Sean D Mooney

Sean D Mooney

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Sean D Mooney

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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Authors:
Naihui Zhou Yuxiang Jiang Timothy R Bergquist Alexandra J Lee Balint Z Kacsoh Alex W Crocker Kimberley A Lewis George Georghiou Huy N Nguyen Md Nafiz Hamid Larry Davis Tunca Dogan Volkan Atalay Ahmet S Rifaioglu Alperen Dalkıran Rengul Cetin Atalay Chengxin Zhang Rebecca L Hurto Peter L Freddolino Yang Zhang Prajwal Bhat Fran Supek José M Fernández Branislava Gemovic Vladimir R Perovic Radoslav S Davidović Neven Sumonja Nevena Veljkovic Ehsaneddin Asgari Mohammad R K Mofrad Giuseppe Profiti Castrense Savojardo Pier Luigi Martelli Rita Casadio Florian Boecker Heiko Schoof Indika Kahanda Natalie Thurlby Alice C McHardy Alexandre Renaux Rabie Saidi Julian Gough Alex A Freitas Magdalena Antczak Fabio Fabris Mark N Wass Jie Hou Jianlin Cheng Zheng Wang Alfonso E Romero Alberto Paccanaro Haixuan Yang Tatyana Goldberg Chenguang Zhao Liisa Holm Petri Törönen Alan J Medlar Elaine Zosa Itamar Borukhov Ilya Novikov Angela Wilkins Olivier Lichtarge Po-Han Chi Wei-Cheng Tseng Michal Linial Peter W Rose Christophe Dessimoz Vedrana Vidulin Saso Dzeroski Ian Sillitoe Sayoni Das Jonathan Gill Lees David T Jones Cen Wan Domenico Cozzetto Rui Fa Mateo Torres Alex Warwick Vesztrocy Jose Manuel Rodriguez Michael L Tress Marco Frasca Marco Notaro Giuliano Grossi Alessandro Petrini Matteo Re Giorgio Valentini Marco Mesiti Daniel B Roche Jonas Reeb David W Ritchie Sabeur Aridhi Seyed Ziaeddin Alborzi Marie-Dominique Devignes Da Chen Emily Koo Richard Bonneau Vladimir Gligorijević Meet Barot Hai Fang Stefano Toppo Enrico Lavezzo Marco Falda Michele Berselli Silvio C E Tosatto Marco Carraro Damiano Piovesan Hafeez Ur Rehman Qizhong Mao Shanshan Zhang Slobodan Vucetic Gage S Black Dane Jo Erica Suh Jonathan B Dayton Dallas J Larsen Ashton R Omdahl Liam J McGuffin Danielle A Brackenridge Patricia C Babbitt Jeffrey M Yunes Paolo Fontana Feng Zhang Shanfeng Zhu Ronghui You Zihan Zhang Suyang Dai Shuwei Yao Weidong Tian Renzhi Cao Caleb Chandler Miguel Amezola Devon Johnson Jia-Ming Chang Wen-Hung Liao Yi-Wei Liu Stefano Pascarelli Yotam Frank Robert Hoehndorf Maxat Kulmanov Imane Boudellioua Gianfranco Politano Stefano Di Carlo Alfredo Benso Kai Hakala Filip Ginter Farrokh Mehryary Suwisa Kaewphan Jari Björne Hans Moen Martti E E Tolvanen Tapio Salakoski Daisuke Kihara Aashish Jain Tomislav Šmuc Adrian Altenhoff Asa Ben-Hur Burkhard Rost Steven E Brenner Christine A Orengo Constance J Jeffery Giovanni Bosco Deborah A Hogan Maria J Martin Claire O'Donovan Sean D Mooney Casey S Greene Predrag Radivojac Iddo Friedberg

Genome Biol 2019 11 19;20(1):244. Epub 2019 Nov 19.

Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.

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http://dx.doi.org/10.1186/s13059-019-1835-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864930PMC
November 2019

Continuing challenges swirl around bioinformatics service delivery.

