Zhaolei Zhang

Zhaolei Zhang

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Zhaolei Zhang

Publications by authors named "Zhaolei Zhang"

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Rad5 Recruits Error-Prone DNA Polymerases for Mutagenic Repair of ssDNA Gaps on Undamaged Templates.

Mol Cell 2019 03 4;73(5):900-914.e9. Epub 2019 Feb 4.

Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.01.001DOI Listing
March 2019

Integrating exosomal microRNAs and electronic health data improved tuberculosis diagnosis.

EBioMedicine 2019 Feb 8;40:564-573. Epub 2019 Feb 8.

Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S23523964193002
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http://dx.doi.org/10.1016/j.ebiom.2019.01.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413343PMC
February 2019

Publisher Correction: N-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

Nat Neurosci 2018 Aug;21(8):1139

Tumor Initiation and Maintenance Program, NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41593-018-0169-2DOI Listing
August 2018

N-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

Nat Neurosci 2018 02 15;21(2):195-206. Epub 2018 Jan 15.

Tumor Initiation and Maintenance Program, NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41593-017-0057-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317335PMC
February 2018

Cholinergic neuron gene expression differences captured by translational profiling in a mouse model of Alzheimer's disease.

Neurobiol Aging 2017 09 25;57:104-119. Epub 2017 May 25.

Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.neurobiolaging.2017.05.014DOI Listing
September 2017

Exome sequencing reveals DNMT3A and ASXL1 variants associate with progression of chronic myeloid leukemia after tyrosine kinase inhibitor therapy.

Leuk Res 2017 08 16;59:142-148. Epub 2017 Jun 16.

Department of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1016/j.leukres.2017.06.009DOI Listing
August 2017

Spectrum of somatic mutation dynamics in chronic myeloid leukemia following tyrosine kinase inhibitor therapy.

Blood 2017 01 12;129(1):38-47. Epub 2016 Oct 12.

Department of Medical Oncology, Princess Margaret Cancer Center, University Health Network, Faculty of Medicine and.

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http://dx.doi.org/10.1182/blood-2016-04-708560DOI Listing
January 2017

Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity.

G3 (Bethesda) 2017 01 5;7(1):95-108. Epub 2017 Jan 5.

Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada

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http://dx.doi.org/10.1534/g3.116.035675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217127PMC
January 2017

Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes.

Genome Biol Evol 2016 12 31;8(11):3433-3445. Epub 2016 Dec 31.

The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China

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http://dx.doi.org/10.1093/gbe/evw239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203780PMC
December 2016

G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis.

Stem Cell Reports 2016 09 18;7(3):454-470. Epub 2016 Aug 18.

Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2016.06.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031922PMC
September 2016

MTE1 Functions with MPH1 in Double-Strand Break Repair.

Genetics 2016 05 26;203(1):147-57. Epub 2016 Feb 26.

Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 3E1, Canada Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada

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http://www.genetics.org/lookup/doi/10.1534/genetics.115.1854
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http://dx.doi.org/10.1534/genetics.115.185454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858770PMC
May 2016

Computational Biology in microRNA.

Wiley Interdiscip Rev RNA 2015 Jul-Aug;6(4):435-52. Epub 2015 Apr 24.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1002/wrna.1286DOI Listing
March 2016

Computational learning on specificity-determining residue-nucleotide interactions.

Nucleic Acids Res 2015 Dec 2;43(21):10180-9. Epub 2015 Nov 2.

Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

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http://dx.doi.org/10.1093/nar/gkv1134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666365PMC
December 2015

Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase.

Genetics 2015 Nov 11;201(3):937-49. Epub 2015 Sep 11.

Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853

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http://dx.doi.org/10.1534/genetics.115.181479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649662PMC
November 2015

Mitophagy induced by nanoparticle-peptide conjugates enabling an alternative intracellular trafficking route.

Biomaterials 2015 Oct 19;65:56-65. Epub 2015 Jun 19.

Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, 199 RenAi Road, Suzhou Industrial Park, Suzhou City, Jiangsu Province 215123, China. Electronic address:

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http://dx.doi.org/10.1016/j.biomaterials.2015.06.029DOI Listing
October 2015

Genome-wide detection of high abundance N6-methyladenosine sites by microarray.

RNA 2015 Aug 19;21(8):1511-8. Epub 2015 Jun 19.

