Publications by authors named "Vineet Bafna"

100Publications

Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification.

Mol Ecol 2020 07 29;29(14):2521-2534. Epub 2020 Jun 29.

Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1111/mec.15507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7496323PMC
July 2020

The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters.

Mol Ecol Resour 2020 May 4;20(3). Epub 2020 Feb 4.

Department of Electrical and Computer Engineering, UC San Diego, CA, USA.

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http://dx.doi.org/10.1111/1755-0998.13135DOI Listing
May 2020

EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA.

iScience 2019 Nov 21;21:428-435. Epub 2019 Oct 21.

Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA; Moores Cancer Center, UC San Diego, La Jolla, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2019.10.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6849072PMC
November 2019

Computing the Statistical Significance of Overlap between Genome Annotations with iStat.

Cell Syst 2019 06 12;8(6):523-529.e4. Epub 2019 Jun 12.

Department of Computer Science & Engineering, University of California, San Diego, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200088PMC
June 2019

Extrachromosomal oncogene amplification in tumour pathogenesis and evolution.

Nat Rev Cancer 2019 05;19(5):283-288

Ludwig Institute for Cancer Research, San Diego, La Jolla, CA, USA.

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http://www.nature.com/articles/s41568-019-0128-6
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http://dx.doi.org/10.1038/s41568-019-0128-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168519PMC
May 2019

Skmer: assembly-free and alignment-free sample identification using genome skims.

Genome Biol 2019 02 13;20(1):34. Epub 2019 Feb 13.

Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, 92093, CA, USA.

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http://dx.doi.org/10.1186/s13059-019-1632-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6374904PMC
February 2019

Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.

Nat Commun 2019 01 23;10(1):392. Epub 2019 Jan 23.

Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.

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http://www.nature.com/articles/s41467-018-08200-y
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http://dx.doi.org/10.1038/s41467-018-08200-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344493PMC
January 2019

Targeted genotyping of variable number tandem repeats with adVNTR.

Genome Res 2018 11 23;28(11):1709-1719. Epub 2018 Oct 23.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.235119.118
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http://dx.doi.org/10.1101/gr.235119.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211647PMC
November 2018

ProteoStorm: An Ultrafast Metaproteomics Database Search Framework.

Cell Syst 2018 10 26;7(4):463-467.e6. Epub 2018 Sep 26.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.08.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231400PMC
October 2018

Identifying the favored mutation in a positive selective sweep.

Nat Methods 2018 04 19;15(4):279-282. Epub 2018 Feb 19.

Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, USA.

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http://www.nature.com/doifinder/10.1038/nmeth.4606
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http://dx.doi.org/10.1038/nmeth.4606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231406PMC
April 2018

Ultraaccurate genome sequencing and haplotyping of single human cells.

Proc Natl Acad Sci U S A 2017 11 24;114(47):12512-12517. Epub 2017 Oct 24.

Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1707609114
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http://dx.doi.org/10.1073/pnas.1707609114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703283PMC
November 2017

The Antibody Repertoire of Colorectal Cancer.

Mol Cell Proteomics 2017 Dec 18;16(12):2111-2124. Epub 2017 Oct 18.

¶Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92037

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http://www.mcponline.org/lookup/doi/10.1074/mcp.RA117.000397
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http://dx.doi.org/10.1074/mcp.RA117.000397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724175PMC
December 2017

High-altitude adaptation in humans: from genomics to integrative physiology.

J Mol Med (Berl) 2017 Dec 26;95(12):1269-1282. Epub 2017 Sep 26.

Division of Respiratory Medicine, Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0735, La Jolla, CA, 92093, USA.

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http://link.springer.com/10.1007/s00109-017-1584-7
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http://dx.doi.org/10.1007/s00109-017-1584-7DOI Listing
December 2017

Clear: Composition of Likelihoods for Evolve and Resequence Experiments.

Genetics 2017 06 10;206(2):1011-1023. Epub 2017 Apr 10.

Department of Computer Science and Engineering, University of California, San Diego, California 92093.

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http://www.genetics.org/lookup/doi/10.1534/genetics.116.1975
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http://dx.doi.org/10.1534/genetics.116.197566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499160PMC
June 2017

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.

Genome Res 2017 05 9;27(5):801-812. Epub 2016 Dec 9.

Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92053, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.213462.116
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http://dx.doi.org/10.1101/gr.213462.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411775PMC
May 2017

Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease.

J Exp Med 2016 11 7;213(12):2729-2744. Epub 2016 Nov 7.

Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093

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http://dx.doi.org/10.1084/jem.20151920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5110013PMC
November 2016

InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms.

