Predrag Radivojac

Predrag Radivojac

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Predrag Radivojac

Publications by authors named "Predrag Radivojac"

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Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies.

Pac Symp Biocomput 2019 ;24:124-135

Northeastern University, Boston, Massachusetts, U.S.A.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417800PMC
August 2019

ISMB/ECCB 2019 Proceedings.

Bioinformatics 2019 Jul;35(14):i1-i2

Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612803PMC
July 2019

Identification of N-terminal protein processing sites by chemical labeling mass spectrometry.

Rapid Commun Mass Spectrom 2019 Jun;33(11):1015-1023

Department of Chemistry, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1002/rcm.8435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522274PMC
June 2019

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

PLoS Comput Biol 2019 Jun 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

Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse.

IEEE/ACM Trans Comput Biol Bioinform 2018 Jul-Aug;15(4):1284-1289. Epub 2015 Sep 18.

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http://dx.doi.org/10.1109/TCBB.2015.2480068DOI Listing
May 2019

The sequencing and interpretation of the genome obtained from a Serbian individual.

PLoS One 2018 19;13(12):e0208901. Epub 2018 Dec 19.

College of Computer and Information Science, Northeastern University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208901PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300249PMC
May 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

Precision Medicine: Improving health through high-resolution analysis of personal data.

Pac Symp Biocomput 2019 ;24:220-223

University of California, Berkeley, USA†Supported by U41 HG007346 and U19 HD077627.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526370PMC
January 2019

Target site specificity and in vivo complexity of the mammalian arginylome.

Sci Rep 2018 11 1;8(1):16177. Epub 2018 Nov 1.

Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1038/s41598-018-34639-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212499PMC
November 2018

Reproductive Longevity Predicts Mutation Rates in Primates.

Curr Biol 2018 10 27;28(19):3193-3197.e5. Epub 2018 Sep 27.

Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09609822183113
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http://dx.doi.org/10.1016/j.cub.2018.08.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177314PMC
October 2018

Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies.

Bioinformatics 2018 07;34(13):i313-i322

Department of Computer Science, Indiana University, Bloomington, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022688PMC
July 2018

ISMB 2018 proceedings.

Bioinformatics 2018 07;34(13):i2-i3

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

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http://dx.doi.org/10.1093/bioinformatics/bty413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022687PMC
July 2018

Community-Wide Evaluation of Computational Function Prediction.

Methods Mol Biol 2017 ;1446:133-146

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

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http://dx.doi.org/10.1007/978-1-4939-3743-1_10DOI Listing
December 2017

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

Physicochemical sequence characteristics that influence S-palmitoylation propensity.

J Biomol Struct Dyn 2017 Aug 7;35(11):2337-2350. Epub 2016 Aug 7.

a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA.

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http://dx.doi.org/10.1080/07391102.2016.1217275DOI Listing
August 2017

COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION.

Pac Symp Biocomput 2017 ;22:1-2

Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA.

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http://dx.doi.org/10.1142/9789813207813_0001DOI Listing
July 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

Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics.

J Proteome Res 2016 10 27;15(10):3656-3665. Epub 2016 Sep 27.

Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767123PMC
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

Protein function in precision medicine: deep understanding with machine learning.

FEBS Lett 2016 08 6;590(15):2327-41. Epub 2016 Aug 6.

Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.

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http://dx.doi.org/10.1002/1873-3468.12307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937700PMC
August 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

XLSearch: a Probabilistic Database Search Algorithm for Identifying Cross-Linked Peptides.

J Proteome Res 2016 06 6;15(6):1830-41. Epub 2016 May 6.

Department of Computer Science and Informatics and ‡Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770149PMC
June 2016

Training the next generation of quantitative biologists in the era of big data.

Pac Symp Biocomput 2015 :488-92

Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA.

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April 2016

Position of Proline Mediates the Reactivity of S-Palmitoylation.

ACS Chem Biol 2015 Nov 19;10(11):2529-36. Epub 2015 Aug 19.

Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University , Bloomington, Indiana 47405, United States.

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http://dx.doi.org/10.1021/acschembio.5b00429DOI Listing
November 2015

Penultimate proline in neuropeptides.

Anal Chem 2015 Aug 29;87(16):8466-72. Epub 2015 Jul 29.

†Department of Chemistry, ‡Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States.

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http://dx.doi.org/10.1021/acs.analchem.5b01889DOI Listing
August 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

On the split personality of penultimate proline.

