Michael Brudno

Michael Brudno

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Michael Brudno

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Identifying Clinical Terms in Medical Text Using Ontology-Guided Machine Learning.

JMIR Med Inform 2019 May 10;7(2):e12596. Epub 2019 May 10.

Department of Computer Science, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.2196/12596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533869PMC
May 2019

Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease.

Am J Hum Genet 2019 Mar 28;104(3):466-483. Epub 2019 Feb 28.

Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297193001
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http://dx.doi.org/10.1016/j.ajhg.2019.01.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407525PMC
March 2019

Impact of assisted reproduction, infertility, sex and paternal factors on the placental DNA methylome.

Hum Mol Genet 2019 02;28(3):372-385

MUHC Reproductive Centre, Department of Obstetrics and Gynecology, Royal Victoria Hospital and Research Institute of McGill University Health Centre, Quebec, Canada.

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http://fdslive.oup.com/www.oup.com/pdf/production_in_progres
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http://dx.doi.org/10.1093/hmg/ddy321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337702PMC
February 2019

Don't brush off buccal data heterogeneity.

Epigenetics 2019 Feb 1;14(2):109-117. Epub 2019 Mar 1.

a Program in Genetics and Genome Biology , The Hospital for Sick Children , Toronto , Ontario , Canada.

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http://dx.doi.org/10.1080/15592294.2019.1581592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557604PMC
February 2019

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Nucleic Acids Res 2019 Jan;47(D1):D1018-D1027

Monarch Initiative, monarchinitiative.org.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky1105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074PMC
January 2019

Harmonising phenomics information for a better interoperability in the rare disease field.

Eur J Med Genet 2018 Nov 7;61(11):706-714. Epub 2018 Feb 7.

INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.ejmg.2018.01.013DOI Listing
November 2018

Tamoxifen therapy in a murine model of myotubular myopathy.

Nat Commun 2018 11 19;9(1):4849. Epub 2018 Nov 19.

Program for Genetics and Genome Biology, Hospital for Sick Children, 686 Bay Street, Toronto, ON, CAN M5G 0A4, Canada.

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http://www.nature.com/articles/s41467-018-07057-5
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http://dx.doi.org/10.1038/s41467-018-07057-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242823PMC
November 2018

Doccurate: A Curation-Based Approach for Clinical Text Visualization.

IEEE Trans Vis Comput Graph 2018 Aug 20. Epub 2018 Aug 20.

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http://dx.doi.org/10.1109/TVCG.2018.2864905DOI Listing
August 2018

CHARGE and Kabuki Syndromes: Gene-Specific DNA Methylation Signatures Identify Epigenetic Mechanisms Linking These Clinically Overlapping Conditions.

Am J Hum Genet 2017 May;100(5):773-788

Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A1, Canada; Department of Pediatrics, University of Toronto, Toronto, Ontario, M5S 1A1, Canada; Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420353PMC
May 2017

PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations.

IEEE Trans Vis Comput Graph 2017 01 5;23(1):191-200. Epub 2016 Aug 5.

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http://dx.doi.org/10.1109/TVCG.2016.2598469DOI Listing
January 2017

Identification of complex genomic rearrangements in cancers using CouGaR.

Genome Res 2017 01 14;27(1):107-117. Epub 2016 Nov 14.

Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 3G4, Canada.

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http://dx.doi.org/10.1101/gr.211201.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5204335PMC
January 2017

Genome-wide placental DNA methylation analysis of severely growth-discordant monochorionic twins reveals novel epigenetic targets for intrauterine growth restriction.

Clin Epigenetics 2016 21;8:70. Epub 2016 Jun 21.

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario Canada ; Department of Paediatrics, University of Toronto, Toronto, Ontario Canada ; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario Canada ; Institute of Medical Science, University of Toronto, Toronto, Ontario Canada.

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http://dx.doi.org/10.1186/s13148-016-0238-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915063PMC
December 2016

An MRspec database query and visualization engine with applications as a clinical diagnostic and research tool.

Mol Genet Metab 2016 12 9;119(4):300-306. Epub 2016 Nov 9.