Tumor Initiation and Maintenance Program, Sanford Burnham Medical Research Institute, San Diego, California 92037, USA.

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http://dx.doi.org/10.1261/rna.051474.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509940PMC
August 2015

Assembly of Slx4 signaling complexes behind DNA replication forks.

EMBO J 2015 Aug 25;34(16):2182-97. Epub 2015 Jun 25.

Department of Biochemistry, University of Toronto, Toronto, ON, Canada Donnelly Centre, University of Toronto, Toronto, ON, Canada

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http://dx.doi.org/10.15252/embj.201591190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557669PMC
August 2015

A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human.

Bioinformatics 2015 Jul 18;31(14):2348-55. Epub 2015 Mar 18.

Department of Computer Science, Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btv159DOI Listing
July 2015

Bichir microRNA repertoire suggests a ray-finned fish affinity of Polypteriforme.

Gene 2015 Jul 24;566(2):242-7. Epub 2015 Apr 24.

The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2015.04.058DOI Listing
July 2015

SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles.

Bioinformatics 2015 Jan 5;31(1):17-24. Epub 2014 Sep 5.

Department of Computer Science and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, CEMSE Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, K.S.A., Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Department of Computer Science and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, CEMSE Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, K.S.A., Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Department of Computer Science and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, CEMSE Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, K.S.A., Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Department of Computer Science and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, CEMSE Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, K.S.A., Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu604DOI Listing
January 2015

Mitochondrial targets for pharmacological intervention in human disease.

J Proteome Res 2015 Jan 12;14(1):5-21. Epub 2014 Dec 12.

Department of Biochemistry, Research and Innovation Centre, University of Regina , Regina, Saskatchewan S4S 0A2, Canada.

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http://dx.doi.org/10.1021/pr500813fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286170PMC
January 2015

Investigating the functional implications of reinforcing feedback loops in transcriptional regulatory networks.

Mol Biosyst 2014 Dec;10(12):3238-48

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

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http://dx.doi.org/10.1039/c4mb00526kDOI Listing
December 2014

Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus.

Genome Biol Evol 2014 Dec 26;7(1):251-61. Epub 2014 Dec 26.

The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China

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http://dx.doi.org/10.1093/gbe/evu279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316632PMC
December 2014

Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis.

Sci Rep 2014 Nov 18;4:7097. Epub 2014 Nov 18.

1] Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada [2] The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada [4] Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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http://dx.doi.org/10.1038/srep07097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235308PMC
November 2014

New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM.

Genome Biol Evol 2014 Oct 15;6(10):2897-917. Epub 2014 Oct 15.

Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Biochemistry, University of Toronto, Ontario, Canada

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http://dx.doi.org/10.1093/gbe/evu228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224354PMC
October 2014

Regression analysis of combined gene expression regulation in acute myeloid leukemia.

PLoS Comput Biol 2014 Oct 23;10(10):e1003908. Epub 2014 Oct 23.

Department of Computer Science, University of Toronto, Toronto, Canada; The Donnelly Centre, University of Toronto, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada; Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1003908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207489PMC
October 2014

Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion.

Bioinformatics 2014 Sep 3;30(18):2627-35. Epub 2014 Jun 3.

Department of Computer Science, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada, College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China and Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada Department of Computer Science, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada, College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China and Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada Department of Computer Science, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada, College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China and Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu373DOI Listing
September 2014

Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach.

Nucleic Acids Res 2014 May 7;42(9):e76. Epub 2014 Mar 7.

Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A4, Canada Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada

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http://dx.doi.org/10.1093/nar/gku182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027195PMC
May 2014

Identifying mRNA sequence elements for target recognition by human Argonaute proteins.

Genome Res 2014 May 24;24(5):775-85. Epub 2014 Mar 24.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada;

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http://dx.doi.org/10.1101/gr.162230.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009607PMC
May 2014

SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences.

Bioinformatics 2014 04 2;30(8):1112-1119. Epub 2014 Jan 2.

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.

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http://dx.doi.org/10.1093/bioinformatics/btt769DOI Listing
April 2014

A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information.

Bioinformatics 2014 Mar 17;30(5):621-8. Epub 2013 Oct 17.

Department of Computer Science, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, 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/btt599DOI Listing
March 2014

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells.

Nat Cell Biol 2014 Feb 7;16(2):191-8. Epub 2014 Jan 7.