J Am Soc Mass Spectrom 2015 Mar 12;26(3):444-52. Epub 2014 Dec 12.

Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.

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http://dx.doi.org/10.1007/s13361-014-1049-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336576PMC
March 2015

Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential.

Sci Rep 2014 Nov 21;4:7155. Epub 2014 Nov 21.

Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232-0700, USA.

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http://dx.doi.org/10.1038/srep07155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239565PMC
November 2014

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective.

Bioinformatics 2014 Sep;30(17):i609-16

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA, Department of Microbiology and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147924PMC
September 2014

Vector quantization kernels for the classification of protein sequences and structures.

Pac Symp Biocomput 2014 :316-27

Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, U.S.A.

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August 2014

The structural and functional signatures of proteins that undergo multiple events of post-translational modification.

Protein Sci 2014 Aug 11;23(8):1077-93. Epub 2014 Jun 11.

Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, 47405.

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http://doi.wiley.com/10.1002/pro.2494
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http://dx.doi.org/10.1002/pro.2494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116656PMC
August 2014

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

ISCB computational biology Wikipedia competition.

PLoS Comput Biol 2013 19;9(9):e1003242. Epub 2013 Sep 19.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777890PMC
April 2014

Bioinformatics curriculum guidelines: toward a definition of core competencies.

PLoS Comput Biol 2014 Mar 6;10(3):e1003496. Epub 2014 Mar 6.

The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945096PMC
March 2014

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

Information-theoretic evaluation of predicted ontological annotations.

Bioinformatics 2013 Jul;29(13):i53-61

Department of Computer Science and Informatics, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694662PMC
July 2013

Computational approaches to protein inference in shotgun proteomics.

BMC Bioinformatics 2012 5;13 Suppl 16:S4. Epub 2012 Nov 5.

School of Informatics and Computing, Indiana University, Bloomington 150 S, Woodlawn Avenue, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1186/1471-2105-13-S16-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489551PMC
May 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

An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors.

PLoS Comput Biol 2012 26;8(7):e1002603. Epub 2012 Jul 26.

Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.

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http://dx.doi.org/10.1371/journal.pcbi.1002603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3405991PMC
January 2013

Post-translational modifications induce significant yet not extreme changes to protein structure.

Bioinformatics 2012 Nov 4;28(22):2905-13. Epub 2012 Sep 4.

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

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http://dx.doi.org/10.1093/bioinformatics/bts541DOI Listing
November 2012

Allosteric post-translational modification codes.

Trends Biochem Sci 2012 Oct 8;37(10):447-55. Epub 2012 Aug 8.

Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory, NCI, Frederick, MD 21702, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S09680004120010
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http://dx.doi.org/10.1016/j.tibs.2012.07.001DOI Listing
October 2012

Protein identification problem from a Bayesian point of view.

Stat Interface 2012 Jan;5(1):21-37

School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.4310/SII.2012.v5.n1.a3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992622PMC
January 2012

Investigation of VUV Photodissociation Propensities Using Peptide Libraries.

Int J Mass Spectrom 2011 Dec;308(2-3):142-154

Department of Chemistry, Indiana University, Bloomington, Indiana 47405, and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47408.

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http://dx.doi.org/10.1016/j.ijms.2011.04.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224043PMC
December 2011

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

Computational methods for identification of functional residues in protein structures.

Curr Protein Pept Sci 2011 Sep;12(6):456-69

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

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http://dx.doi.org/10.2174/138920311796957685DOI Listing
September 2011

Analysis of protein function and its prediction from amino acid sequence.

Proteins 2011 Jul 19;79(7):2086-96. Epub 2011 Apr 19.

School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA.

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http://www.cs.indiana.edu/~predrag/papers/clark_proteins_201
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http://doi.wiley.com/10.1002/prot.23029
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http://dx.doi.org/10.1002/prot.23029DOI Listing
July 2011

Testing the ortholog conjecture with comparative functional genomic data from mammals.

PLoS Comput Biol 2011 Jun 9;7(6):e1002073. Epub 2011 Jun 9.

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

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http://dx.doi.org/10.1371/journal.pcbi.1002073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111532PMC
June 2011

Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity.

Am J Hum Genet 2011 Apr 31;88(4):433-9. Epub 2011 Mar 31.

Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.

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http://dx.doi.org/10.1016/j.ajhg.2011.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071914PMC
April 2011

On the accuracy and limits of peptide fragmentation spectrum prediction.

