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Joel Bader

Research Profile

Living Beings

Saccharomyces cerevisiae

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Occupations

Computational Biology

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Chemicals & Drugs

Genes & Molecular Sequences

Physiology

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Publications

TOP 3
Pritam Chanda; Eran Elhaik; Joel S Bader
HapZipper: sharing HapMap populations just got easier.
Liang-Hui Chu; Aleksander S Popel; Corban G Rivera; Joel S Bader
Constructing the angiome: a global angiogenesis protein interaction network.
Pritam Chanda; Alex Hartz; Man Li; Naoya Yuhki; WEN KAO; Joel S Bader; Eric Boerwinkle; Dan E Arking
Comprehensive evaluation of imputation performance in African Americans.

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All Publications

2012: Pritam Chanda; Eran Elhaik; Joel S Bader
HapZipper: sharing HapMap populations just got easier.
Nucleic acids research 2012;40(20):e159.
2012: Liang-Hui Chu; Aleksander S Popel; Corban G Rivera; Joel S Bader
Constructing the angiome: a global angiogenesis protein interaction network.
Physiological genomics 2012;44(19):915-24.
2012: Pritam Chanda; Alex Hartz; Man Li; Naoya Yuhki; WEN KAO; Joel S Bader; Eric Boerwinkle; Dan E Arking
Comprehensive evaluation of imputation performance in African Americans.
Journal of human genetics 2012;57(7):411-21.
2012: Yongjin Park; Joel S Bader
How networks change with time.
Bioinformatics (Oxford, England) 2012;28(12):i40-8.
2012: Yu-Yi Lin; Shang-Yun Liu; Jin-ying Lu; Yasir Suhail; Yi-hsuan Chou; Rafael A Irizarry; Chin Ni Khor; Samara Kiihl; Zheng Kuang; Chi-Long Lin; Joel S Bader; Jef Boeke
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.
Nature 2012;482(7384):251-5.
2012: Eric M Cooper; Helöise Müller; Joel S Bader; Srinivasan Chandrasegaran; Jef Boeke
The Build-a-Genome course.
Methods in molecular biology (Clifton, N.J.) 2012;852():273-83.
2012: Sarah M Richardson; Jef Boeke; Steffi Liu; Joel S Bader
Design-A-Gene with GeneDesign.
Methods in molecular biology (Clifton, N.J.) 2012;852():235-47.
2012: Héloïse Muller; Sarah M Richardson; Joy Wu Schwerzmann; Eric M Cooper; Jessica S Dymond; Narayana Annaluru; Joel S Bader; Jef Boeke; Srinivasan Chandrasegaran
Assembling large DNA segments in yeast.
Methods in molecular biology (Clifton, N.J.) 2012;852():133-50.
2012: Narayana Annaluru; Joel S Bader; Jef Boeke; Eric M Cooper; Jessica S Dymond; Karthikeyan Kandavelou; Viktoriya London; Héloïse Muller; Sivaprakash Ramalingam; Sarah M Richardson; Srinivasan Chandrasegaran
Assembling DNA fragments by USER fusion.
Methods in molecular biology (Clifton, N.J.) 2012;852():77-95.
2011: Corban G Rivera; Elena V Rosca; Joel S Bader; Jacob E Koskimaki; Niranjan Pandey; Aleksander S Popel
Novel peptide-specific quantitative structure-activity relationship (QSAR) analysis applied to collagen IV peptides with antiangiogenic activity.
Journal of medicinal chemistry 2011;54(19):6492-500.
2011: Jessica S Dymond; Daniel E Gottschling; Derek L Lindstrom; Héloïse Muller; Sarah M Richardson; Joy W Schwerzmann; Narayana Annaluru; Timothy Babatz; Joel S Bader; William J Blake; Annabel C Boeke; Srinivasan Chandrasegaran; Candice E Coombes; Junbiao Dai; Jef Boeke
Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.
Nature 2011;477(7365):471-6.
2011: Corban G Rivera; Joel S Bader; Aleksander S Popel
Angiogenesis-associated crosstalk between collagens, CXC chemokines, and thrombospondin domain-containing proteins.
