Joel S Bader

Joel S Bader

UNVERIFIED PROFILE

Are you Joel S Bader?   Register this Author

Register author
Joel S Bader

Joel S Bader

Publications by authors named "Joel S Bader"

Are you Joel S Bader?   Register this Author

99Publications

2165Reads

22Profile Views

E-cadherin is required for metastasis in multiple models of breast cancer.

Nature 2019 Sep 4;573(7774):439-444. Epub 2019 Sep 4.

Department of Cell Biology, Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-019-1526-3DOI Listing
September 2019

Genome analysis of Mycobacterium avium subspecies hominissuis strain 109.

Sci Data 2018 12 4;5:180277. Epub 2018 Dec 4.

Center for Systems Approaches to Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/sdata2018277
Publisher Site
http://dx.doi.org/10.1038/sdata.2018.277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278689PMC
December 2018

PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity.

Authors:
Jessica van Setten Jennifer A Brody Yalda Jamshidi Brenton R Swenson Anne M Butler Harry Campbell Fabiola M Del Greco Daniel S Evans Quince Gibson Daniel F Gudbjartsson Kathleen F Kerr Bouwe P Krijthe Leo-Pekka Lyytikäinen Christian Müller Martina Müller-Nurasyid Ilja M Nolte Sandosh Padmanabhan Marylyn D Ritchie Antonietta Robino Albert V Smith Maristella Steri Toshiko Tanaka Alexander Teumer Stella Trompet Sheila Ulivi Niek Verweij Xiaoyan Yin David O Arnar Folkert W Asselbergs Joel S Bader John Barnard Josh Bis Stefan Blankenberg Eric Boerwinkle Yuki Bradford Brendan M Buckley Mina K Chung Dana Crawford Marcel den Hoed Josh C Denny Anna F Dominiczak Georg B Ehret Mark Eijgelsheim Patrick T Ellinor Stephan B Felix Oscar H Franco Lude Franke Tamara B Harris Hilma Holm Gandin Ilaria Annamaria Iorio Mika Kähönen Ivana Kolcic Jan A Kors Edward G Lakatta Lenore J Launer Honghuang Lin Henry J Lin Ruth J F Loos Steven A Lubitz Peter W Macfarlane Jared W Magnani Irene Mateo Leach Thomas Meitinger Braxton D Mitchell Thomas Munzel George J Papanicolaou Annette Peters Arne Pfeufer Peter P Pramstaller Olli T Raitakari Jerome I Rotter Igor Rudan Nilesh J Samani David Schlessinger Claudia T Silva Aldana Moritz F Sinner Jonathan D Smith Harold Snieder Elsayed Z Soliman Timothy D Spector David J Stott Konstantin Strauch Kirill V Tarasov Unnur Thorsteinsdottir Andre G Uitterlinden David R Van Wagoner Uwe Völker Henry Völzke Melanie Waldenberger Harm Jan Westra Philipp S Wild Tanja Zeller Alvaro Alonso Christy L Avery Stefania Bandinelli Emelia J Benjamin Francesco Cucca Marcus Dörr Luigi Ferrucci Paolo Gasparini Vilmundur Gudnason Caroline Hayward Susan R Heckbert Andrew A Hicks J Wouter Jukema Stefan Kääb Terho Lehtimäki Yongmei Liu Patricia B Munroe Afshin Parsa Ozren Polasek Bruce M Psaty Dan M Roden Renate B Schnabel Gianfranco Sinagra Kari Stefansson Bruno H Stricker Pim van der Harst Cornelia M van Duijn James F Wilson Sina A Gharib Paul I W de Bakker Aaron Isaacs Dan E Arking Nona Sotoodehnia

Nat Commun 2018 07 25;9(1):2904. Epub 2018 Jul 25.

Departments of Medicine and Epidemiology, Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, 98101, WA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-018-04766-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060178PMC
July 2018

Heterozygous diploid and interspecies SCRaMbLEing.

Nat Commun 2018 05 22;9(1):1934. Epub 2018 May 22.