Department of Paediatrics, University of Toronto, Toronto, Canada; Genetics and Genome Biology, Peter Gilgan Center for Research and Learning, The Hospital for Sick Children, Toronto, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ymgme.2016.11.003DOI Listing
December 2016

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors.

Authors:
Jonathon Torchia Brian Golbourn Shengrui Feng King Ching Ho Patrick Sin-Chan Alexandre Vasiljevic Joseph D Norman Paul Guilhamon Livia Garzia Natalia R Agamez Mei Lu Tiffany S Chan Daniel Picard Pasqualino de Antonellis Dong-Anh Khuong-Quang Aline C Planello Constanze Zeller Dalia Barsyte-Lovejoy Lucie Lafay-Cousin Louis Letourneau Mathieu Bourgey Man Yu Deena M A Gendoo Misko Dzamba Mark Barszczyk Tiago Medina Alexandra N Riemenschneider A Sorana Morrissy Young-Shin Ra Vijay Ramaswamy Marc Remke Christopher P Dunham Stephen Yip Ho-Keung Ng Jian-Qiang Lu Vivek Mehta Steffen Albrecht Jose Pimentel Jennifer A Chan Gino R Somers Claudia C Faria Lucia Roque Maryam Fouladi Lindsey M Hoffman Andrew S Moore Yin Wang Seung Ah Choi Jordan R Hansford Daniel Catchpoole Diane K Birks Nicholas K Foreman Doug Strother Almos Klekner Laszló Bognár Miklós Garami Péter Hauser Tibor Hortobágyi Beverly Wilson Juliette Hukin Anne-Sophie Carret Timothy E Van Meter Eugene I Hwang Amar Gajjar Shih-Hwa Chiou Hideo Nakamura Helen Toledano Iris Fried Daniel Fults Takafumi Wataya Chris Fryer David D Eisenstat Katrin Scheinemann Adam J Fleming Donna L Johnston Jean Michaud Shayna Zelcer Robert Hammond Samina Afzal David A Ramsay Nongnuch Sirachainan Suradej Hongeng Noppadol Larbcharoensub Richard G Grundy Rishi R Lulla Jason R Fangusaro Harriet Druker Ute Bartels Ronald Grant David Malkin C Jane McGlade Theodore Nicolaides Tarik Tihan Joanna Phillips Jacek Majewski Alexandre Montpetit Guillaume Bourque Gary D Bader Alyssa T Reddy G Yancey Gillespie Monika Warmuth-Metz Stefan Rutkowski Uri Tabori Mathieu Lupien Michael Brudno Ulrich Schüller Torsten Pietsch Alexander R Judkins Cynthia E Hawkins Eric Bouffet Seung-Ki Kim Peter B Dirks Michael D Taylor Anat Erdreich-Epstein Cheryl H Arrowsmith Daniel D De Carvalho James T Rutka Nada Jabado Annie Huang

Cancer Cell 2016 Dec;30(6):891-908

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500911PMC
December 2016

deBGA: read alignment with de Bruijn graph-based seed and extension.

Bioinformatics 2016 11 4;32(21):3224-3232. Epub 2016 Jul 4.

Center for Bioinformatics, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.

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http://dx.doi.org/10.1093/bioinformatics/btw371DOI Listing
November 2016

Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data.

PLoS One 2015 5;10(10):e0139656. Epub 2015 Oct 5.

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; Hospital of Sick Children, Toronto, Ontario, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139656PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593641PMC
June 2016

Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction.

Bioinformatics 2016 06 5;32(11):1662-9. Epub 2016 Apr 5.

Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada and Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btw178DOI Listing
June 2016

The genomic birthday paradox: how much is enough?

Hum Mutat 2015 Oct 20;36(10):989-97. Epub 2015 Aug 20.

Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany.

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http://dx.doi.org/10.1002/humu.22848DOI Listing
October 2015

The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection.

Nucleic Acids Res 2015 Sep 30;43(15):7217-28. Epub 2015 Jun 30.

Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada Department of Computer Science, University of Toronto, Toronto, ON, M5S 3G4, Canada

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http://dx.doi.org/10.1093/nar/gkv677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551921PMC
September 2015

Phenotyping: targeting genotype's rich cousin for diagnosis.