Annals of biomedical engineering 2011;39(8):2213-22.
2011: Hailiang Huang; Alvaro Alonso; Joel S Bader; Pritam Chanda; Dan E Arking
Gene-based tests of association.
PLoS genetics 2011;7(7):e1002177.
2011: Corban G Rivera; Joel S Bader; Lena Claesson-Welsh; Sofie Mellberg; Aleksander S Popel
Analysis of VEGF--a regulated gene expression in endothelial cells to identify genes linked to angiogenesis.
PloS one 2011;6(9):e24887.
2011: Joel S Bader
Grand network convergence.
Genome biology 2011;12(6):306.
2011: Yongjin Park; Joel S Bader
Resolving the structure of interactomes with hierarchical agglomerative clustering.
BMC bioinformatics 2011;12 Suppl 1():S44.
2010: Beiyan Zou; Haibo Yu; Joseph J Babcock; Pritam Chanda; Joel S Bader; Owen B McManus; Min Li
Profiling diverse compounds by flux- and electrophysiology-based primary screens for inhibition of human Ether-à-go-go related gene potassium channels.
Assay and drug development technologies 2010;8(6):743-54.
2010: Jun Zhong; Sarah A Krawczyk; Raghothama Chaerkady; Hailiang Huang; renu goel; Joel S Bader; GUANG WILLIAM WONG; Barbara E Corkey; Akhilesh Pandey
Temporal profiling of the secretome during adipogenesis in humans.
Journal of proteome research 2010;9(10):5228-38.
2010: Pablo A Lee; Jessica S Dymond; Lisa Z Scheifele; Sarah M Richardson; Katrina J Foelber; Jef Boeke; Joel S Bader
CLONEQC: lightweight sequence verification for synthetic biology.
Nucleic acids research 2010;38(8):2617-23.
2010: Sarah M Richardson; Paul W Nunley; Robert M Yarrington; Jef Boeke; Joel S Bader
GeneDesign 3.0 is an updated synthetic biology toolkit.
Nucleic acids research 2010;38(8):2603-6.
2010: Balaji Veeramani; Joel S Bader
Predicting functional associations from metabolism using bi-partite network algorithms.
BMC systems biology 2010;4():95.
2010: Corban G Rivera; Rachit Vakil; Joel S Bader
NeMo: Network Module identification in Cytoscape.
BMC bioinformatics 2010;11 Suppl 1():S61.
2010: Yongjin Park; Cristopher Moore; Joel S Bader
Dynamic networks from hierarchical bayesian graph clustering.
PloS one 2010;5(1):e8118.
2009: Hailiang Huang; Alexandra M Maertens; Edel Hyland; Junbiao Dai; Anne Norris; Jef Boeke; Joel S Bader
HistoneHits: a database for histone mutations and their phenotypes.
Genome research 2009;19(4):674-81.
2009: Balaji Veeramani; Joel S Bader
Metabolic flux correlations, genetic interactions, and disease.
Journal of computational biology : a journal of computational molecular cell biology 2009;16(2):291-302.
2009: Hailiang Huang; Joel S Bader
Precision and recall estimates for two-hybrid screens.
Bioinformatics (Oxford, England) 2009;25(3):372-8.
2009: Joel S Bader
New connections, new components, real dynamics.
Science signaling 2009;2(82):pe48.
2009: Carmen Kut; Vahid Golkhou; Joel S Bader
Analytical approximations for the amplitude and period of a relaxation oscillator.
BMC systems biology 2009;3():6.
2009: Jessica S Dymond; Lisa Z Scheifele; Sarah Richardson; Pablo Lee; Srinivasan Chandrasegaran; Joel S Bader; Jef Boeke
Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course.
Genetics 2009;181(1):13-21.
2008: Yan Qi; Yasir Suhail; Yu-Yi Lin; Jef Boeke; Joel S Bader
Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions.
Genome research 2008;18(12):1991-2004.
2008: Junbiao Dai; Edel Hyland; Daniel S Yuan; Hailiang Huang; Joel S Bader; Jef Boeke
Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants.
Cell 2008;134(6):1066-78.