Nucleic Acids Res 2016 07 21;44(12):e111. Epub 2016 Apr 21.

Bioinformatics and Systems Biology Program, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093, USA Department of Computer Science and Engineering, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/nar/gkw281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937317PMC
July 2016

Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele.

PLoS Genet 2015 Sep 24;11(9):e1005527. Epub 2015 Sep 24.

Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, United States of America.

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https://rosenberglab.stanford.edu/papers/RonenEtAl2015-PlosG
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http://dx.plos.org/10.1371/journal.pgen.1005527
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http://dx.doi.org/10.1371/journal.pgen.1005527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581834PMC
September 2015

Endothelin receptor B, a candidate gene from human studies at high altitude, improves cardiac tolerance to hypoxia in genetically engineered heterozygote mice.

Proc Natl Acad Sci U S A 2015 Aug 3;112(33):10425-30. Epub 2015 Aug 3.

Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA 92093; Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093; Rady Children's Hospital, San Diego, CA 92123

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http://www.pnas.org/lookup/doi/10.1073/pnas.1507486112
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http://dx.doi.org/10.1073/pnas.1507486112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547246PMC
August 2015

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer.

J Proteome Res 2015 Sep 21;14(9):3555-67. Epub 2015 Jul 21.

Department of Biomedical Informatics, Vanderbilt University , Nashville, Tennessee 37203, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868822PMC
September 2015

Reconstructing breakage fusion bridge architectures using noisy copy numbers.

J Comput Biol 2015 Jun;22(6):577-94

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California.

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http://dx.doi.org/10.1089/cmb.2014.0166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449712PMC
June 2015

The genetic basis of chronic mountain sickness.

Physiology (Bethesda) 2014 Nov;29(6):403-12

Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, California; Department of Neurosciences, University of California San Diego, La Jolla, California; and Rady Children's Hospital, San Diego, California.

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http://dx.doi.org/10.1152/physiol.00008.2014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280153PMC
November 2014

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data.

Proteomics 2014 Dec 17;14(23-24):2719-30. Epub 2014 Nov 17.

Department of Electrical and Computer Engineering, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1002/pmic.201400206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256132PMC
December 2014

Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.

Mol Cell Proteomics 2014 Nov 24;13(11):3184-98. Epub 2014 Jul 24.

From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205

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http://dx.doi.org/10.1074/mcp.M114.038299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223501PMC
November 2014

The elusive evidence for chromothripsis.

Nucleic Acids Res 2014 Jul 17;42(13):8231-42. Epub 2014 Jun 17.

Department of Computer Science and Engineering, University of California, San Diego, CA, 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/gku525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117757PMC
July 2014

Inferring gene ontologies from pairwise similarity data.

Bioinformatics 2014 Jun;30(12):i34-42

Department of Medicine and Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, 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/btu282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058954PMC
June 2014

Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations.

Genome Res 2014 Feb 4;24(2):318-28. Epub 2013 Dec 4.

Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California 92093, USA;

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http://dx.doi.org/10.1101/gr.161497.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912422PMC
February 2014

An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays.

Mol Cell Proteomics 2014 Jan 18;13(1):157-67. Epub 2013 Oct 18.

Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92092;

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http://dx.doi.org/10.1074/mcp.M113.031260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879611PMC
January 2014

Proteogenomic database construction driven from large scale RNA-seq data.

J Proteome Res 2014 Jan 17;13(1):21-8. Epub 2013 Jul 17.

Department of Electrical and Computing Engineering, ¶Department of Bioinformatics and Systems Biology, and §Department of Computer Science, University of California, San Diego , La Jolla, California 92093, United States.

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http://dx.doi.org/10.1021/pr400294cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034692PMC
January 2014

Learning natural selection from the site frequency spectrum.

Genetics 2013 Sep 14;195(1):181-93. Epub 2013 Jun 14.

Bioinformatics and Systems Biology Program, University of California, San Diego, California 92093.

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http://dx.doi.org/10.1534/genetics.113.152587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3761300PMC
September 2013

Evaluating genome architecture of a complex region via generalized bipartite matching.

BMC Bioinformatics 2013 10;14 Suppl 5:S13. Epub 2013 Apr 10.

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

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http://dx.doi.org/10.1186/1471-2105-14-S5-S13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622632PMC
December 2013

Using Genome Query Language to uncover genetic variation.

Bioinformatics 2014 Jan 10;30(1):1-8. Epub 2013 Jun 10.

Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, San Diego, CA 92123 and Microsoft Research, 1065 La Avenida, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866549PMC
January 2014

Reprever: resolving low-copy duplicated sequences using template driven assembly.