J Paediatr Child Health 2015 Apr 11;51(4):381-6. Epub 2014 Aug 11.

Genetic Services of Western Australia, Princess Margaret Hospital for Children, Perth, Western Australia, Australia; School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia; Office of Population Health Genomics, Department of Health, Government of Western Australia, Perth, Western Australia, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia.

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http://dx.doi.org/10.1111/jpc.12705DOI Listing
April 2015

Alignathon: a competitive assessment of whole-genome alignment methods.

Genome Res 2014 Dec 1;24(12):2077-89. Epub 2014 Oct 1.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA;

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http://dx.doi.org/10.1101/gr.174920.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248324PMC
December 2014

Assembly and characterization of novel inserts detected from next-generation sequencing data.

Mob Genet Elements 2014 Oct 12;4(5):1-7. Epub 2014 Dec 12.

Department of Computer Science; University of Toronto ; Toronto, Canada ; Centre for Computational Medicine; Hospital for Sick Children ; Toronto, Canada.

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http://dx.doi.org/10.4161/21592543.2014.969584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589995PMC
October 2014

GenomeVISTA--an integrated software package for whole-genome alignment and visualization.

Bioinformatics 2014 Sep 23;30(18):2654-5. Epub 2014 May 23.

US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155257PMC
September 2014

Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing.

Bioinformatics 2014 Jun;30(12):i212-8

Department of Computer Science, University of Toronto, Toronto M5S 2E4, Centre for Computational Medicine and Genetics and Genome Biology, Hospital for Sick Children, Toronto M5G 1L7, CanadaDepartment of Computer Science, University of Toronto, Toronto M5S 2E4, Centre for Computational Medicine and Genetics and Genome Biology, Hospital for Sick Children, Toronto M5G 1L7, CanadaDepartment of Computer Science, University of Toronto, Toronto M5S 2E4, Centre for Computational Medicine and Genetics and Genome Biology, Hospital for Sick Children, Toronto M5G 1L7, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058944PMC
June 2014

Similarity network fusion for aggregating data types on a genomic scale.

Nat Methods 2014 Mar 26;11(3):333-7. Epub 2014 Jan 26.

1] Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada. [2] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.2810DOI Listing
March 2014

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D966-74. Epub 2013 Nov 11.

Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke's Hospital, Cambridge CB2 2QQ, UK, Université Paul Sabatier, Faculté de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine. Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada, Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds LS2 9NS, UK, MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, The Jackson Laboratory, Bar Harbor, ME 04609, USA, Center for Molecular and Vascular Biology, University of Leuven, Belgium, Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel Campus, 24105 Kiel, Germany, NE Thames Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK, Drexel University College of Medicine, Philadelphia, PA 19102, USA, Department of Haematology, University of Cambridge and NHS Blood and Transplant Cambridge, CB2 0PT Cambridge, UK, Autism and Developmental Medicine Institute, Geisinger Health System

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http://dx.doi.org/10.1093/nar/gkt1026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965098PMC
January 2014

Mixture model for sub-phenotyping in GWAS.

Pac Symp Biocomput 2012 :363-74

Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.

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December 2013

Detecting Alu insertions from high-throughput sequencing data.

Nucleic Acids Res 2013 Sep 5;41(17):e169. Epub 2013 Aug 5.

Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada and Centre for Computational Medicine, Genetics and Genome Biology Program, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada.

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http://nar.oxfordjournals.org/content/early/2013/08/05/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt612
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http://dx.doi.org/10.1093/nar/gkt612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783187PMC
September 2013

PhenoTips: patient phenotyping software for clinical and research use.

Hum Mutat 2013 Aug 24;34(8):1057-65. Epub 2013 May 24.

Department of Computer Science, University of Toronto, Ontario, Canada.

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http://dx.doi.org/10.1002/humu.22347DOI Listing
August 2013

Identification of deleterious synonymous variants in human genomes.

Bioinformatics 2013 Aug 4;29(15):1843-50. Epub 2013 Jun 4.

Department of Computer Science, University of Toronto, Toronto, ON M5S 3H5, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btt308DOI Listing
August 2013

iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data.

