Works by Garber, Manuel

Results: 33

A single cell atlas of the mouse seminal vesicle Open Access.

Published in:

G3: Genes | Genomes | Genetics, 2025, v. 15, n. 5, p. 1, doi. 10.1093/g3journal/jkaf045

By:

Sun, Fengyun;
Desevin, Kathleen;
Fu, Yu;
Parameswaran, Shanmathi;
Mayall, Jemma;
Rinaldi, Vera;
Krietenstein, Nils;
Manukyan, Artür;
Yin, Qiangzong;
Galan, Carolina;
Yang, Chih-Hsiang;
Shindyapina, Anastasia V;
Gladyshev, Vadim N;
Garber, Manuel;
Schjenken, John E;
Rando, Oliver J

Publication type:

Article

Identifying novel constrained elements by exploiting biased substitution patterns.

Published in:

Bioinformatics, 2009, v. 25, n. 12, p. i54, doi. 10.1093/bioinformatics/btp190

By:

Manuel Garber;
Mitchell Guttman;
Michele Clamp;
Michael C. Zody;
Nir Friedman;
Xiaohui Xie

Publication type:

Article

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

Published in:

Frontiers in Molecular Neuroscience, 2013, v. 6, p. 1, doi. 10.3389/fnmol.2013.00049

By:

Mezan, Shaul;
Ashwal-Fluss, Reut;
Shenhav, Rom;
Garber, Manuel;
Kadener, Sebastian

Publication type:

Article

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells.

Published in:

Nature Genetics, 2010, v. 42, n. 12, p. 1113, doi. 10.1038/ng.710

By:

Loewer, Sabine;
Cabili, Moran N.;
Guttman, Mitchell;
Loh, Yuin-Han;
Thomas, Kelly;
In Hyun Park;
Garber, Manuel;
Curran, Matthew;
Onder, Tamer;
Agarwal, Suneet;
Manos, Philip D.;
Datta, Sumon;
Lander, Eric S.;
Schlaeger, Thorsten M.;
Daley, George Q.;
Rinn, John L.

Publication type:

Article

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

Published in:

FASEB Journal, 2020, v. 34, n. 1, p. 1901, doi. 10.1096/fj.201901022RR

By:

Redick, Sambra D.;
Leehy, Linda;
Rittenhouse, Ann R.;
Blodgett, David M.;
Derr, Alan G.;
Kucukural, Alper;
Garber, Manuel G.;
Shultz, Leonard D.;
Greiner, Dale L.;
Wang, Jennifer P.;
Harlan, David M.;
Bortell, Rita;
Jurczyk, Agata

Publication type:

Article

DolphinNext: a distributed data processing platform for high throughput genomics.

Published in:

BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-6714-x

By:

Yukselen, Onur;
Turkyilmaz, Osman;
Ozturk, Ahmet Rasit;
Garber, Manuel;
Kucukural, Alper

Publication type:

Article

scRNA-seq of human vitiligo reveals complex networks of subclinical immune activation and a role for CCR5 in T<sub>reg</sub> function.

Published in:

Science Translational Medicine, 2021, v. 13, n. 610, p. 1, doi. 10.1126/scitranslmed.abd8995

By:

Gellatly, Kyle J.;
Strassner, James P.;
Essien, Kingsley;
Refat, Maggi Ahmed;
Murphy, Rachel L.;
Coffin-Schmitt, Anthony;
Pandya, Amit G.;
Tovar-Garza, Andrea;
Frisoli, Michael L.;
Fan, Xueli;
Ding, Xiaolan;
Kim, Evangeline E.;
Abbas, Zainab;
McDonel, Patrick;
Garber, Manuel;
Harris, John E.

Publication type:

Article

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.

Published in:

Nature Biotechnology, 2011, v. 29, n. 5, p. 436, doi. 10.1038/nbt.1861

By:

Rabani, Michal;
Levin, Joshua Z.;
Lin Fan;
Xian Adiconis;
Raychowdhury, Raktima;
Garber, Manuel;
Gnirke, Andreas;
Nusbaum, Chad;
Hacohen, Nir;
Friedman, Nir;
Amit, Ido;
Regev, Aviv

Publication type:

Article

Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.