Authors:
Sean D Mooney

J Biomed Inform 2019 Jun 9;94:103209. Epub 2019 May 9.

Department of Biomedical Informatics and Medical Education, University of Washington, 98109, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2019.103209DOI Listing
June 2019

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome.

PLoS Comput Biol 2019 06 14;15(6):e1007112. Epub 2019 Jun 14.

School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594643PMC
June 2019

The accuracy of passive phone sensors in predicting daily mood.

Depress Anxiety 2019 01 21;36(1):72-81. Epub 2018 Aug 21.

Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, Washington.

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http://dx.doi.org/10.1002/da.22822DOI Listing
January 2019

New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods.

G3 (Bethesda) 2019 01 9;9(1):251-267. Epub 2019 Jan 9.

Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA

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http://dx.doi.org/10.1534/g3.118.200867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325913PMC
January 2019

Using Mobile Apps to Assess and Treat Depression in Hispanic and Latino Populations: Fully Remote Randomized Clinical Trial.

J Med Internet Res 2018 08 9;20(8):e10130. Epub 2018 Aug 9.

Department of Neurology, University of California San Francisco, San Francisco, WA, United States.

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http://www.jmir.org/2018/8/e10130/
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http://dx.doi.org/10.2196/10130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107735PMC
August 2018

Smartphone-Based Passive Assessment of Mobility in Depression: Challenges and Opportunities.

Ment Health Phys Act 2018 Mar 18;14:136-139. Epub 2018 Apr 18.

Department of Psychiatry & Behavioral Sciences, University of Washington, 1959 NE Pacific St. Box 356560, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1016/j.mhpa.2018.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095666PMC
March 2018

PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY.

Pac Symp Biocomput 2016 ;21:243-8

Stanford University School of Medicine & Khosla Ventures, Stanford, CA, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180448PMC
February 2018

Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges.

Hum Mutat 2017 09 12;38(9):1092-1108. Epub 2017 Jun 12.

Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana.

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http://dx.doi.org/10.1002/humu.23258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5561458PMC
September 2017

Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society.

Hum Mutat 2017 04 14;38(4):460-463. Epub 2017 Feb 14.

Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1002/humu.23169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546288PMC
April 2017

Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.

Hum Mutat 2016 11 31;37(11):1137-1143. Epub 2016 Aug 31.

Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington.

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http://dx.doi.org/10.1002/humu.23049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192032PMC
November 2016

USE OF GENOME DATA IN NEWBORNS AS A STARTING POINT FOR LIFE-LONG PRECISION MEDICINE.

Pac Symp Biocomput 2016 ;21:568-75

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA,

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October 2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease.

PLoS Comput Biol 2016 08 26;12(8):e1005091. Epub 2016 Aug 26.

Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001644PMC
August 2016

High-performance web services for querying gene and variant annotation.

Genome Biol 2016 05 6;17(1):91. Epub 2016 May 6.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1186/s13059-016-0953-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858870PMC
May 2016

Progress towards the integration of pharmacogenomics in practice.

Authors:
Sean D Mooney

Hum Genet 2015 May 11;134(5):459-65. Epub 2014 Sep 11.

Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA,

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http://dx.doi.org/10.1007/s00439-014-1484-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362928PMC
May 2015

Biotinidase deficiency due to a de novo mutation or gonadal mosaicism in a first child.

Clin Chim Acta 2015 May 18;445:70-2. Epub 2015 Mar 18.

Molecular and Cell Biology Laboratory, Paediatric Neurology Unit and Laboratories, Neuroscience Department, A. Meyer Children's Hospital, Florence, Italy; Department of Neurosciences, Psychology, Pharmacology and Child Health, University of Florence, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.cca.2015.03.010DOI Listing
May 2015

Ten simple rules for a community computational challenge.

PLoS Comput Biol 2015 Apr 23;11(4):e1004150. Epub 2015 Apr 23.

Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1004150
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http://dx.doi.org/10.1371/journal.pcbi.1004150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408123PMC
April 2015

Germline & somatic mosaicism: the 2014 annual scientific meeting of the Human Genome Variation Society.