Tumor Initiation and Maintenance Program, NCI-designated Cancer Center, Sanford Burnham Medical Research Institute, La Jolla, California 92037, USA.

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http://www.nature.com/articles/ncb2902
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http://dx.doi.org/10.1038/ncb2902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640932PMC
February 2014

DNA motif elucidation using belief propagation.

Nucleic Acids Res 2013 Sep 29;41(16):e153. Epub 2013 Jun 29.

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, KSA, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/nar/gkt574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763557PMC
September 2013

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.

Nucleic Acids Res 2013 Apr 28;41(8):e94. Epub 2013 Feb 28.

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

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http://dx.doi.org/10.1093/nar/gkt142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632129PMC
April 2013

miRNA regulatory variation in human evolution.

Trends Genet 2013 Feb 2;29(2):116-24. Epub 2012 Nov 2.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.tig.2012.10.008DOI Listing
February 2013

Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution.

PLoS Genet 2012 22;8(3):e1002578. Epub 2012 Mar 22.

Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1371/journal.pgen.1002578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310733PMC
September 2012

Characterization and evolutionary analysis of protein-protein interaction networks.

Methods Mol Biol 2012 ;856:363-80

Cardiovascular Division, Brigham & Women's Hospital, Boston, MA, USA.

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http://dx.doi.org/10.1007/978-1-61779-585-5_15DOI Listing
July 2012

Bioinformatic approach to identify chaperone pathway relationship from large-scale interaction networks.

Methods Mol Biol 2011 ;787:189-203

Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1007/978-1-61779-295-3_15DOI Listing
February 2012

Filtering and interpreting large-scale experimental protein-protein interaction data.

Methods Mol Biol 2011 ;781:295-309

Cardiovascular Division, Brigham & Women's Hospital, Boston, MA, USA.

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http://dx.doi.org/10.1007/978-1-61779-276-2_14DOI Listing
January 2012

PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae.

Nucleic Acids Res 2012 Jan 18;40(Database issue):D687-94. Epub 2011 Oct 18.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1093/nar/gkr827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245137PMC
January 2012

Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans-regulation effects.

Nucleic Acids Res 2011 Feb 8;39(3):837-47. Epub 2010 Oct 8.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada.

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http://dx.doi.org/10.1093/nar/gkq874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035465PMC
February 2011

Gene expression variations are predictive for stochastic noise.

Nucleic Acids Res 2011 Jan 21;39(2):403-13. Epub 2010 Sep 21.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/nar/gkq844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025572PMC
January 2011

DAnCER: disease-annotated chromatin epigenetics resource.

Nucleic Acids Res 2011 Jan 28;39(Database issue):D889-94. Epub 2010 Sep 28.

Hospital for Sick Children, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/nar/gkq857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013761PMC
January 2011

Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective.

Bioinformatics 2011 Jan 11;27(2):147-52. Epub 2010 Nov 11.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btq637DOI Listing
January 2011

The cellular robustness by genetic redundancy in budding yeast.

PLoS Genet 2010 Nov 4;6(11):e1001187. Epub 2010 Nov 4.

Department of Molecular Genetics, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1371/journal.pgen.1001187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2973813PMC
November 2010

Gene expression variability within and between human populations and implications toward disease susceptibility.

PLoS Comput Biol 2010 Aug 26;6(8). Epub 2010 Aug 26.

Department of Molecular Genetics, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1000910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928754PMC
August 2010

The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses.

Proteins 2010 Jul;78(9):2075-89

Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1002/prot.22723DOI Listing
July 2010

Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise.

Proc Natl Acad Sci U S A 2010 Jun 20;107(23):10472-7. Epub 2010 May 20.

Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1073/pnas.0914302107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890810PMC
June 2010

PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation.

Mol Cell Proteomics 2010 Apr 8;9(4):623-34. Epub 2009 Dec 8.

Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M900273-MCP2
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http://dx.doi.org/10.1074/mcp.M900273-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860229PMC
April 2010

Evolution of an X-linked primate-specific micro RNA cluster.

Mol Biol Evol 2010 Mar 19;27(3):671-83. Epub 2009 Nov 19.

Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/molbev/msp284DOI Listing
March 2010

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.

Nucleic Acids Res 2010 Jan 25;38(Database issue):D155-60. Epub 2009 Sep 25.

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.