Published in:

2010

By:

Guttman, Mitchell;
Garber, Manuel;
Levin, Joshua Z;
Donaghey, Julie;
Robinson, James;
Adiconis, Xian;
Fan, Lin;
Koziol, Magdalena J;
Gnirke, Andreas;
Nusbaum, Chad;
Rinn, John L;
Lander, Eric S;
Regev, Aviv

Publication type:

Correction Notice

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.

Published in:

Nature Biotechnology, 2010, v. 28, n. 5, p. 503, doi. 10.1038/nbt.1633

By:

Guttman, Mitchell;
Garber, Manuel;
Levin, Joshua Z.;
Donaghey, Julie;
Robinson, James;
Adiconis, Xian;
Lin Fan;
Koziol, Magdalena J.;
Gnirke, Andreas;
Nusbaum, Chad;
Rinn, John L.;
Lander, Eric S.;
Regev, Aviv

Publication type:

Article

Single cell transcriptomics reveals dysregulated cellular and molecular networks in a fragile X syndrome model.

Published in:

PLoS Genetics, 2022, v. 18, n. 6, p. 1, doi. 10.1371/journal.pgen.1010221

By:

Donnard, Elisa;
Shu, Huan;
Garber, Manuel

Publication type:

Article

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60154-0

By:

Zhang, Hefei;
Li, Xuhang;
Song, Dongyuan;
Yukselen, Onur;
Nanda, Shivani;
Kucukural, Alper;
Li, Jingyi Jessica;
Garber, Manuel;
Walhout, Albertha J. M.

Publication type:

Article

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60154-0

By:

Zhang, Hefei;
Li, Xuhang;
Song, Dongyuan;
Yukselen, Onur;
Nanda, Shivani;
Kucukural, Alper;
Li, Jingyi Jessica;
Garber, Manuel;
Walhout, Albertha J. M.

Publication type:

Article

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

Published in:

Nature Methods, 2015, v. 12, n. 5, p. 401, doi. 10.1038/nmeth.3325

By:

Kearns, Nicola A;
Pham, Hannah;
Tabak, Barbara;
Genga, Ryan M;
Silverstein, Noah J;
Garber, Manuel;
Maehr, René

Publication type:

Article

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

Published in:

Nature Methods, 2015, v. 12, n. 4, p. 323, doi. 10.1038/nmeth.3313

By:

Shishkin, Alexander A;
Giannoukos, Georgia;
Kucukural, Alper;
Ciulla, Dawn;
Busby, Michele;
Surka, Christine;
Chen, Jenny;
Bhattacharyya, Roby P;
Rudy, Robert F;
Patel, Milesh M;
Novod, Nathaniel;
Hung, Deborah T;
Gnirke, Andreas;
Garber, Manuel;
Guttman, Mitchell;
Livny, Jonathan

Publication type:

Article

Computational methods for transcriptome annotation and quantification using RNA-seq.

Published in:

Nature Methods, 2011, v. 8, n. 6, p. 469, doi. 10.1038/nmeth.1613

By:

Garber, Manuel;
Grabherr, Manfred G;
Guttman, Mitchell;
Trapnell, Cole

Publication type:

Article

Semiconductor-based DNA sequencing of histone modification states.

Published in:

Nature Communications, 2013, v. 4, n. 10, p. 2672, doi. 10.1038/ncomms3672

By:

Cheng, Christine S.;
Rai, Kunal;
Garber, Manuel;
Hollinger, Andrew;
Robbins, Dana;
Anderson, Scott;
Macbeth, Alyssa;
Tzou, Austin;
Carneiro, Mauricio O.;
Raychowdhury, Raktima;
Russ, Carsten;
Hacohen, Nir;
Gershenwald, Jeffrey E.;
Lennon, Niall;
Nusbaum, Chad;
Chin, Lynda;
Regev, Aviv;
Amit, Ido

Publication type:

Article

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.

Published in:

2009

By:

Guttman, Mitchell;
Amit, Ido;
Garber, Manuel;
French, Courtney;
Lin, Michael F.;
Feldser, David;
Huarte, Maite;
Zuk, Or;
Carey, Bryce W.;
Cassady, John P.;
Cabili, Moran N.;
Jaenisch, Rudolf;
Mikkelsen, Tarjei S.;
Jacks, Tyler;
Hacohen, Nir;
Bernstein, Bradley E.;
Kellis, Manolis;
Regev, Aviv;
Rinn, John L.;
Lander, Eric S.

