Works matching AU Bader, Joel S.

Results: 63

Proteomic signature of HIV-associated subclinical left atrial remodeling and incident heart failure.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-55911-0

By:

Peterson, Tess E.;
Hahn, Virginia S.;
Moaddel, Ruin;
Zhu, Min;
Haberlen, Sabina A.;
Palella, Frank J.;
Plankey, Michael;
Bader, Joel S.;
Lima, Joao A. C.;
Gerszten, Robert E.;
Rotter, Jerome I.;
Rich, Stephen S.;
Heckbert, Susan R.;
Kirk, Gregory D.;
Piggott, Damani A.;
Ferrucci, Luigi;
Margolick, Joseph B.;
Brown, Todd T.;
Wu, Katherine C.;
Post, Wendy S.

Publication type:

Article

The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-54130-3

By:

Zhou, Chun;
Wang, Yun;
Huang, Yikun;
An, Yongpan;
Fu, Xian;
Yang, Daqian;
Wang, Yilin;
Zhang, Jintao;
Mitchell, Leslie A.;
Bader, Joel S.;
Cai, Yizhi;
Dai, Junbiao;
Boeke, Jef D.;
Cai, Zhiming;
Xie, Zhengwei;
Shen, Yue;
Huang, Weiren

Publication type:

Article

Gaining confidence in high-throughput protein interaction networks.

Published in:

Nature Biotechnology, 2004, v. 22, n. 1, p. 78, doi. 10.1038/nbt924

By:

Chaudhuri, Amitabha;
Chant, John;
Bader, Joel S.;
Rothberg, Jonathan M.

Publication type:

Article

Hypoxia Sensing and Persistence Genes Are Expressed during the Intragranulomatous Survival of Mycobacterium tuberculosis.

Published in:

American Journal of Respiratory Cell & Molecular Biology, 2017, v. 56, n. 5, p. 637, doi. 10.1165/rcmb.2016-0239OC

By:

Hudock, Teresa A.;
Foreman, Taylor W.;
Bandyopadhyay, Nirmalya;
Gautam, Uma S.;
Veatch, Ashley V.;
LoBato, Denae N.;
Gentry, Kaylee M.;
Golden, Nadia A.;
Cavigli, Amy;
Mueller, Michelle;
Hwang, Shen-An;
Hunter, Robert L.;
Alvarez, Xavier;
Lackner, Andrew A.;
Bader, Joel S.;
Mehra, Smriti;
Kaushal, Deepak

Publication type:

Article

Corrigendum: Genome sequencing in microfabricated high-density picolitre reactors.

Published in:

2006

By:

Margulies, Marcel;
Egholm, Michael;
Altman, William E.;
Attiya, Said;
Bader, Joel S.;
Bemben, Lisa A.;
Berka, Jan;
Braverman, Michael S.;
Yi-Ju Chen;
Zhoutao Chen;
Dewell, Scott B.;
de Winter, Alex;
Drake, James;
Lei Du;
Fierro, Joseph M.;
Forte, Robin;
Gomes, Xavier V.;
Godwin, Brian C.;
Wen He;
Helgesen, Scott

Publication type:

Correction Notice

Corrigendum: Genome sequencing in microfabricated high-density picolitre reactors.

Published in:

2006

By:

Margulies, Marcel;
Egholm, Michael;
Altman, William E.;
Attiya, Said;
Bader, Joel S.;
Bemben, Lisa A.;
Berka, Jan;
Braverman, Michael S.;
Yi-Ju Chen;
Zhoutao Chen;
Dewell, Scott B.;
de Winter, Alex;
Drake, James;
Lei Du;
Fierro, Joseph M.;
Forte, Robin;
Gomes, Xavier V.;
Goodwin, Brian C.;
Wen He;
Helgesen, Scott

Publication type:

Correction Notice

Genome sequencing in microfabricated high-density picolitre reactors.