Department of Biochemistry Molecular Pharmacology and Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41467-018-04157-0
Publisher Site
http://dx.doi.org/10.1038/s41467-018-04157-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964232PMC
May 2018

Gene Enrichment Analysis Reveals Major Regulators of Gene Expression in Two Models of Antibiotic Tolerance.

Front Microbiol 2018 4;9:610. Epub 2018 Apr 4.

Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2018.00610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893760PMC
April 2018

Design of a synthetic yeast genome.

Science 2017 03;355(6329):1040-1044

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aaf4557DOI Listing
March 2017

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

Bioinformatics 2016 11 13;32(22):3519-3521. Epub 2016 Jul 13.

Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181553PMC
November 2016

Molecular and systems approaches towards drought-tolerant canola crops.

New Phytol 2016 06 16;210(4):1169-89. Epub 2016 Feb 16.

Biology Department, Pennsylvania State University, University Park, PA, 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.13866DOI Listing
June 2016

Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions.

Infect Immun 2016 05 22;84(5):1650-1669. Epub 2016 Apr 22.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/IAI.01438-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862722PMC
May 2016

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

Bioinformatics 2016 03 14;32(6):937-9. Epub 2015 Nov 14.

Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803390PMC
March 2016

Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters.

Proc Natl Acad Sci U S A 2016 Feb 1;113(7):E854-63. Epub 2016 Feb 1.

Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205; Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1508541113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763783PMC
February 2016

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.

Genome Res 2016 Jan 13;26(1):36-49. Epub 2015 Nov 13.

High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA; Department of Biomedical Engineering, School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.193433.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691749PMC
January 2016

Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

PLoS One 2014 16;9(10):e110871. Epub 2014 Oct 16.

Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America; Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110871PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199761PMC
December 2015

Tissue matrix arrays for high-throughput screening and systems analysis of cell function.

Nat Methods 2015 Dec 19;12(12):1197-204. Epub 2015 Oct 19.

Translational Tissue Engineering Center, Wilmer Eye Institute and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3619DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666781PMC
December 2015

PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease.

Physiol Genomics 2015 Aug 9;47(8):331-43. Epub 2015 Jun 9.

Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1152/physiolgenomics.00125.2014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525078PMC
August 2015

RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae.

ACS Synth Biol 2015 Mar 4;4(3):213-20. Epub 2014 Jun 4.

†Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, PR China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/sb500241eDOI Listing
March 2015

Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes.

Proc Natl Acad Sci U S A 2015 Feb 26;112(6):1803-8. Epub 2015 Jan 26.

School of Medicine, The Johns Hopkins University, Baltimore, MD 21205; Institute for Systems Genetics, NYU Langone Medical Center, New York, NY 10016; and

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1424704112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330768PMC
February 2015

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

Nat Commun 2014 Dec 10;5:5748. Epub 2014 Dec 10.

Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms6748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270294PMC
December 2014

