list of publications from Garber Lab

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

Source: Cell

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

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

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

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

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

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

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

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

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

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

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

Source: BMC genomics

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

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

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

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

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

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

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

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

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

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

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

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

DolphinNext: a distributed data processing platform for high throughput genomics

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

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

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

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

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

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

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

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

Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon

HIV-1 unmasks the plasticity of innate lymphoid cells

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

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

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

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

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

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

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

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

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

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

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

Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

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

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

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

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

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

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

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

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

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

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

Semiconductor-based DNA sequencing of histone modification states

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

The Bioinformatics Core and The Garber Lab

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

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