Published in:

Nature, 2005, v. 437, n. 7057, p. 376, doi. 10.1038/nature03959

By:

Margulies, Marcel;
Egholm, Michael;
Altman, William E.;
Attiya, Said;
Bader, Joel S.;
Bemben, Lisa A.;
Berka, Jan;
Braverman, Michael S.;
Yi-Ju Chen;
Zhoutao Chen;
Dewell, Scott B.;
Lei Du;
Fierro, Joseph M.;
Gomes, Xavier V.;
Godwin, Brian C.;
Wen He;
Helgesen, Scott;
Chun He Ho;
Irzyk, Gerard P.;
Jando, Szilveszter C.

Publication type:

Article

Comprehensive evaluation of imputation performance in African Americans.

Published in:

Journal of Human Genetics, 2012, v. 57, n. 7, p. 411, doi. 10.1038/jhg.2012.43

By:

Chanda, Pritam;
Yuhki, Naoya;
Li, Man;
Bader, Joel S;
Hartz, Alex;
Boerwinkle, Eric;
Kao, WH Linda;
Arking, Dan E

Publication type:

Article

HapZipper: sharing HapMap populations just got easier.

Published in:

Nucleic Acids Research, 2012, v. 40, n. 20, p. e159, doi. 10.1093/nar/gks709

By:

Chanda, Pritam;
Elhaik, Eran;
Bader, Joel S.

Publication type:

Article

CLONEQC: lightweight sequence verification for synthetic biology.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 8, p. 2617, doi. 10.1093/nar/gkq093

By:

Lee, Pablo A.;
Dymond, Jessica S.;
Scheifele, Lisa Z.;
Richardson, Sarah M.;
Foelber, Katrina J.;
Boeke, Jef D.;
Bader, Joel S.

Publication type:

Article

GeneDesign 3.0 is an updated synthetic biology toolkit.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 8, p. 2603, doi. 10.1093/nar/gkq143

By:

Richardson, Sarah M.;
Nunley, Paul W.;
Yarrington, Robert M.;
Boeke, Jef D.;
Bader, Joel S.

Publication type:

Article

A configurational bias Monte Carlo method for linear and cyclic peptides.

Published in:

Molecular Physics, 1996, v. 87, n. 6, p. 1245, doi. 10.1080/00268979600100841

By:

Deem, Michael W.;
Bader, Joel S.

Publication type:

Article

Family-based association tests for quantitative traits using pooled DNA.

Published in:

European Journal of Human Genetics, 2002, v. 10, n. 12, p. 870, doi. 10.1038/sj.ejhg.5200893

By:

Bader, Joel S;
Sham, Pak

Publication type:

Article

Optimal selection strategies for QTL mapping using pooled DNA samples.

Published in:

European Journal of Human Genetics, 2002, v. 10, n. 2, p. 125, doi. 10.1038/sj.ejhg.5200771

By:

Jawaid, Ansar;
Bader, Joel S.;
Purcell, Shaun;
Cherny, Stacey S.;
Sham, Pak

Publication type:

Article

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets.

Published in:

Nature Genetics, 2006, v. 38, n. 3, p. 285, doi. 10.1038/ng1747

By:

Gandhi, T. K. B.;
Zhong, Jun;
Mathivanan, Suresh;
Karthick, L.;
Chandrika, K. N.;
Mohan, S. Sujatha;
Sharma, Salil;
Pinkert, Stefan;
Nagaraju, Shilpa;
Periaswamy, Balamurugan;
Mishra, Goparani;
Nandakumar, Kannabiran;
Beiyi Shen;
Deshpande, Nandan;
Nayak, Rashmi;
Sarker, Malabika;
Boeke, Jef D.;
Parmigiani, Giovanni;
Schultz, Jörg;
Bader, Joel S.

Publication type:

Article

Gene-Based Tests of Association.

Published in:

PLoS Genetics, 2011, v. 7, n. 7, p. 1, doi. 10.1371/journal.pgen.1002177

By:

Hailiang Huang;
Chanda, Pritam;
Alonso, Alvaro;
Bader, Joel S.;
Arking, Dan E.