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

Authors:
Dan E Arking Sara L Pulit Lia Crotti Pim van der Harst Patricia B Munroe Tamara T Koopmann Nona Sotoodehnia Elizabeth J Rossin Michael Morley Xinchen Wang Andrew D Johnson Alicia Lundby Daníel F Gudbjartsson Peter A Noseworthy Mark Eijgelsheim Yuki Bradford Kirill V Tarasov Marcus Dörr Martina Müller-Nurasyid Annukka M Lahtinen Ilja M Nolte Albert Vernon Smith Joshua C Bis Aaron Isaacs Stephen J Newhouse Daniel S Evans Wendy S Post Daryl Waggott Leo-Pekka Lyytikäinen Andrew A Hicks Lewin Eisele David Ellinghaus Caroline Hayward Pau Navarro Sheila Ulivi Toshiko Tanaka David J Tester Stéphanie Chatel Stefan Gustafsson Meena Kumari Richard W Morris Åsa T Naluai Sandosh Padmanabhan Alexander Kluttig Bernhard Strohmer Andrie G Panayiotou Maria Torres Michael Knoflach Jaroslav A Hubacek Kamil Slowikowski Soumya Raychaudhuri Runjun D Kumar Tamara B Harris Lenore J Launer Alan R Shuldiner Alvaro Alonso Joel S Bader Georg Ehret Hailiang Huang W H Linda Kao James B Strait Peter W Macfarlane Morris Brown Mark J Caulfield Nilesh J Samani Florian Kronenberg Johann Willeit J Gustav Smith Karin H Greiser Henriette Meyer Zu Schwabedissen Karl Werdan Massimo Carella Leopoldo Zelante Susan R Heckbert Bruce M Psaty Jerome I Rotter Ivana Kolcic Ozren Polašek Alan F Wright Maura Griffin Mark J Daly David O Arnar Hilma Hólm Unnur Thorsteinsdottir Joshua C Denny Dan M Roden Rebecca L Zuvich Valur Emilsson Andrew S Plump Martin G Larson Christopher J O'Donnell Xiaoyan Yin Marco Bobbo Adamo P D'Adamo Annamaria Iorio Gianfranco Sinagra Angel Carracedo Steven R Cummings Michael A Nalls Antti Jula Kimmo K Kontula Annukka Marjamaa Lasse Oikarinen Markus Perola Kimmo Porthan Raimund Erbel Per Hoffmann Karl-Heinz Jöckel Hagen Kälsch Markus M Nöthen Marcel den Hoed Ruth J F Loos Dag S Thelle Christian Gieger Thomas Meitinger Siegfried Perz Annette Peters Hanna Prucha Moritz F Sinner Melanie Waldenberger Rudolf A de Boer Lude Franke Pieter A van der Vleuten Britt Maria Beckmann Eimo Martens Abdennasser Bardai Nynke Hofman Arthur A M Wilde Elijah R Behr Chrysoula Dalageorgou John R Giudicessi Argelia Medeiros-Domingo Julien Barc Florence Kyndt Vincent Probst Alice Ghidoni Roberto Insolia Robert M Hamilton Stephen W Scherer Jeffrey Brandimarto Kenneth Margulies Christine E Moravec Fabiola del Greco M Christian Fuchsberger Jeffrey R O'Connell Wai K Lee Graham C M Watt Harry Campbell Sarah H Wild Nour E El Mokhtari Norbert Frey Folkert W Asselbergs Irene Mateo Leach Gerjan Navis Maarten P van den Berg Dirk J van Veldhuisen Manolis Kellis Bouwe P Krijthe Oscar H Franco Albert Hofman Jan A Kors André G Uitterlinden Jacqueline C M Witteman Lyudmyla Kedenko Claudia Lamina Ben A Oostra Gonçalo R Abecasis Edward G Lakatta Antonella Mulas Marco Orrú David Schlessinger Manuela Uda Marcello R P Markus Uwe Völker Harold Snieder Timothy D Spector Johan Ärnlöv Lars Lind Johan Sundström Ann-Christine Syvänen Mika Kivimaki Mika Kähönen Nina Mononen Olli T Raitakari Jorma S Viikari Vera Adamkova Stefan Kiechl Maria Brion Andrew N Nicolaides Bernhard Paulweber Johannes Haerting Anna F Dominiczak Fredrik Nyberg Peter H Whincup Aroon D Hingorani Jean-Jacques Schott Connie R Bezzina Erik Ingelsson Luigi Ferrucci Paolo Gasparini James F Wilson Igor Rudan Andre Franke Thomas W Mühleisen Peter P Pramstaller Terho J Lehtimäki Andrew D Paterson Afshin Parsa Yongmei Liu Cornelia M van Duijn David S Siscovick Vilmundur Gudnason Yalda Jamshidi Veikko Salomaa Stephan B Felix Serena Sanna Marylyn D Ritchie Bruno H Stricker Kari Stefansson Laurie A Boyer Thomas P Cappola Jesper V Olsen Kasper Lage Peter J Schwartz Stefan Kääb Aravinda Chakravarti Michael J Ackerman Arne Pfeufer Paul I W de Bakker Christopher Newton-Cheh

Nat Genet 2014 Aug 22;46(8):826-36. Epub 2014 Jun 22.

1] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA. [4] Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA. [5].

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.3014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124521PMC
August 2014

Total synthesis of a functional designer eukaryotic chromosome.

Science 2014 04 27;344(6179):55-8. Epub 2014 Mar 27.