Genome Res 2013 Mar 29;23(3):519-29. Epub 2012 Nov 29.

Department of Computer Science, University of Toronto, Ontario M5S 2E4, Canada.

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http://dx.doi.org/10.1101/gr.142232.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589540PMC
March 2013

SCARPA: scaffolding reads with practical algorithms.

Bioinformatics 2013 Feb 29;29(4):428-34. Epub 2012 Dec 29.

Department of Computer Science, University of Toronto, Toronto, ON, Canada M5S 3E1.

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http://dx.doi.org/10.1093/bioinformatics/bts716DOI Listing
February 2013

PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants.

Bioinformatics 2012 Oct 31;28(20):2576-83. Epub 2012 Jul 31.

Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.

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http://dx.doi.org/10.1093/bioinformatics/bts484DOI Listing
October 2012

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

Nucleic Acids Res 2012 Jul 25;40(Web Server issue):W615-21. Epub 2012 May 25.

Department of Computer Science, University of Toronto, Ontario, Canada M5S 2E4.

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http://dx.doi.org/10.1093/nar/gks427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394255PMC
July 2012

Genomic sequencing and characterization of cynomolgus macaque cytomegalovirus.

J Virol 2011 Dec 12;85(24):12995-3009. Epub 2011 Oct 12.

Department of Microbiology, Mount Sinai Hospital, Room 1484, 600 University Avenue, Toronto, ON, Canada.

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http://dx.doi.org/10.1128/JVI.05840-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233177PMC
December 2011

SHRiMP2: sensitive yet practical SHort Read Mapping.

Bioinformatics 2011 Apr 28;27(7):1011-2. Epub 2011 Jan 28.

Department of Computer Science, Princeton University, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr046DOI Listing
April 2011

Detecting copy number variation with mated short reads.

Genome Res 2010 Nov 30;20(11):1613-22. Epub 2010 Aug 30.

Department of Computer Science, University of Toronto, Toronto, Ontario M5R 3G4, Canada.

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http://dx.doi.org/10.1101/gr.106344.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2963824PMC
November 2010

Savant: genome browser for high-throughput sequencing data.

Bioinformatics 2010 Aug 20;26(16):1938-44. Epub 2010 Jun 20.

Department of Computer Science, University of Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btq332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271355PMC
August 2010

VARiD: a variation detection framework for color-space and letter-space platforms.

Bioinformatics 2010 Jun;26(12):i343-9

Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881369PMC
June 2010

Genome variation discovery with high-throughput sequencing data.

Brief Bioinform 2010 Jan 6;11(1):3-14. Epub 2010 Jan 6.

Computer Science, MIT, USA.

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http://dx.doi.org/10.1093/bib/bbp058DOI Listing
January 2010

A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG).

Bioinformatics 2009 Nov 24;25(21):2863-4. Epub 2009 Sep 24.

Department of Computer Science, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btp525DOI Listing
November 2009

Computational methods for discovering structural variation with next-generation sequencing.

Nat Methods 2009 Nov;6(11 Suppl):S13-20

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://www.nature.com/articles/nmeth.1374
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http://dx.doi.org/10.1038/nmeth.1374DOI Listing
November 2009

Conservation of core gene expression in vertebrate tissues.

J Biol 2009 16;8(3):33. Epub 2009 Apr 16.

Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1186/jbiol130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689434PMC
October 2009

Maximum likelihood genome assembly.

J Comput Biol 2009 Aug;16(8):1101-16

Department of Computer Science, University of Toronto , Toronto, Canada.

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http://dx.doi.org/10.1089/cmb.2009.0047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154397PMC
August 2009

SHRiMP: accurate mapping of short color-space reads.

PLoS Comput Biol 2009 May 22;5(5):e1000386. Epub 2009 May 22.

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1000386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678294PMC
May 2009

Multiple whole-genome alignments without a reference organism.

Genome Res 2009 Apr 28;19(4):682-9. Epub 2009 Jan 28.

Genome Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.081778.108
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http://dx.doi.org/10.1101/gr.081778.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665786PMC
April 2009

Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi.