Publication type:

Letter

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

Published in:

Nature, 2007, v. 447, n. 7141, p. 167, doi. 10.1038/nature05805

By:

Mikkelsen, Tarjei S.;
Wakefield, Matthew J.;
Aken, Bronwen;
Amemiya, Chris T.;
Chang, Jean L.;
Duke, Shannon;
Garber, Manuel;
Gentles, Andrew J.;
Goodstadt, Leo;
Heger, Andreas;
Jurka, Jerzy;
Kamal, Michael;
Mauceli, Evan;
Searle, Stephen M. J.;
Sharpe, Ted;
Baker, Michelle L.;
Batzer, Mark A.;
Benos, Panayiotis V.;
Belov, Katherine;
Clamp, Michele

Publication type:

Article

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

Published in:

2006

By:

Zody, Michael C.;
Garber, Manuel;
Adams, David J.;
Sharpe, Ted;
Harrow, Jennifer;
Lupski, James R.;
Nicholson, Christine;
Searle, Steven M.;
Wilming, Laurens;
Young, Sarah K.;
Abouelleil, Amr;
Allen, Nicole R.;
Weimin Bi;
Bloom, Toby;
Borowsky, Mark L.;
Bugalter, Boris E.;
Butler, Jonathan;
Chang, Jean L.;
Chao-Kung Chen;
Cook, April

Publication type:

Letter

Analysis of the DNA sequence and duplication history of human chromosome 15.

Published in:

2006

By:

Zody, Michael C.;
Garber, Manuel;
Sharpe, Ted;
Young, Sarah K.;
Rowen, Lee;
O'Neill, Keith;
Whittaker, Charles A.;
Kamal, Michael;
Chang, Jean L.;
Cuomo, Christina A.;
Dewar, Ken;
FitzGerald, Michael G.;
Kodira, Chinnappa D.;
Madan, Anup;
Shizhen Qin;
Xiaoping Yang;
Abbasi, Nissa;
Abouelleil, Amr;
Arachchi, Harindra M.;
Baradarani, Lida

Publication type:

Letter

DNA sequence and analysis of human chromosome 8.

Published in:

Nature, 2006, v. 439, n. 7074, p. 331, doi. 10.1038/nature04406

By:

Nusbaum, Chad;
Mikkelsen, Tarjei S.;
Zody, Michael C.;
Asakawa, Shuichi;
Taudien, Stefan;
Garber, Manuel;
Kodira, Chinnappa D.;
Schueler, Mary G.;
Shimizu, Atsushi;
Whittaker, Charles A.;
Chang, Jean L.;
Cuomo, Christina A.;
Dewar, Ken;
FitzGerald, Michael G.;
Xiaoping Yang;
Allen, Nicole R.;
Anderson, Scott;
Asakawa, Teruyo;
Blechschmidt, Karin;
Bloom, Toby

Publication type:

Article

An Early Islet Transcriptional Signature is Associated with Local Inflammation in Autoimmune Diabetes.

Published in:

Diabetes, 2023, v. 72, n. 2, p. 261, doi. 10.2337/db22-0521

By:

Derr, Alan G.;
Arowosegbe, Adediwura;
Satish, Basanthi;
Redick, Sambra D.;
Qaisar, Natasha;
Guo, Zhiru;
Vanderleeden, Emma;
Trombly, Melanie I.;
Baer, Christina E.;
Harlan, David M.;
Greiner, Dale L.;
Garber, Manuel;
Wang, Jennifer P.

Publication type:

Article

HLA Class II Antigen Processing and Presentation Pathway Components Demonstrated by Transcriptome and Protein Analyses of Islet β-Cells From Donors With Type 1 Diabetes.

Published in:

2019

By:

Russell, Mark A.;
Richardson, Sarah J.;
Leete, Pia;
Morgan, Noel G.;
Derr, Alan G.;
Kucukural, Alper;
Garber, Manuel G.;
Yang, Chaoxing;
Redick, Sambra D.;
Chaoxing Yang;
Babon, Jenny Aurielle B.;
Kent, Sally C.;
Harlan, David M.;
Blodgett, David M.;
Krogvold, Lars;
Dahl-Jørgensen, Knut;
Bottino, Rita;
Brissova, Marcela;
Powers, Alvin C.;
Spaeth, Jason M.