Nucleic Acids Res 2013 Jul 8;41(12):e128. Epub 2013 May 8.

Department of Computer Science and Engineering, 9500 Gilman Dr University of California at San Diego, La Jolla, CA 92122, USA.

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http://dx.doi.org/10.1093/nar/gkt339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695505PMC
July 2013

An algorithmic approach for breakage-fusion-bridge detection in tumor genomes.

Proc Natl Acad Sci U S A 2013 Apr 15;110(14):5546-51. Epub 2013 Mar 15.

University of California at San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1073/pnas.1220977110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619374PMC
April 2013

Wessim: a whole-exome sequencing simulator based on in silico exome capture.

Bioinformatics 2013 Apr 14;29(8):1076-7. Epub 2013 Feb 14.

Department of Computer Science and Engineering and Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624799PMC
April 2013

Abstractions for Genomics.

Commun ACM 2013 Jan;56(1):83-93

Computer Science and Engineering, UC San Diego.

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http://dx.doi.org/10.1145/2398356.2398376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183138PMC
January 2013

Speeding up tandem mass spectral identification using indexes.

Bioinformatics 2012 Jul 27;28(13):1692-7. Epub 2012 Apr 27.

Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3381964PMC
July 2012

Combinatorics of the breakage-fusion-bridge mechanism.

J Comput Biol 2012 Jun 16;19(6):662-78. Epub 2012 Apr 16.

Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1089/cmb.2012.0020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375649PMC
June 2012

Accurate mass spectrometry based protein quantification via shared peptides.

J Comput Biol 2012 Apr 13;19(4):337-48. Epub 2012 Mar 13.

Department of Computer Science and Engineering, UC San Diego, San Diego, California, USA.

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http://dx.doi.org/10.1089/cmb.2009.0267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317402PMC
April 2012

Sample reproducibility of genetic association using different multimarker TDTs in genome-wide association studies: characterization and a new approach.

PLoS One 2012 17;7(2):e29613. Epub 2012 Feb 17.

Departamento de Lenguajes y Sistemas Informáticos, ETS Ingeniera Informática y de Telecomunicaciones-CITIC, Universidad de Granada, Granada, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029613PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281822PMC
June 2012

Tests of selection in pooled case-control data: an empirical study.

Front Genet 2011 28;2:83. Epub 2011 Nov 28.

Bioinformatics and Systems Biology Graduate Program, University of California San Diego La Jolla, CA, USA.

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http://dx.doi.org/10.3389/fgene.2011.00083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268381PMC
October 2012

Protein identification using top-down.

Mol Cell Proteomics 2012 Jun 25;11(6):M111.008524. Epub 2011 Oct 25.

Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, San Diego, California 92093, USA.

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http://dx.doi.org/10.1074/mcp.M111.008524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433905PMC
June 2012

AMASS: algorithm for MSI analysis by semi-supervised segmentation.

J Proteome Res 2011 Oct 25;10(10):4734-43. Epub 2011 Aug 25.

University of California, San Diego, La Jolla, California, United States.

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http://dx.doi.org/10.1021/pr2005378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190602PMC
October 2011

Compressing genomic sequence fragments using SlimGene.

J Comput Biol 2011 Mar;18(3):401-13

Department of Computer Science and Engineering, University of California, San Diego, California, USA.

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http://dx.doi.org/10.1089/cmb.2010.0253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123913PMC
March 2011

Strobe sequence design for haplotype assembly.

BMC Bioinformatics 2011 Feb 15;12 Suppl 1:S24. Epub 2011 Feb 15.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1186/1471-2105-12-S1-S24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044279PMC
February 2011

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.

Bioinformatics 2011 Apr 16;27(8):1068-75. Epub 2011 Feb 16.

Bioinformatics and Systems Biology Program, Moores UCSD Cancer Center, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072550PMC
April 2011

Experimental selection of hypoxia-tolerant Drosophila melanogaster.

Proc Natl Acad Sci U S A 2011 Feb 24;108(6):2349-54. Epub 2011 Jan 24.

Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1073/pnas.1010643108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038716PMC
February 2011

Practical 4'-phosphopantetheine active site discovery from proteomic samples.

J Proteome Res 2011 Jan 13;10(1):320-9. Epub 2010 Dec 13.

Department of Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla California 92093, USA.

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http://dx.doi.org/10.1021/pr100953bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042426PMC
January 2011

A covering method for detecting genetic associations between rare variants and common phenotypes.

PLoS Comput Biol 2010 Oct 14;6(10):e1000954. Epub 2010 Oct 14.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2954823PMC
October 2010

RAPID detection of gene-gene interactions in genome-wide association studies.

