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The Garber Lab for Evolutionary Non-coding Genomics
Program in Bioinformatics and Integrative Biology
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Publications
Total:
33
results
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 Seminar Series
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
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