Publication type:

journal article

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

Published in:

Diabetes, 2015, v. 64, n. 9, p. 3172, doi. 10.2337/db15-0039

By:

Blodgett, David M.;
Nowosielska, Anetta;
Afik, Shaked;
Pechhold, Susanne;
Cura, Anthony J.;
Kennedy, Norman J.;
Soyoung Kim;
Kucukural, Alper;
Davis, Roger J.;
Kent, Sally C.;
Greiner, Dale L.;
Garber, Manuel G.;
Harlan, David M.;
diIorio, Philip

Publication type:

Article

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

Published in:

Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-0880-9

By:

Chen, Jenny;
Shishkin, Alexander A.;
Xiaopeng Zhu;
Kadri, Sabah;
Maza, Itay;
Guttman, Mitchell;
Hanna, Jacob H.;
Regev, Aviv;
Garber, Manuel

Publication type:

Article

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

Published in:

2014

By:

Luzuriaga, Katherine;
Tabak, Barbara;
Garber, Manuel;
Chen, Ya Hui;
Ziemniak, Carrie;
McManus, Margaret M;
Murray, Danielle;
Strain, Matthew C;
Richman, Douglas D;
Chun, Tae-Wook;
Cunningham, Coleen K;
Persaud, Deborah

Publication type:

journal article

HIV Type 1 (HIV-1) Proviral Reservoirs Decay Continuously Under Sustained Virologic Control in HIV-1–Infected Children Who Received Early Treatment.

Published in:

Journal of Infectious Diseases, 2014, v. 210, n. 10, p. 1529, doi. 10.1093/infdis/jiu297

By:

Luzuriaga, Katherine;
Tabak, Barbara;
Garber, Manuel;
Chen, Ya Hui;
Ziemniak, Carrie;
McManus, Margaret M.;
Murray, Danielle;
Strain, Matthew C.;
Richman, Douglas D.;
Chun, Tae-Wook;
Cunningham, Coleen K.;
Persaud, Deborah

Publication type:

Article

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

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5362-x

By:

Kucukural, Alper;
Yukselen, Onur;
Ozata, Deniz M.;
Moore, Melissa J.;
Garber, Manuel

Publication type:

Article

A high-resolution map of human evolutionary constraint using 29 mammals.

Published in:

Nature, 2011, v. 478, n. 7370, p. 476, doi. 10.1038/nature10530

By:

Lindblad-Toh, Kerstin;
Garber, Manuel;
Zuk, Or;
Lin, Michael F.;
Parker, Brian J.;
Washietl, Stefan;
Kheradpour, Pouya;
Ernst, Jason;
Jordan, Gregory;
Mauceli, Evan;
Ward, Lucas D.;
Lowe, Craig B.;
Holloway, Alisha K.;
Clamp, Michele;
Gnerre, Sante;
Alföldi, Jessica;
Beal, Kathryn;
Chang, Jean;
Clawson, Hiram;
Cuff, James

Publication type:

Article

lincRNAs act in the circuitry controlling pluripotency and differentiation.

Published in:

Nature, 2011, v. 477, n. 7364, p. 295, doi. 10.1038/nature10398

By:

Guttman, Mitchell;
Donaghey, Julie;
Carey, Bryce W.;
Garber, Manuel;
Grenier, Jennifer K.;
Munson, Glen;
Young, Geneva;
Lucas, Anne Bergstrom;
Ach, Robert;
Bruhn, Laurakay;
Yang, Xiaoping;
Amit, Ido;
Meissner, Alexander;
Regev, Aviv;
Rinn, John L.;
Root, David E.;
Lander, Eric S.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2017, v. 45, n. 11, p. 1, doi. 10.1093/nar/gkx133

By:

Afik, Shaked;
Bartok, Osnat;
Artyomov, Maxim N.;
Shishkin, Alexander A.;
Kadri, Sabah;
Hanan, Mor;
Xiaopeng Zhu;
Garber, Manuel;
Kadener, Sebastian

Publication type:

Article

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

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3746-y

By:

Zhu, Lihua Julie;
Lawrence, Michael;
Gupta, Ankit;
Pagès, Hervé;
Kucukural, Alper;
Garber, Manuel;
Wolfe, Scot A.

Publication type:

Article