Bioinformatics 2010 Nov 24;26(22):2856-62. Epub 2010 Sep 24.

Life Technologies, Foster City, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493125PMC
November 2010

Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach.

Mol Cell Proteomics 2010 Dec 20;9(12):2772-82. Epub 2010 Sep 20.

Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M110.002766
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http://dx.doi.org/10.1074/mcp.M110.002766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101958PMC
December 2010

Proteogenomics to discover the full coding content of genomes: a computational perspective.

J Proteomics 2010 Oct 8;73(11):2124-35. Epub 2010 Jul 8.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093-0404, USA.

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http://dx.doi.org/10.1016/j.jprot.2010.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949459PMC
October 2010

Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance.

BMC Genomics 2010 Jun 18;11:385. Epub 2010 Jun 18.

Dept, of Computer Science and Engineering, UC San Diego, La Jolla, CA, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-11-385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091630PMC
June 2010

Protein-protein interaction network evaluation for identifying potential drug targets.

J Comput Biol 2010 May;17(5):669-84

School of Computing Science, Simon Fraser University, Burnaby, Canada.

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http://dx.doi.org/10.1089/cmb.2009.0032DOI Listing
May 2010

TCLUST: a fast method for clustering genome-scale expression data.

IEEE/ACM Trans Comput Biol Bioinform 2011 May-Jun;8(3):808-18

Department of Computer Science and Engineering, University of California, San Diego, CA 92093, USA.

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http://dx.doi.org/10.1109/TCBB.2010.34DOI Listing
August 2011

Optimizing PCR assays for DNA-based cancer diagnostics.

J Comput Biol 2010 Mar;17(3):369-81

Department of Computer Science, University of California, San Diego, La Jolla, California 92129, USA.

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http://dx.doi.org/10.1089/cmb.2009.0203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213025PMC
March 2010

Template proteogenomics: sequencing whole proteins using an imperfect database.

Mol Cell Proteomics 2010 Jun 17;9(6):1260-70. Epub 2010 Feb 17.

Department of Computer Science, University of California, San Diego, San Diego, California 92093, USA.

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http://dx.doi.org/10.1074/mcp.M900504-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877985PMC
June 2010

Expansion of the mycobacterial "PUPylome".

Mol Biosyst 2010 Feb 16;6(2):376-85. Epub 2009 Nov 16.

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Ave., BSB 4090 MC 0636, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1039/b916104jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846642PMC
February 2010

Fast and accurate alignment of multiple protein networks.

J Comput Biol 2009 Aug;16(8):989-99

1 School of Computer Science, Tel Aviv University , Tel Aviv, Israel.

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http://dx.doi.org/10.1089/cmb.2009.0136DOI Listing
August 2009

Discovery and revision of Arabidopsis genes by proteogenomics.

Proc Natl Acad Sci U S A 2008 Dec 19;105(52):21034-8. Epub 2008 Dec 19.

Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1073/pnas.0811066106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605632PMC
December 2008

QNet: a tool for querying protein interaction networks.

J Comput Biol 2008 Sep;15(7):913-25

Computer Science and Engineering, University of California, San Diego, California, USA.

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http://dx.doi.org/10.1089/cmb.2007.0172DOI Listing
September 2008

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem.

Bioinformatics 2008 Aug;24(16):i153-9

Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0404, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn298DOI Listing
August 2008

An MCMC algorithm for haplotype assembly from whole-genome sequence data.

Genome Res 2008 Aug;18(8):1336-46

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1101/gr.077065.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493424PMC
August 2008

Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis.

J Proteome Res 2008 Aug 19;7(8):3373-81. Epub 2008 Jun 19.

Bioinformatics Program, University of California San Diego, Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1021/pr800129mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566938PMC
August 2008

Structural alignment of pseudoknotted RNA.

J Comput Biol 2008 Jun;15(5):489-504

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1089/cmb.2007.0214DOI Listing
June 2008

A multidimensional chromatography technology for in-depth phosphoproteome analysis.

Mol Cell Proteomics 2008 Jul 11;7(7):1389-96. Epub 2008 Apr 11.

Ludwig Institute for Cancer Research, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1074/mcp.M700468-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493382PMC
July 2008

Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer.

PLoS Comput Biol 2008 Apr 25;4(4):e1000051. Epub 2008 Apr 25.

Bioinformatics Graduate Program, University of California San Diego, San Diego, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278375PMC
April 2008

A decomposition theory for phylogenetic networks and incompatible characters.

J Comput Biol 2007 Dec;14(10):1247-72

Department of Computer Science, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1089/cmb.2006.0137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581772PMC
December 2007