Publication type:

Article

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012725

By:

Mousavi, Zeinab;
Arvanitis, Marios;
Duong, ThuyVy;
Brody, Jennifer A.;
Battle, Alexis;
Sotoodehnia, Nona;
Shojaie, Ali;
Arking, Dan E.;
Bader, Joel S.

Publication type:

Article

Probabilistic inference of molecular networks from noisy data sources.

Published in:

Bioinformatics, 2004, v. 20, n. 8, p. 1205, doi. 10.1093/bioinformatics/bth061

By:

Ivan Iossifov;
Michael Krauthammer;
Carol Friedman;
Vasileios Hatzivassiloglou;
Joel S. Bader;
Kevin P. White;
Andrey Rzhetsky

Publication type:

Article

Profiling Diverse Compounds by Flux- and Electrophysiology-Based Primary Screens for Inhibition of Human Ether-à-go-goRelated Gene Potassium Channels.

Published in:

Assay & Drug Development Technologies, 2010, v. 8, n. 6, p. 743, doi. 10.1089/adt.2010.0339

By:

Beiyan Zou;
Haibo Yu;
Joseph J. Babcock;
Pritam Chanda;
Joel S. Bader;
Owen B. McManus;
Min Li

Publication type:

Article

Transcriptomic dynamics of ABA response in Brassica napus guard cells.

Published in:

Stress Biology, 2024, v. 4, n. 1, p. 1, doi. 10.1007/s44154-024-00169-7

By:

Villiers, Florent;
Suhail, Yasir;
Lee, Jade;
Hauser, Felix;
Hwang, Jaeung;
Bader, Joel S.;
McKay, John K.;
Peck, Scott C.;
Schroeder, Julian I.;
Kwak, June M.

Publication type:

Article

Next-generation large-scale binary protein interaction network for Drosophila melanogaster.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37876-0

By:

Tang, Hong-Wen;
Spirohn, Kerstin;
Hu, Yanhui;
Hao, Tong;
Kovács, István A.;
Gao, Yue;
Binari, Richard;
Yang-Zhou, Donghui;
Wan, Kenneth H.;
Bader, Joel S.;
Balcha, Dawit;
Bian, Wenting;
Booth, Benjamin W.;
Coté, Atina G.;
de Rouck, Steffi;
Desbuleux, Alice;
Goh, Kah Yong;
Kim, Dae-Kyum;
Knapp, Jennifer J.;
Lee, Wen Xing

Publication type:

Article

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 11, p. e214, doi. 10.1371/journal.pcbi.0030214

By:

Huang, Hailiang;
Jedynak, Bruno M;
Bader, Joel S

Publication type:

Article

OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3292, doi. 10.1093/bioinformatics/btaa096

By:

Hasnain, Zaki;
Fraser, Andrew K;
Georgess, Dan;
Choi, Alex;
Macklin, Paul;
Bader, Joel S;
Peyton, Shelly R;
Ewald, Andrew J;
Newton, Paul K

Publication type:

Article

BioPartsDB: a synthetic biology workflow web-application for education and research.

Published in:

Bioinformatics, 2016, v. 32, n. 22, p. 3519, doi. 10.1093/bioinformatics/btw394

By:

Stracquadanio, Giovanni;
Kun Yang;
Boeke, Jef D.;
Bader, Joel S.

Publication type:

Article

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.

Published in:

Bioinformatics, 2016, v. 32, n. 6, p. 937, doi. 10.1093/bioinformatics/btv664

By:

Kun Yang;
Stracquadanio, Giovanni;
Jingchuan Luo;
Boeke, Jef D.;
Bader, Joel S.

Publication type:

Article

How networks change with time.

Published in:

Bioinformatics, 2012, v. 28, n. 12, p. i40, doi. 10.1093/bioinformatics/bts211

By:

Park, Yongjin;
Bader, Joel S.

Publication type:

Article

Editorial.

Published in:

Bioinformatics, 2010, v. 26, n. 12, p. i1, doi. 10.1093/bioinformatics/btq238

By:

Singh, Mona;
Bader, Joel S.

Publication type:

Article

Precision and recall estimates for two-hybrid screens.