Department of Environmental Health Sciences, Johns Hopkins University (JHU) School of Public Health, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1249252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033833PMC
April 2014

Fast association tests for genes with FAST.

PLoS One 2013 23;8(7):e68585. Epub 2013 Jul 23.

Department of Biomedical Engineering and Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068585PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720833PMC
March 2014

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

J Cell Biol 2014 Mar;204(5):839-56

Department of Cell Biology and 2 Department of Oncology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1083/jcb.201306088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941052PMC
March 2014

RNA-Seq optimization with eQTL gold standards.

BMC Genomics 2013 Dec 17;14:892. Epub 2013 Dec 17.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-14-892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890578PMC
December 2013

Modeling intercellular transfer of biomolecules through tunneling nanotubes.

Bull Math Biol 2013 Aug 16;75(8):1400-16. Epub 2013 Feb 16.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11538-013-9819-4DOI Listing
August 2013

Molecular immunologic correlates of spontaneous latency in a rabbit model of pulmonary tuberculosis.

Cell Commun Signal 2013 Feb 28;11(1):16. Epub 2013 Feb 28.

Laboratory of Mycobacterial Immunity and Pathogenesis, The Public Health Research Institute (PHRI) Center at the University of Medicine and Dentistry of New Jersey (UMDNJ), 225 Warren Street, 07103, Newark, NJ, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1478-811X-11-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598925PMC
February 2013

HapZipper: sharing HapMap populations just got easier.

Nucleic Acids Res 2012 Nov 27;40(20):e159. Epub 2012 Jul 27.

Department of Biomedical Engineering, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, McKusick-Nathans Institute of Genetic Medicine, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gks709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488212PMC
November 2012

Constructing the angiome: a global angiogenesis protein interaction network.

Physiol Genomics 2012 Oct 21;44(19):915-24. Epub 2012 Aug 21.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1152/physiolgenomics.00181.2011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472464PMC
October 2012

Comprehensive evaluation of imputation performance in African Americans.

J Hum Genet 2012 Jul 31;57(7):411-21. Epub 2012 May 31.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/jhg.2012.43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477509PMC
July 2012

How networks change with time.

Bioinformatics 2012 Jun;28(12):i40-8

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bts211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371843PMC
June 2012

Assembling large DNA segments in yeast.

Methods Mol Biol 2012 ;852:133-50

Department of Environmental Health Sciences, Johns Hopkins University School of Public Health, Baltimore, MD, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-61779-564-0_11DOI Listing
May 2012

Design-A-Gene with GeneDesign.

Methods Mol Biol 2012 ;852:235-47

High Throughput Biology Center, Johns Hopkins University School of Public Health, Baltimore, MD, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-61779-564-0_18DOI Listing
May 2012

The Build-a-Genome course.

Methods Mol Biol 2012 ;852:273-83

High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-61779-564-0_20DOI Listing
May 2012

Analysis of VEGF--a regulated gene expression in endothelial cells to identify genes linked to angiogenesis.

PLoS One 2011 13;6(9):e24887. Epub 2011 Sep 13.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024887PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3172305PMC
February 2012

Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.

Nature 2012 Feb 8;482(7384):251-5. Epub 2012 Feb 8.

Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature10804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277212PMC
February 2012

Novel peptide-specific quantitative structure-activity relationship (QSAR) analysis applied to collagen IV peptides with antiangiogenic activity.

J Med Chem 2011 Oct 13;54(19):6492-500. Epub 2011 Sep 13.

Department of Biomedical Engineering, 613 Traylor Building, Johns Hopkins University, 720 Rutland Avenue, Baltimore, Maryland 21205, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jm200114fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195544PMC
October 2011

Angiogenesis-associated crosstalk between collagens, CXC chemokines, and thrombospondin domain-containing proteins.

Ann Biomed Eng 2011 Aug 18;39(8):2213-22. Epub 2011 May 18.

Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10439-011-0325-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150481PMC
August 2011

Gene-based tests of association.

PLoS Genet 2011 Jul 28;7(7):e1002177. Epub 2011 Jul 28.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1002177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145613PMC
July 2011

Grand network convergence.

Authors:
Joel S Bader

Genome Biol 2011 Jun 17;12(6):306. Epub 2011 Jun 17.

Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
Publisher Site
http://dx.doi.org/10.1186/gb-2011-12-6-306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218839PMC
June 2011

Resolving the structure of interactomes with hierarchical agglomerative clustering.

BMC Bioinformatics 2011 Feb 15;12 Suppl 1:S44. Epub 2011 Feb 15.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-12-S1-S44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044301PMC
February 2011

Profiling diverse compounds by flux- and electrophysiology-based primary screens for inhibition of human Ether-à-go-go related gene potassium channels.

Assay Drug Dev Technol 2010 Dec;8(6):743-54

Department of Neuroscience, High Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/adt.2010.0339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002177PMC
December 2010

Temporal profiling of the secretome during adipogenesis in humans.

J Proteome Res 2010 Oct;9(10):5228-38

McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Oncology, Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr100521cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2948433PMC
October 2010

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

BMC Syst Biol 2010 Jul 14;4:95. Epub 2010 Jul 14.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1752-0509-4-95DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919484PMC
July 2010

GeneDesign 3.0 is an updated synthetic biology toolkit.

Nucleic Acids Res 2010 May 8;38(8):2603-6. Epub 2010 Mar 8.

McKusick-Nathans Institute of Genetic Medicine, High Throughput Biology Center, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkq143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860129PMC
May 2010

CLONEQC: lightweight sequence verification for synthetic biology.

Nucleic Acids Res 2010 May 7;38(8):2617-23. Epub 2010 Mar 7.

Department of Computer Science, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21215, USA.

View Article

Download full-text PDF

Source
https://nar.oxfordjournals.org/content/38/8/2617.full-text-l
Web Search
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkq093
Publisher Site
http://dx.doi.org/10.1093/nar/gkq093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860120PMC
May 2010

Dynamic networks from hierarchical bayesian graph clustering.

PLoS One 2010 Jan 11;5(1):e8118. Epub 2010 Jan 11.

Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland, USA.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008118PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799515PMC
January 2010

NeMo: Network Module identification in Cytoscape.

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S61. Epub 2010 Jan 18.

Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-11-S1-S61DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009535PMC
January 2010

New connections, new components, real dynamics.

Authors:
Joel S Bader

Sci Signal 2009 Aug 4;2(82):pe48. Epub 2009 Aug 4.

Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/scisignal.282pe48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892287PMC
August 2009

Structure-based ab initio prediction of transcription factor-binding sites.

Methods Mol Biol 2009 ;541:23-41

Department of Biomedical Engineering and Institute for Multiscale Modeling of Biological Interactions, John Hopkins University, Baltimore, MD, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-59745-243-4_2DOI Listing
June 2009

HistoneHits: a database for histone mutations and their phenotypes.

Genome Res 2009 Apr 13;19(4):674-81. Epub 2009 Feb 13.

Department of Biomedical Engineering, Johns Hopkins University and School of Medicine, Baltimore, Maryland 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.083402.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666297PMC
April 2009

Precision and recall estimates for two-hybrid screens.

Bioinformatics 2009 Feb 17;25(3):372-8. Epub 2008 Dec 17.

Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University, Baltimore, MD, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btn640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639075PMC
February 2009

Gene synthesis demystified.

Trends Biotechnol 2009 Feb 26;27(2):63-72. Epub 2008 Dec 26.

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S016777990800285
Publisher Site
http://dx.doi.org/10.1016/j.tibtech.2008.10.007DOI Listing
February 2009

Metabolic flux correlations, genetic interactions, and disease.

J Comput Biol 2009 Feb;16(2):291-302

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2008.14TTDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909654PMC
February 2009

Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course.

Genetics 2009 Jan 17;181(1):13-21. Epub 2008 Nov 17.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.108.096784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621162PMC
January 2009

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

BMC Syst Biol 2009 Jan 14;3. Epub 2009 Jan 14.

Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1752-0509-3-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657111PMC
January 2009

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 Res 2008 Dec 2;18(12):1991-2004. Epub 2008 Oct 2.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.077693.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593582PMC
December 2008

Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants.

Cell 2008 Sep;134(6):1066-78

High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2008.07.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701395PMC
September 2008

A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation.