2008: Yu-Yi Lin; Yan Qi; Jin-ying Lu; Xuewen Pan; Daniel S Yuan; Yingming Zhao; Joel S Bader; Jef Boeke
A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation.
Genes & development 2008;22(15):2062-74.
2008: Joel S Bader
Systems approaches for pharmacogenetics and pharmacogenomics.
Pharmacogenomics 2008;9(3):257-62.
2007: Hailiang Huang; Bruno M Jedynak; Joel S Bader
Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps.
PLoS computational biology 2007;3(11):e214.
2007: L Angela Liu; Joel S Bader
Ab initio prediction of transcription factor binding sites.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007;():484-95.
2006: Ron Bose; Henrik Molina; A Scott Patterson; John K Bitok; Balamurugan Periaswamy; Joel S Bader; Akhilesh Pandey; Philip A Cole
Phosphoproteomic analysis of Her2/neu signaling and inhibition.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(26):9773-8.
2006: Xuewen Pan; Ping Ye; Daniel S Yuan; Xiaoling Wang; Joel S Bader; Jef Boeke
A DNA integrity network in the yeast Saccharomyces cerevisiae.
Cell 2006;124(5):1069-81.
2006: T K B Gandhi; Jun Zhong; M Suresh; L Karthick; K N Chandrika; S Sujatha Mohan; Salil Sharma; Stefan Pinkert; Shilpa Nagaraju; Balamurugan Periaswamy; Goparani Mishra; Kannabiran Nandakumar; Beiyi Shen; Nandan Deshpande; Rashmi Nayak; Malabika Sarker; Jef Boeke; Giovanni Parmigiani; Jörg Schultz; Joel S Bader; Akhilesh Pandey
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets.
Nature genetics 2006;38(3):285-93.
2006: Joel S Bader; Chant John
Systems biology. When proteomes collide.
Science (New York, N.Y.) 2006;311(5758):187-8.
2006: Siew Loon Ooi; Xuewen Pan; Brian D Peyser; Ping Ye; Pamela B Meluh; Daniel S Yuan; Rafael A Irizarry; Joel S Bader; Forrest Spencer; Jef Boeke
Global synthetic-lethality analysis and yeast functional profiling.
Trends in genetics : TIG 2006;22(1):56-63.
2005: Ping Ye; Brian D Peyser; Xuewen Pan; Jef Boeke; Forrest Spencer; Joel S Bader
Gene function prediction from congruent synthetic lethal interactions in yeast.
Molecular systems biology 2005;1():2005.0026.
2005: Yan Qi; Ping Ye; Joel S Bader
Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethality.
BMC bioinformatics 2005;6():288.
2005: Ping Ye; Brian D Peyser; Forrest Spencer; Joel S Bader
Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast.
BMC bioinformatics 2005;6():270.
2004: Xuewen Pan; Daniel S Yuan; Dong Xiang; Xiaoling Wang; Sharon Sookhai-Mahadeo; Joel S Bader; Philip Hieter; Forrest Spencer; Jef Boeke
A robust toolkit for functional profiling of the yeast genome.
Molecular cell 2004;16(3):487-96.
2004: Joel S Bader; Amitabha Chaudhuri; Jonathan M Rothberg; Chant John
Gaining confidence in high-throughput protein interaction networks.
Nature biotechnology 2004;22(1):78-85.
2003: Joel S Bader
Greedily building protein networks with confidence.
Bioinformatics (Oxford, England) 2003;19(15):1869-74.
2002: Joel S Bader; Pak Sham
Family-based association tests for quantitative traits using pooled DNA.
European journal of human genetics : EJHG 2002;10(12):870-8.
2000: R W Hammond; Joel S Bader; S A Henck; M W Deem; G A McDermott; J M Bustillo; Jonathan M Rothberg
Differential transport of DNA by a rectified Brownian motion device.
Electrophoresis 2000;21(1):74-80.
1999: Joel S Bader; R W Hammond; S A Henck; M W Deem; G A McDermott; J M Bustillo; JW Simpson; G T Mulhern; Jonathan M Rothberg
DNA transport by a micromachined Brownian ratchet device.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(23):13165-9.