Published in:

Bioinformatics, 2009, v. 25, n. 3, p. 372, doi. 10.1093/bioinformatics/btn640

By:

Hailiang Huang;
Joel S. Bader

Publication type:

Article

DNA Pooling: a tool for large-scale association studies.

Published in:

Nature Reviews Genetics, 2002, v. 3, n. 11, p. 862, doi. 10.1038/nrg930

By:

Sham, Pak;
Bader, Joel S.;
Craig, Ian;
O'Donovan, Michael;
Owen, Michael

Publication type:

Article

Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-57845-7

By:

Matern, William M.;
Jenquin, Robert L.;
Bader, Joel S.;
Karakousis, Petros C.

Publication type:

Article

Molecular and systems approaches towards drought-tolerant canola crops.

Published in:

New Phytologist, 2016, v. 210, n. 4, p. 1169, doi. 10.1111/nph.13866

By:

Zhu, Mengmeng;
Monroe, J. Grey;
Suhail, Yasir;
Villiers, Florent;
Mullen, Jack;
Pater, Dianne;
Hauser, Felix;
Jeon, Byeong Wook;
Bader, Joel S.;
Kwak, June M.;
Schroeder, Julian I.;
McKay, John K.;
Assmann, Sarah M.

Publication type:

Article

Predicting functional associations from metabolism using bi-partite network algorithms.

Published in:

BMC Systems Biology, 2010, v. 4, p. 95, doi. 10.1186/1752-0509-4-95

By:

Veeramani, Balaji;
Bader, Joel S.

Publication type:

Article

Analytical approximations for the amplitude and period of a relaxation oscillator.

Published in:

BMC Systems Biology, 2009, v. 3, p. 1, doi. 10.1186/1752-0509-3-6

By:

Kut, Carmen;
Golkhou, Vahid;
Bader, Joel S.

Publication type:

Article

RNA-Seq optimization with eQTL gold standards.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-892

By:

Ellis, Shannon E.;
Gupta, Simone;
Ashar, Foram N.;
Bader, Joel S.;
West, Andrew B.;
Arking, Dan E.

Publication type:

Article

RNA Interference Analysis of Legionella<br /> in Drosophila Cells: Exploitation of Early<br /> Secretory Apparatus Dynamics.

Published in:

PLoS Pathogens, 2006, v. 2, n. 4, p. e34, doi. 10.1371/journal.ppat.0020034

By:

Dorer, Marion S.;
Kirton, Donald;
Bader, Joel S.;
Isberg, Ralph R.;
Portnoy, Daniel

Publication type:

Article

Cancer cells educate natural killer cells to a metastasis-promoting cell state.

Published in:

Journal of Cell Biology, 2020, v. 219, n. 9, p. 1, doi. 10.1083/jcb.202001134

By:

Chan, Isaac S.;
Knútsdóttir, Hildur;
Ramakrishnan, Gayathri;
Padmanaban, Veena;
Warrier, Manisha;
Ramirez, Juan Carlos;
Dunworth, Matthew;
Hao Zhang;
Jaffee, Elizabeth M.;
Bader, Joel S.;
Ewald, Andrew Josef

Publication type:

Article

Twist1-induced dissemination preserves epithelial identity and requires E-cadherin.

Published in:

Journal of Cell Biology, 2014, v. 204, n. 5, p. 839, doi. 10.1083/jcb.201306088

By:

Shamir, Eliah R.;
Pappalardo, Elisa;
Jorgens, Danielle M.;
Coutinho, Kester;
Wen-Ting Tsai;
Aziz, Khaled;
Auer, Manfred;
Tran, Phuoc T.;
Bader, Joel S.;
Ewald, Andrew J.

Publication type:

Article

Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism.

Published in:

Nature Communications, 2014, v. 5, n. 12, p. 5748, doi. 10.1038/ncomms6748

By:

Gupta, Simone;
Ellis, Shannon E.;
Ashar, Foram N.;
Moes, Anna;
Bader, Joel S.;
Zhan, Jianan;
West, Andrew B.;
Arking, Dan E.

Publication type:

Article

New Connections, New Components, Real Dynamics.