Genes Dev 2008 Aug;22(15):2062-74

High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

View Article

Download full-text PDF

Source
http://genesdev.cshlp.org/cgi/doi/10.1101/gad.1679508
Publisher Site
http://dx.doi.org/10.1101/gad.1679508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492751PMC
August 2008

Systems approaches for pharmacogenetics and pharmacogenomics.

Authors:
Joel S Bader

Pharmacogenomics 2008 Mar;9(3):257-62

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2217/14622416.9.3.257DOI Listing
March 2008

Human Proteinpedia enables sharing of human protein data.

Authors:
Suresh Mathivanan Mukhtar Ahmed Natalie G Ahn Hainard Alexandre Ramars Amanchy Philip C Andrews Joel S Bader Brian M Balgley Marcus Bantscheff Keiryn L Bennett Erik Björling Blagoy Blagoev Ron Bose Samir K Brahmachari Alma S Burlingame Xosé R Bustelo Gerard Cagney Greg T Cantin Helene L Cardasis Julio E Celis Raghothama Chaerkady Feixia Chu Philip A Cole Catherine E Costello Robert J Cotter David Crockett James P DeLany Angelo M De Marzo Leroi V DeSouza Eric W Deutsch Eric Dransfield Gerard Drewes Arnaud Droit Michael J Dunn Kojo Elenitoba-Johnson Rob M Ewing Jennifer Van Eyk Vitor Faca Jayson Falkner Xiangming Fang Catherine Fenselau Daniel Figeys Pierre Gagné Cecilia Gelfi Kris Gevaert Jeffrey M Gimble Florian Gnad Renu Goel Pavel Gromov Samir M Hanash William S Hancock H C Harsha Gerald Hart Faith Hays Fuchu He Prashantha Hebbar Kenny Helsens Heiko Hermeking Winston Hide Karin Hjernø Denis F Hochstrasser Oliver Hofmann David M Horn Ralph H Hruban Nieves Ibarrola Peter James Ole N Jensen Pia Hønnerup Jensen Peter Jung Kumaran Kandasamy Indu Kheterpal Reiko F Kikuno Ulrike Korf Roman Körner Bernhard Kuster Min-Seok Kwon Hyoung-Joo Lee Young-Jin Lee Michael Lefevre Minna Lehvaslaiho Pierre Lescuyer Fredrik Levander Megan S Lim Christian Löbke Joseph A Loo Matthias Mann Lennart Martens Juan Martinez-Heredia Mark McComb James McRedmond Alexander Mehrle Rajasree Menon Christine A Miller Harald Mischak S Sujatha Mohan Riaz Mohmood Henrik Molina Michael F Moran James D Morgan Robert Moritz Martine Morzel David C Muddiman Anuradha Nalli J Daniel Navarro Thomas A Neubert Osamu Ohara Rafael Oliva Gilbert S Omenn Masaaki Oyama Young-Ki Paik Kyla Pennington Rainer Pepperkok Balamurugan Periaswamy Emanuel F Petricoin Guy G Poirier T S Keshava Prasad Samuel O Purvine B Abdul Rahiman Prasanna Ramachandran Y L Ramachandra Robert H Rice Jens Rick Ragna H Ronnholm Johanna Salonen Jean-Charles Sanchez Thierry Sayd Beerelli Seshi Kripa Shankari Shi Jun Sheng Vivekananda Shetty K Shivakumar Richard J Simpson Ravi Sirdeshmukh K W Michael Siu Jeffrey C Smith Richard D Smith David J States Sumio Sugano Matthew Sullivan Giulio Superti-Furga Maarit Takatalo Visith Thongboonkerd Jonathan C Trinidad Mathias Uhlen Joël Vandekerckhove Julian Vasilescu Timothy D Veenstra José-Manuel Vidal-Taboada Mauno Vihinen Robin Wait Xiaoyue Wang Stefan Wiemann Billy Wu Tao Xu John R Yates Jun Zhong Ming Zhou Yunping Zhu Petra Zurbig Akhilesh Pandey

Nat Biotechnol 2008 Feb;26(2):164-7

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt0208-164DOI Listing
February 2008

Ab initio prediction of transcription factor binding sites.