Hum Mutat 2015 Mar;36(3):390-3

Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota.

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http://dx.doi.org/10.1002/humu.22757DOI Listing
March 2015

The automated function prediction SIG looks back at 2013 and prepares for 2014.

Bioinformatics 2014 Jul 3;30(14):2091-2. Epub 2014 Mar 3.

School of Biosciences, University of Kent, Canterbury, Kent CT2 7NH, UK, The Buck Institute for Research on Aging, Novato, CA 94945, USA, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem Israel, Department of Computer Science and Informatics, Indiana University, Bloomington, IN 47405, USA, Department of Microbiology, Miami University and Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USASchool of Biosciences, University of Kent, Canterbury, Kent CT2 7NH, UK, The Buck Institute for Research on Aging, Novato, CA 94945, USA, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem Israel, Department of Computer Science and Informatics, Indiana University, Bloomington, IN 47405, USA, Department of Microbiology, Miami University and Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080736PMC
July 2014

Medium-chain acyl-CoA deficiency: outlines from newborn screening, in silico predictions, and molecular studies.

ScientificWorldJournal 2013 31;2013:625824. Epub 2013 Oct 31.

Department of Neurosciences, Psychology, Pharmacology and Child Health, University of Florence, Viale Pieraccini 24, 50139 Florence, Italy ; Molecular and Cell Biology Laboratory, Paediatric Neurology Unit and Laboratories, Neuroscience Department, A. Meyer Children's Hospital, Viale Pieraccini 24, 50139 Florence, Italy.

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http://dx.doi.org/10.1155/2013/625824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833120PMC
June 2014

Genome and proteome annotation using automatically recognized concepts and functional networks.

AMIA Jt Summits Transl Sci Proc 2013 18;2013:26. Epub 2013 Mar 18.

Buck Institute for Research on Aging, Novato, CA.

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December 2013

Loss of post-translational modification sites in disease.

Pac Symp Biocomput 2010 :337-47

School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813771PMC
http://dx.doi.org/10.1142/9789814295291_0036DOI Listing
November 2013

A large-scale evaluation of computational protein function prediction.

Authors:
Predrag Radivojac Wyatt T Clark Tal Ronnen Oron Alexandra M Schnoes Tobias Wittkop Artem Sokolov Kiley Graim Christopher Funk Karin Verspoor Asa Ben-Hur Gaurav Pandey Jeffrey M Yunes Ameet S Talwalkar Susanna Repo Michael L Souza Damiano Piovesan Rita Casadio Zheng Wang Jianlin Cheng Hai Fang Julian Gough Patrik Koskinen Petri Törönen Jussi Nokso-Koivisto Liisa Holm Domenico Cozzetto Daniel W A Buchan Kevin Bryson David T Jones Bhakti Limaye Harshal Inamdar Avik Datta Sunitha K Manjari Rajendra Joshi Meghana Chitale Daisuke Kihara Andreas M Lisewski Serkan Erdin Eric Venner Olivier Lichtarge Robert Rentzsch Haixuan Yang Alfonso E Romero Prajwal Bhat Alberto Paccanaro Tobias Hamp Rebecca Kaßner Stefan Seemayer Esmeralda Vicedo Christian Schaefer Dominik Achten Florian Auer Ariane Boehm Tatjana Braun Maximilian Hecht Mark Heron Peter Hönigschmid Thomas A Hopf Stefanie Kaufmann Michael Kiening Denis Krompass Cedric Landerer Yannick Mahlich Manfred Roos Jari Björne Tapio Salakoski Andrew Wong Hagit Shatkay Fanny Gatzmann Ingolf Sommer Mark N Wass Michael J E Sternberg Nives Škunca Fran Supek Matko Bošnjak Panče Panov Sašo Džeroski Tomislav Šmuc Yiannis A I Kourmpetis Aalt D J van Dijk Cajo J F ter Braak Yuanpeng Zhou Qingtian Gong Xinran Dong Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Barbara Di Camillo Stefano Toppo Liang Lan Nemanja Djuric Yuhong Guo Slobodan Vucetic Amos Bairoch Michal Linial Patricia C Babbitt Steven E Brenner Christine Orengo Burkhard Rost Sean D Mooney Iddo Friedberg

Nat Methods 2013 Mar 27;10(3):221-7. Epub 2013 Jan 27.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1038/nmeth.2340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584181PMC
March 2013

Comparative protein interactomics of neuroglobin and myoglobin.