Published in:

Science Signaling, 2009, v. 2, n. 82, p. 1, doi. 10.1126/scisignal.282pe48

By:

Bader, Joel S.

Publication type:

Article

Resolving the structure of interactomes with hierarchical agglomerative clustering.

Published in:

BMC Bioinformatics, 2011, v. 12, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-12-S1-S44

By:

Park, Yongjin;
Bader, Joel S.

Publication type:

Article

NeMo: Network Module identification in Cytoscape.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 1, doi. 10.1186/1471-2105-11-S1-S61

By:

Rivera, Corban G.;
Vakil, Rachit;
Bader, Joel S.

Publication type:

Article

Heterozygous diploid and interspecies SCRaMbLEing.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-04157-0

By:

Shen, Michael J.;
Yi Wu;
Kun Yang;
Yunxiang Li;
Hui Xu;
Haoran Zhang;
Bing-Zhi Li;
Xia Li;
Wen-Hai Xiao;
Xiao Zhou;
Mitchell, Leslie A.;
Bader, Joel S.;
Yingjin Yuan;
Boeke, Jef D.

Publication type:

Article

Grand network convergence.

Published in:

Genome Biology, 2011, v. 12, n. 6, p. 306, doi. 10.1186/gb-2011-12-6-306

By:

Bader, Joel S.

Publication type:

Article

Priors, population sizes, and power in genome-wide hypothesis tests.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05261-9

By:

Cai, Jitong;
Zhan, Jianan;
Arking, Dan E.;
Bader, Joel S.

Publication type:

Article

Gene function prediction from congruent synthetic lethal interactions in yeast.

Published in:

Molecular Systems Biology, 2005, v. 1, n. 1, p. E1, doi. 10.1038/msb4100034

By:

Ye, Ping;
Peyser, Brian D;
Pan, Xuewen;
Boeke, Jef D;
Spencer, Forrest A;
Bader, Joel S

Publication type:

Article

Schizophrenia risk alleles often affect the expression of many genes and each gene may have a different effect on the risk: A mediation analysis.

Published in:

American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 2021, v. 186, n. 4, p. 251, doi. 10.1002/ajmg.b.32841

By:

Peng, Xi;
Bader, Joel S.;
Avramopoulos, Dimitrios

Publication type:

Article

Lesion-Specific Immune Response in Granulomas of Patients with Pulmonary Tuberculosis: A Pilot Study.

Published in:

PLoS ONE, 2015, v. 10, n. 7, p. 1, doi. 10.1371/journal.pone.0132249

By:

Subbian, Selvakumar;
Tsenova, Liana;
Kim, Mi-Jeong;
Wainwright, Helen C.;
Visser, Annalie;
Bandyopadhyay, Nirmalya;
Bader, Joel S.;
Karakousis, Petros C.;
Murrmann, Gabriele B.;
Bekker, Linda-Gail;
Russell, David G.;
Kaplan, Gilla

Publication type:

Article

Angiogenesis Interactome and Time Course Microarray Data Reveal the Distinct Activation Patterns in Endothelial Cells.

Published in:

PLoS ONE, 2014, v. 9, n. 10, p. 1, doi. 10.1371/journal.pone.0110871

By:

Chu, Liang-Hui;
Lee, Esak;
Bader, Joel S.;
Popel, Aleksander S.

Publication type:

Article

The Housekeeping Gene Hypoxanthine Guanine Phosphoribosyltransferase (HPRT) Regulates Multiple Developmental and Metabolic Pathways of Murine Embryonic Stem Cell Neuronal Differentiation.

Published in:

PLoS ONE, 2013, v. 8, n. 10, p. 1, doi. 10.1371/journal.pone.0074967

By:

Kang, Tae Hyuk;
Park, Yongjin;
Bader, Joel S.;
Friedmann, Theodore

Publication type:

Article

Fast Association Tests for Genes with FAST.

Published in:

PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0068585

By:

Chanda, Pritam;
Huang, Hailiang;
Arking, Dan E.;
Bader, Joel S.

Publication type:

Article