Pac Symp Biocomput 2007 :484-95

Department of Biomedical Engineering, High-Throughput Biology Center, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://www.cs.huji.ac.il/~tommy/Papers/Kaplan+al-PLCB2005.pd
Web Search
http://psb.stanford.edu/psb-online/proceedings/psb07/liu_l.p
Web Search
December 2007

Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps.

PLoS Comput Biol 2007 Nov 21;3(11):e214. Epub 2007 Sep 21.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.0030214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2082503PMC
November 2007

Decoding transcriptional regulatory interactions.

Physica D 2006 Dec;224(1-2):174-181

Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21215 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.physd.2006.09.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1827156PMC
December 2006

Gene function prediction from congruent synthetic lethal interactions in yeast.

Mol Syst Biol 2005 22;1:2005.0026. Epub 2005 Nov 22.

Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/msb4100034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681444PMC
August 2006

Phosphoproteomic analysis of Her2/neu signaling and inhibition.

Proc Natl Acad Sci U S A 2006 Jun 19;103(26):9773-8. Epub 2006 Jun 19.

Department of Pharmacology, McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0603948103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1502529PMC
June 2006

RNA interference analysis of Legionella in Drosophila cells: exploitation of early secretory apparatus dynamics.

PLoS Pathog 2006 Apr 28;2(4):e34. Epub 2006 Apr 28.

Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.0020034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1447669PMC
April 2006

A DNA integrity network in the yeast Saccharomyces cerevisiae.

Cell 2006 Mar 16;124(5):1069-81. Epub 2006 Feb 16.

Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S009286740600118
Publisher Site
http://dx.doi.org/10.1016/j.cell.2005.12.036DOI Listing
March 2006

Global synthetic-lethality analysis and yeast functional profiling.

Trends Genet 2006 Jan 23;22(1):56-63. Epub 2005 Nov 23.

High Throughput Biology Center, Institute of Genetic Medicine, Department of Biostatistics, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tig.2005.11.003DOI Listing
January 2006

Systems biology. When proteomes collide.

Science 2006 Jan;311(5758):187-8

Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1123221DOI Listing
January 2006

Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethality.

BMC Bioinformatics 2005 Dec 6;6:288. Epub 2005 Dec 6.

Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-6-288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1334220PMC
December 2005

Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast.

BMC Bioinformatics 2005 Nov 9;6:270. Epub 2005 Nov 9.

The Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-6-270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1310633PMC
November 2005

A robust toolkit for functional profiling of the yeast genome.

Mol Cell 2004 Nov;16(3):487-96

Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2004.09.035DOI Listing
November 2004

Probabilistic inference of molecular networks from noisy data sources.

Bioinformatics 2004 May 10;20(8):1205-13. Epub 2004 Feb 10.

Department of Medical Informatics, Columbia University, New York, NY 10032, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bth061DOI Listing
May 2004

Gaining confidence in high-throughput protein interaction networks.

Nat Biotechnol 2004 Jan 14;22(1):78-85. Epub 2003 Dec 14.

Department of Biomedical Engineering, 201C Clark Hall, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt924DOI Listing
January 2004

Greedily building protein networks with confidence.

Authors:
Joel S Bader

Bioinformatics 2003 Oct;19(15):1869-74

CuraGen Corporation, 555 Long Wharf Drive, New Haven, CT 06511, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btg358DOI Listing
October 2003

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

Eur J Hum Genet 2002 Dec;10(12):870-8

CuraGen Corporation, 555 Long Wharf Drive, New Haven, Connecticut, CT 06511 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/sj.ejhg.5200893DOI Listing
December 2002

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

Nat Rev Genet 2002 Nov;3(11):862-71

P080, Institute of Psychiatry, King's College, Denmark Hill, London SE5 8AF, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrg930DOI Listing
November 2002

Optimal selection strategies for QTL mapping using pooled DNA samples.

Eur J Hum Genet 2002 Feb;10(2):125-32

Department of Psychological Medicine, Institute of Psychiatry, King's College London, London SE5 8AF, UK.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/5200771
Publisher Site
http://dx.doi.org/10.1038/sj.ejhg.5200771DOI Listing
February 2002