J Neurochem 2012 Oct 14;123(1):192-8. Epub 2012 Aug 14.

Buck Institute for Research on Aging, Novato, CA 94945, USA.

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http://dx.doi.org/10.1111/j.1471-4159.2012.07881.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438380PMC
October 2012

Collaborative software for traditional and translational research.

Hum Genomics 2012 Sep 25;6:21. Epub 2012 Sep 25.

Buck Institute for Research on Aging, Bioinformatics Core, Novato, CA 94945, USA.

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http://dx.doi.org/10.1186/1479-7364-6-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500217PMC
September 2012

DEFOG: discrete enrichment of functionally organized genes.

Integr Biol (Camb) 2012 Jul 18;4(7):795-804. Epub 2012 Jun 18.

Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA.

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http://dx.doi.org/10.1039/c2ib00136eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3469163PMC
July 2012

Functional organization and its implication in evolution of the human protein-protein interaction network.

BMC Genomics 2012 Apr 24;13:150. Epub 2012 Apr 24.

Buck Institute for Research on Aging, Novato, California, USA.

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http://dx.doi.org/10.1186/1471-2164-13-150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375200PMC
April 2012

Prediction of functional regulatory SNPs in monogenic and complex disease.

Hum Mutat 2011 Oct 9;32(10):1183-90. Epub 2011 Sep 9.

Buck Institute for Research on Aging, Novato, California 94945, USA.

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http://dx.doi.org/10.1002/humu.21559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957483PMC
October 2011

Characterization of ligand type of estrogen receptor by MD simulation and mm-PBSA free energy analysis.

Int J Biochem Mol Biol 2011 23;2(2):190-198. Epub 2011 Apr 23.

Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine Indianapolis, Indiana USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180098PMC
April 2011

An ontology-neutral framework for enrichment analysis.

AMIA Annu Symp Proc 2010 Nov 13;2010:797-801. Epub 2010 Nov 13.

Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041299PMC
November 2010

Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease.

Bioinformatics 2010 Aug 15;26(16):1975-82. Epub 2010 Jun 15.

School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916715PMC
August 2010

Bioinformatic tools for identifying disease gene and SNP candidates.

Methods Mol Biol 2010 ;628:307-19

Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA.

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http://dx.doi.org/10.1007/978-1-60327-367-1_17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957484PMC
May 2010

Automated inference of molecular mechanisms of disease from amino acid substitutions.

Bioinformatics 2009 Nov 3;25(21):2744-50. Epub 2009 Sep 3.

School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140805PMC
November 2009

Connecting protein interaction data, mutations, and disease using bioinformatics.

Methods Mol Biol 2009 ;541:449-61

Informatics and Technology Complex (IT), Indiana University School of Informatics, IUPUI, Indianapolis, IN, USA.

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http://link.springer.com/10.1007/978-1-59745-243-4_19
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http://dx.doi.org/10.1007/978-1-59745-243-4_19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2793329PMC
June 2009

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.

Genome Res 2009 Mar 30;19(3):381-94. Epub 2008 Dec 30.

Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.082503.108
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http://dx.doi.org/10.1101/gr.082503.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661799PMC
March 2009

Gain and loss of phosphorylation sites in human cancer.

Bioinformatics 2008 Aug;24(16):i241-7

School of Informatics, Indiana University, 901 East Tenth Street, Bloomington, IN 47408, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732209PMC
August 2008

Using RNase sequence specificity to refine the identification of RNA-protein binding regions.