Genetics 2009 Feb 15;181(2):685-90. Epub 2008 Dec 15.

Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109-2216.

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http://dx.doi.org/10.1534/genetics.108.097535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644956PMC
February 2009

A robust framework for detecting structural variations in a genome.

Bioinformatics 2008 Jul;24(13):i59-67

Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btn176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718654PMC
July 2008

An introduction to the Lagan alignment toolkit.

Authors:
Michael Brudno

Methods Mol Biol 2007 ;395:205-20

Department of Computer Science, University of Toronto.

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http://dx.doi.org/10.1007/978-1-59745-514-5_13DOI Listing
March 2008

Extensive parallelism in protein evolution.

Biol Direct 2007 Aug 16;2:20. Epub 2007 Aug 16.

Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA.

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http://dx.doi.org/10.1186/1745-6150-2-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2020468PMC
August 2007

Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

Nucleic Acids Res 2007 Jul 8;35(Web Server issue):W669-74. Epub 2007 May 8.

Department of Computer Science, Banting and Best Department of Medical Research, University of Toronto, 6 King's College Road, Toronto, ON, Canada M5S 3G4.

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http://dx.doi.org/10.1093/nar/gkm279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933192PMC
July 2007

A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome.

Genome Biol 2007 ;8(3):R41

Department of Pathology, Stanford University Medical Center, Stanford, California 94305-5324, USA.

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http://dx.doi.org/10.1186/gb-2007-8-3-r41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868934PMC
June 2007

Extreme genomic variation in a natural population.

Proc Natl Acad Sci U S A 2007 Mar 19;104(13):5698-703. Epub 2007 Mar 19.

Departments of Genetics and Pathology, Stanford University Medical Center, Stanford, CA 94305-5324, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0700890104
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http://dx.doi.org/10.1073/pnas.0700890104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838466PMC
March 2007

Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter.

J Bioinform Comput Biol 2006 Oct;4(5):981-98

Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.

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http://dx.doi.org/10.1142/s0219720006002284DOI Listing
October 2006

Fast and sensitive alignment of large genomic sequences.

Proc IEEE Comput Soc Bioinform Conf 2002 ;1:138-47

Computer Science Department, Stanford University, Stanford, CA 94305, USA.

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May 2005

ProbCons: Probabilistic consistency-based multiple sequence alignment.

Genome Res 2005 Feb;15(2):330-40

Department of Computer Science, Stanford University, Stanford, California 94305, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.2821705
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http://dx.doi.org/10.1101/gr.2821705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546535PMC
February 2005

Glocal alignment: finding rearrangements during alignment.

Bioinformatics 2003 ;19 Suppl 1:i54-62

Department of Computer Science, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1005DOI Listing
October 2004

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W41-4

Department of Computer Science, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/nar/gkh361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441499PMC
July 2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004

Characterization of evolutionary rates and constraints in three Mammalian genomes.

Genome Res 2004 Apr;14(4):539-48

Department of Genetics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.2034704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383297PMC
April 2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

Bioinformatics 2004 Mar 22;20(5):636-43. Epub 2004 Jan 22.

Center for Image Processing and Integrated Computing, Department of Computer Science, One Shields Avenue, University of California, Davis, CA 95616-8562, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg459DOI Listing
March 2004

Fast and sensitive multiple alignment of large genomic sequences.

BMC Bioinformatics 2003 Dec 23;4:66. Epub 2003 Dec 23.

Department of Computer Science, Stanford University, Stanford, CA 94305, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-4-66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC521198PMC
December 2003

AGenDA: homology-based gene prediction.

Bioinformatics 2003 Aug;19(12):1575-7

International Graduate School for Bioinformatics and Genome Research University of Bielefeld, Postfach 10 01 31, 33501 Bielefeld, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btg181DOI Listing
August 2003

Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.

Genome Res 2003 May;13(5):813-20

Department of Genetics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.1064503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430923PMC
May 2003

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

Genome Res 2003 Apr 12;13(4):721-31. Epub 2003 Mar 12.

Department of Computer Science, Stanford University, Stanford, California 94305-9010, USA.

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http://dx.doi.org/10.1101/gr.926603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430158PMC
April 2003