Anal Chem 2011 Feb 22;83(3):790-6. Epub 2010 Dec 22.

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

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http://dx.doi.org/10.1021/ac102272rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3036742PMC
February 2011

The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics.

J Proteome Res 2010 Dec 10;9(12):6288-97. Epub 2010 Nov 10.

Department of Chemistry, School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States.

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http://dx.doi.org/10.1021/pr1005586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006185PMC
December 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

Graphlet kernels for prediction of functional residues in protein structures.

J Comput Biol 2010 Jan;17(1):55-72

Department of Computer Science and Engineering, University of California, Riverside, California, USA.

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http://dx.doi.org/10.1089/cmb.2009.0029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921594PMC
January 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

Influence of sequence changes and environment on intrinsically disordered proteins.

PLoS Comput Biol 2009 Sep 4;5(9):e1000497. Epub 2009 Sep 4.

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

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http://dx.doi.org/10.1371/journal.pcbi.1000497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727479PMC
September 2009

Analysis of AML genes in dysregulated molecular networks.

BMC Bioinformatics 2009 Sep 17;10 Suppl 9:S2. Epub 2009 Sep 17.

Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, South Korea.

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http://dx.doi.org/10.1186/1471-2105-10-S9-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745689PMC
September 2009

A bayesian approach to protein inference problem in shotgun proteomics.

J Comput Biol 2009 Aug;16(8):1183-93

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

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http://dx.doi.org/10.1089/cmb.2009.0018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799497PMC
August 2009

Analysis of AML Genes in Dysregulated Molecular Networks.

Summit Transl Bioinform 2009 Mar 1;2009:1-18. Epub 2009 Mar 1.

Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, South Korea.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041561PMC
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

From protein-disease associations to disease informatics.

Front Biosci 2008 May 1;13:3391-407. Epub 2008 May 1.

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

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http://dx.doi.org/10.2741/2934DOI Listing
May 2008

Prediction of intrinsic disorder and its use in functional proteomics.

Methods Mol Biol 2007 ;408:69-92

School of Medicine, Indiana University, Indianapolis, USA.

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http://dx.doi.org/10.1007/978-1-59745-547-3_5DOI Listing
April 2008

Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes.

Mol Biosyst 2008 Apr 21;4(4):328-40. Epub 2008 Feb 21.

School of Informatics, Indiana University, Bloomington, IN 47401, USA.

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http://dx.doi.org/10.1039/b719168eDOI Listing
April 2008

HIP2: an online database of human plasma proteins from healthy individuals.

BMC Med Genomics 2008 Apr 25;1:12. Epub 2008 Apr 25.

School of Informatics, Indiana University - Purdue University, Indianapolis, USA.

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http://dx.doi.org/10.1186/1755-8794-1-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396660PMC
April 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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http://dx.doi.org/10.1093/nar/gkm659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238958PMC
January 2008

Advancement in protein inference from shotgun proteomics using peptide detectability.

Pac Symp Biocomput 2007 :409-20

School of Informatics, Indiana University, Bloomington, USA.

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December 2007

Characterization of molecular recognition features, MoRFs, and their binding partners.

J Proteome Res 2007 Jun 9;6(6):2351-66. Epub 2007 May 9.

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

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http://dx.doi.org/10.1021/pr0701411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570643PMC
June 2007

Intrinsic disorder and functional proteomics.

Biophys J 2007 Mar 8;92(5):1439-56. Epub 2006 Dec 8.

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

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http://dx.doi.org/10.1529/biophysj.106.094045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1796814PMC
March 2007

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

A machine learning approach to predicting peptide fragmentation spectra.

Pac Symp Biocomput 2006 :219-30

Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.

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January 2007

Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map.

Comput Biol Chem 2006 Aug 22;30(4):241-8. Epub 2006 Jun 22.

Indiana University School of Informatics, 1900 East Tenth Street, Bloomington, IN 47406, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2006.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1992444PMC
August 2006

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments.

Bioinformatics 2006 Jun 21;22(12):1536-7. Epub 2006 Apr 21.

Computer Science and Engineering Department, University of California Riverside, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl151DOI Listing
June 2006

Length-dependent prediction of protein intrinsic disorder.

BMC Bioinformatics 2006 Apr 17;7:208. Epub 2006 Apr 17.

Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA.

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http://dx.doi.org/10.1186/1471-2105-7-208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479845PMC
April 2006