BMC Genomics 2008 ;9 Suppl 1:S17

Division of Biostatistics Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.1186/1471-2164-9-S1-S17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386059PMC
June 2008

MutDB: update on development of tools for the biochemical analysis of genetic variation.

Nucleic Acids Res 2008 Jan 7;36(Database issue):D815-9. Epub 2007 Sep 7.

Center for Computational Biology and Bioinfomatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W. 10th Street, Suite 5000, Indianapolis, IN 46202, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkm659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238958PMC
January 2008

Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group.

Brief Bioinform 2008 Jan 5;9(1):69-74. Epub 2007 Dec 5.

Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th St, Suite 5000, Indianapolis, IN 46202, USA.

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http://bib.oxfordjournals.org/content/9/1/69.full.pdf
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http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbm057
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http://dx.doi.org/10.1093/bib/bbm057DOI Listing
January 2008

Evaluation of features for catalytic residue prediction in novel folds.

Protein Sci 2007 Feb 22;16(2):216-26. Epub 2006 Dec 22.

Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.1110/ps.062523907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203287PMC
February 2007

Structural characterization of proteins using residue environments.

Proteins 2005 Dec;61(4):741-7

Department of Genetics, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1002/prot.20661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483305PMC
December 2005

Fibroblast growth factor-23 mutants causing familial tumoral calcinosis are differentially processed.

Endocrinology 2005 Sep 16;146(9):3883-91. Epub 2005 Jun 16.

Department of Medical and Molecular Genetics, 975 West Walnut Street, IB130, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.

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http://dx.doi.org/10.1210/en.2005-0431DOI Listing
September 2005

A novel recessive mutation in fibroblast growth factor-23 causes familial tumoral calcinosis.

J Clin Endocrinol Metab 2005 Apr 1;90(4):2424-7. Epub 2005 Feb 1.

Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.

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http://dx.doi.org/10.1210/jc.2004-2238DOI Listing
April 2005

Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure.

Pac Symp Biocomput 2005 :319-21

Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA.

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April 2005

MutDB: annotating human variation with functionally relevant data.

Bioinformatics 2003 Sep;19(14):1858-60

Department of Genetics, Stanford Medical Informatics, Stanford University, 251 Campus Drive, MSOB X-215 Stanford, CA 94305-5479, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg241DOI Listing
September 2003

Nitric-oxide synthase (NOS) reductase domain models suggest a new control element in endothelial NOS that attenuates calmodulin-dependent activity.

J Biol Chem 2003 Aug 12;278(34):31814-24. Epub 2003 Jun 12.

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-2280, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M303267200
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http://dx.doi.org/10.1074/jbc.M303267200DOI Listing
August 2003

A functional analysis of disease-associated mutations in the androgen receptor gene.

Nucleic Acids Res 2003 Apr;31(8):e42

Stanford Medical Informatics, Department of Genetics, Stanford University, MSOB X-215, 251 Campus Drive, Stanford, CA 94305-5479, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC153754PMC
http://dx.doi.org/10.1093/nar/gng042DOI Listing
April 2003

Structural models of osteogenesis imperfecta-associated variants in the COL1A1 gene.

Mol Cell Proteomics 2002 Nov;1(11):868-75

Department of Genetics, School of Medicine, Stanford University, Stanford, California 94305-5479, USA.

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http://dx.doi.org/10.1074/mcp.m200064-mcp200DOI Listing
November 2002

The functional importance of disease-associated mutation.

BMC Bioinformatics 2002 Sep 9;3:24. Epub 2002 Sep 9.

Department of Genetics and Stanford Medical Informatics Division, Stanford University, Stanford, California, 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC128831PMC
http://dx.doi.org/10.1186/1471-2105-3-24DOI Listing
September 2002

Conformational preferences of substituted prolines in the collagen triple helix.

Biopolymers 2002 Jul;64(2):63-71

Stanford Medical Informatics, 251 Campus Drive, MSOB X-215, Stanford University, Stanford, CA 94305-5479, USA.

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http://dx.doi.org/10.1002/bip.10123DOI Listing
July 2002