Works by Bader, Joel S.

Results: 63

Human Proteinpedia enables sharing of human protein data.
Published in:
2008
By:
- Mathivanan, Suresh;
- Ahmed, Mukhtar;
- Ahn, Natalie G.;
- Alexandre, Hainard;
- Amanchy, Ramars;
- Andrews, Philip C.;
- Bader, Joel S.;
- Balgley, Brian M.;
- Bantscheff, Marcus;
- Bennett, Keiryn L.;
- Björling, Erik;
- Blagoev, Blagoy;
- Bose, Ron;
- Brahmachari, Samir K.;
- Burlingame, Alma S.;
- Bustelo, Xosé R.;
- Cagney, Gerard;
- Cantin, Greg T.;
- Cardasis, Helene L.;
- Celis, Julio E.
Publication type:
Letter
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
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
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
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
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
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
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
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
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
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
Retraction: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.
Published in:
Nature, 2013, v. 503, n. 7474, p. 146, doi. 10.1038/nature12727
By:
- Lin, Yu-yi;
- Kiihl, Samara;
- Suhail, Yasir;
- Liu, Shang-Yun;
- Chou, Yi-hsuan;
- Kuang, Zheng;
- Lu, Jin-ying;
- Khor, Chin Ni;
- Lin, Chi-Long;
- Bader, Joel S.;
- Irizarry, Rafael;
- Boeke, Jef D.
Publication type:
Article
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.
Published in:
Nature, 2012, v. 482, n. 7384, p. 251, doi. 10.1038/nature10804
By:
- Lin, Yu-yi;
- Kiihl, Samara;
- Suhail, Yasir;
- Liu, Shang-Yun;
- Chou, Yi-hsuan;
- Kuang, Zheng;
- Lu, Jin-ying;
- Khor, Chin Ni;
- Lin, Chi-Long;
- Bader, Joel S.;
- Irizarry, Rafael;
- Boeke, Jef D.
Publication type:
Article
Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.
Published in:
Nature, 2011, v. 477, n. 7365, p. 471, doi. 10.1038/nature10403
By:
- Dymond, Jessica S.;
- Richardson, Sarah M.;
- Coombes, Candice E.;
- Babatz, Timothy;
- Muller, Héloïse;
- Annaluru, Narayana;
- Blake, William J.;
- Schwerzmann, Joy W.;
- Dai, Junbiao;
- Lindstrom, Derek L.;
- Boeke, Annabel C.;
- Gottschling, Daniel E.;
- Chandrasegaran, Srinivasan;
- Bader, Joel S.;
- Boeke, Jef D.
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
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
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
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
Between-tumor and within-tumor heterogeneity in invasive potential.
Published in:
PLoS Computational Biology, 2020, v. 16, n. 1, p. 1, doi. 10.1371/journal.pcbi.1007464
By:
- Padmanaban, Veena;
- Tsehay, Yohannes;
- Cheung, Kevin J.;
- Ewald, Andrew J.;
- Bader, Joel S.
Publication type:
Article
Functional Whole Genome Screen of Nutrient-Starved Mycobacterium tuberculosis Identifies Genes Involved in Rifampin Tolerance.
Published in:
Microorganisms, 2023, v. 11, n. 9, p. 2269, doi. 10.3390/microorganisms11092269
By:
- Matern, William M.;
- Harris, Harley T.;
- Danchik, Carina;
- McDonald, Marissa;
- Patel, Gopi;
- Srivastava, Aashish;
- Ioerger, Thomas R.;
- Bader, Joel S.;
- Karakousis, Petros C.
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
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
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
Early innate immunity determines outcome of Mycobacterium tuberculosis pulmonary infection in rabbits.
Published in:
Cell Communication & Signaling, 2013, v. 11, n. 1, p. 1, doi. 10.1186/1478-811X-11-60
By:
- Subbian, Selvakumar;
- Bandyopadhyay, Nirmalya;
- Tsenova, Liana;
- O'Brien, Paul;
- Khetani, Viraj;
- Kushner, Nicole L.;
- Peixoto, Blas;
- Soteropoulos, Patricia;
- Bader, Joel S.;
- Karakousis, Petros C.;
- Fallows, Dorothy;
- Kaplan, Gilla
Publication type:
Article
Molecular immunologic correlates of spontaneous latency in a rabbit model of pulmonary tuberculosis.
Published in:
Cell Communication & Signaling, 2012, v. 11, n. 1, p. 1, doi. 10.1186/1478-811X-11-16
By:
- Subbian, Selvakumar;
- O'Brien, Paul;
- Kushner, Nicole L.;
- Yang, Guibin;
- Tsenova, Liana;
- Peixoto, Blas;
- Bandyopadhyay, Nirmalya;
- Bader, Joel S.;
- Karakousis, Petros C.;
- Fallows, Dorothy;
- Kaplan, Gilla
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
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
Differential transport of DNA by a rectified Brownian motion device.
Published in:
Electrophoresis, 2000, v. 21, n. 1, p. 74, doi. 10.1002/(SICI)1522-2683(20000101)21:1<74::AID-ELPS74>3.0.CO;2-K
By:
- Hammond, Richard W.;
- Bader, Joel S.;
- Henck, Steven A.;
- Deem, Michael W.;
- McDermott, Gregory A.;
- Bustillo, James M.;
- Rothberg, Jonathan M.
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
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
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
Prioritizing drug targets by perturbing biological network response functions.
Published in:
PLoS Computational Biology, 2024, v. 20, n. 6, p. 1, doi. 10.1371/journal.pcbi.1012195
By:
- Perrone, Matthew C.;
- Lerner, Michael G.;
- Dunworth, Matthew;
- Ewald, Andrew J.;
- Bader, Joel S.
Publication type:
Article
Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course.
Published in:
Genetics, 2009, v. 181, n. 1, p. 13, doi. 10.1534/genetics.108.096784
By:
- Dymond, Jessica S.;
- Scheifele, Lisa Z.;
- Richardson, Sarah;
- Lee, Pablo;
- Chandrasegaran, Srinivasan;
- Bader, Joel S.;
- Boeke, Jef D.
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
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
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
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