American Societies for Experimental Biology; © 2019 The Authors. The FASEB Journal published by Wiley Periodicals, Inc. on behalf of Federatio...

Frequent Loss of IRF2 in Cancers Leads to Immune Evasion through Decreased MHC Class I Antigen Presentation and Increased PD-L1 Expression

Tuesday, October 01, 2019

Author(s): Barry Kriegsman, Pranitha Vangala, Benjamin J. Chen, Paul Meraner, Abraham L. Brass, Manuel Garber, Kenneth L. Rock

Source: Journal of immunology (Baltimore, Md. : 1950)

Diverse repertoire of human adipocyte subtypes develops from transcriptionally distinct mesenchymal progenitor cells

Tuesday, September 03, 2019

Author(s): 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, Silvia Corvera

Source: Proceedings of the National Academy of Sciences of the United States of America; Copyright © 2019 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attri...

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

Wednesday, May 01, 2019

Author(s): Mark A. Russell, Sambra D. Redick, David Blodgett, Jenny Aurielle B. Babon, Chaoxing Yang, Sally C. Kent, Alan G. Derr, Alper Kucukural, Manuel Garber, David M. Harlan

Source: Diabetes

DEBrowser: interactive differential expression analysis and visualization tool for count data

Saturday, January 05, 2019

Author(s): Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber

Source: BMC genomics; © The Author(s). 2019. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/...

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

Monday, June 04, 2018

Author(s): Sofia A. Quinodoz, Barbara Tabak, Patrick McDonel, Manuel Garber, Mitchell Guttman

Source: Cell

Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon

Wednesday, March 28, 2018

Author(s): 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, Manuel Gar...

Source: Cell systems

HIV-1 unmasks the plasticity of innate lymphoid cells [preprint]

Thursday, January 04, 2018

Author(s): Yetao Wang, Kyle Gellatly, Alan G. Derr, Smita Jaiswal, Alper Kucukural, Patrick McDonel, Thomas C. Greenough, JeanMarie Houghton, Manuel Garber, Jeremy Luban

Source: bioRxiv; The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.

Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection

Tuesday, January 02, 2018

Author(s): Eric R. Weiss, Susanna L. Lamers, Jennifer L. Henderson, Alexandre Melnikov, Mohan Somasundaran, Manuel Garber, Liisa K. Selin, Chad Nusbaum, Katherine Luzuriaga

Source: Journal of virology; Copyright © 2018, American Society for Microbiology. Publisher PDF posted as allowed by the publisher's author rights policy at http://journals.asm.org/site/misc/ASM_Author_State...

Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation

Thursday, December 07, 2017

Author(s): Hsin-Jung Chou, Elisa Donnard, H. Tobias Gustafsson, Manuel Garber, Oliver J. Rando

Source: Molecular cell

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases

Monday, May 15, 2017

Author(s): Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Herve Pages, Alper Kucukural, Manuel Garber, Scot A. Wolfe

Defining the 5 and 3 landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq

Wednesday, February 22, 2017

Author(s): Shaked Afik, Osnat Bartok, Maxim N. Artyomov, Alexander A. Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, Sebastian Kadener

Source: Nucleic acids research; © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

High Epstein-Barr Virus Load and Genomic Diversity Are Associated with Generation of gp350-Specific Neutralizing Antibodies following Acute Infectious Mononucleosis

Friday, December 16, 2016

Author(s): Eric R. Weiss, Galit Alter, Javier Gordon Ogembo, Jennifer L. Henderson, Barbara Tabak, Yasin Bakis, Mohan Somasundaran, Manuel Garber, Liisa K. Selin, Katherine Luzuriaga

Source: Journal of virology; Copyright © 2016, American Society for Microbiology. Publisher PDF posted as allowed by the publisher's author rights policy at http://journals.asm.org/site/misc/ASM_Author_State...

Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic

Thursday, November 03, 2016

Author(s): William E. Diehl, Kyusik Kim, Pyae Phyo Kyawe, Sean M. McCauley, Elisa Donnard, Alper Kucukural, Patrick E. McDonel, Manuel Garber, Jeremy Luban

Source: Cell

End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data

Saturday, October 01, 2016

Author(s): 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, Maxi...

Source: Genome research; © 2016 Derr et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.or...

Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

Tuesday, February 02, 2016

Author(s): Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Mitchell Guttman, Jacob H. Hanna, Aviv Regev, Manuel Garber

Source: Genome biology; Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unre...

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

Friday, January 22, 2016

Author(s): 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...

Source: Science (New York, N.Y.)

Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome

Monday, December 21, 2015

Author(s): 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,...

Source: Developmental cell

DNA-binding-domain fusions enhance the targeting range and precision of Cas9

Tuesday, December 01, 2015

Author(s): Mehmet Fatih Bolukbasi, Ankit Gupta, Sarah Oikemus, Alan G. Derr, Manuel Garber, Michael H. Brodsky, Lihua Julie Zhu, Scot A. Wolfe

Source: Nature methods

Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs [preprint]

Wednesday, November 11, 2015

Author(s): Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Jacob H. Hanna, Aviv Regev, Manuel Garber

Source: bioRxiv; The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.

Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets

Tuesday, September 01, 2015

Author(s): 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, D...

Source: Diabetes

Functional annotation of native enhancers with a Cas9-histone demethylase fusion

Friday, May 01, 2015

Author(s): Nicola A. Kearns, Hannah Pham, Barbara Tabak, Ryan M. J. Genga, Noah J. Silverstein, Manuel Garber, Rene Maehr

Source: Nature methods

Simultaneous generation of many RNA-seq libraries in a single reaction

Wednesday, April 01, 2015

Author(s): 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....

Source: Nature methods

A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States

Thursday, December 18, 2014

Author(s): Chamutal Bornstein, Deborah Winter, Zohar Barnett-Itzhaki, Eyal David, Sabah Kadri, Manuel Garber, Ido Amit

Source: Molecular cell

HIV type 1 (HIV-1) proviral reservoirs decay continuously under sustained virologic control in HIV-1-infected children who received early treatment

Saturday, November 15, 2014

Author(s): 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, Deborah Per...

Source: The Journal of infectious diseases

The PPARalpha-FGF21 hormone axis contributes to metabolic regulation by the hepatic JNK signaling pathway

Tuesday, September 02, 2014

Author(s): 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, Roger J. Davis

Source: Cell metabolism

Epstein-barr virus latent membrane protein 1 genetic variability in peripheral blood B cells and oropharyngeal fluids

Tuesday, April 01, 2014

Author(s): 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, Katherine Ruiz De Lu...

Source: Journal of virology; Publisher PDF posted as allowed by the publisher's author rights policy at http://journals.asm.org/site/misc/ASM_Author_Statement.xhtml.

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

Tuesday, April 01, 2014

Author(s): Stefan Washietl, Manolis Kellis, Manuel Garber

Source: Genome research; Copyright 2014 Washietl et al.; Published by Cold Spring Harbor Laboratory Press. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six mont...

Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells

Wednesday, January 01, 2014

Author(s): Nicola A. Kearns, Ryan M. J. Genga, Metewo Selase Enuameh, Manuel Garber, Scot A. Wolfe, Rene Maehr

Source: Development (Cambridge, England)

Genome-wide assessment of post-transcriptional control in the fly brain

Monday, December 09, 2013

Author(s): Shaul Mezan, Reut Ashwal-Fluss, Rom Shenhav, Manuel Garber, Sebastian Kadener

Source: Frontiers in molecular neuroscience; Copyright 2013 Mezan, Ashwal-Fluss, Shenhav, Garber and Kadener. This is an open-access article distributed under the terms of the Creative Commons Attribution Lic...

Semiconductor-based DNA sequencing of histone modification states

Friday, October 25, 2013

Author(s): Christine S. Cheng, Manuel Garber, Lynda Chin, Aviv Regev, Ido Amit

Source: Nature communications

Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis

Thursday, May 23, 2013

Author(s): Gal Haimovich, Daniel A. Medina, Sebastien Z. Causse, Manuel Garber, Gonzalo Millan-Zambrano, Oren Barkai, Sebastian Chavez, Jose E. Perez-Ortin, Xavier Darzacq, Mordechai Choder

Source: Cell

The Bioinformatics Core and The Garber Lab

Thursday, November 29, 2012

Author(s): Manuel Garber

Source: UMass Center for Clinical and Translational Science Seminars; Copyright the Author(s)

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

Friday, September 14, 2012

Author(s): Manuel Garber, Ido Amit

Source: Molecular cell

Publications