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http://dx.doi.org/10.1093/nar/gkp784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808993PMC
January 2010

The sequence and de novo assembly of the giant panda genome.

Nature 2010 Jan 13;463(7279):311-7. Epub 2009 Dec 13.

BGI-Shenzhen, Shenzhen 518083, China.

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http://dx.doi.org/10.1038/nature08696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951497PMC
January 2010

A probabilistic framework to improve microrna target prediction by incorporating proteomics data.

J Bioinform Comput Biol 2009 Dec;7(6):955-72

Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada.

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December 2009

An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.

Mol Syst Biol 2009 16;5:275. Epub 2009 Jun 16.

Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/msb.2009.26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2710862PMC
September 2009

Evolution of olfactory receptor genes in primates dominated by birth-and-death process.

Genome Biol Evol 2009 Aug 4;1:258-64. Epub 2009 Aug 4.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/gbe/evp026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817421PMC
August 2009

Small RNAs originated from pseudogenes: cis- or trans-acting?

PLoS Comput Biol 2009 Jul 31;5(7):e1000449. Epub 2009 Jul 31.

Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Albert Einstein College of Medicine, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708354PMC
July 2009

Learned random-walk kernels and empirical-map kernels for protein sequence classification.

J Comput Biol 2009 Mar;16(3):457-74

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

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http://dx.doi.org/10.1089/cmb.2008.0031DOI Listing
March 2009

Global robustness and identifiability of random, scale-free, and small-world networks.

Ann N Y Acad Sci 2009 Mar;1158:82-92

Centre for the Analysis of Genome Evolution & Function, Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada.

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http://doi.wiley.com/10.1111/j.1749-6632.2008.03752.x
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March 2009

Preferential regulation of duplicated genes by microRNAs in mammals.

Genome Biol 2008 26;9(8):R132. Epub 2008 Aug 26.

Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.

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http://dx.doi.org/10.1186/gb-2008-9-8-r132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575522PMC
December 2008

The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast.

Genome Res 2008 Jul 7;18(7):1092-9. Epub 2008 May 7.

Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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http://www.genome.org/cgi/doi/10.1101/gr.076174.108
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http://dx.doi.org/10.1101/gr.076174.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493398PMC
July 2008

MAID : an effect size based model for microarray data integration across laboratories and platforms.

BMC Bioinformatics 2008 Jul 10;9:305. Epub 2008 Jul 10.

Banting and Best Department of Medical Research, University of Toronto, 112 College St, Toronto, ON M5G1L6, Canada.

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http://dx.doi.org/10.1186/1471-2105-9-305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483727PMC
July 2008

A hybrid model for robust detection of transcription factor binding sites.

Bioinformatics 2008 Feb 9;24(4):484-91. Epub 2008 Jan 9.

Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto ON, Canada M5S 3E1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btm629DOI Listing
February 2008

The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment.

BMC Evol Biol 2008 Jan 24;8:23. Epub 2008 Jan 24.

Banting & Best Department of Medical Research (BBDMR), Donnelly Centre for Cellular & Biomolecular Research (CCBR), University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada. wagied.davids@utoronto

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http://dx.doi.org/10.1186/1471-2148-8-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2259305PMC
January 2008

CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks.

Ann N Y Acad Sci 2007 Dec 9;1115:249-66. Epub 2007 Oct 9.

Banting & Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1196/annals.1407.010DOI Listing
December 2007

Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments.

Ann N Y Acad Sci 2007 Dec 9;1115:267-85. Epub 2007 Oct 9.

Banting & Best Department of Medical Research, Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Ontario M5S 3E1, Canada.

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http://doi.wiley.com/10.1196/annals.1407.011
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December 2007

Experimental and computational procedures for the assessment of protein complexes on a genome-wide scale.

Chem Rev 2007 Aug 14;107(8):3585-600. Epub 2007 Jul 14.

Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1.

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http://dx.doi.org/10.1021/cr0682857DOI Listing
August 2007

Retention of protein complex membership by ancient duplicated gene products in budding yeast.

Trends Genet 2007 Jun 10;23(6):266-9. Epub 2007 Apr 10.

Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada.

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http://www.cell.com/cms/attachment/584209/4419725/mmc1.pdf
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http://dx.doi.org/10.1016/j.tig.2007.03.012DOI Listing
June 2007

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

BMC Evol Biol 2007 Feb 8;7 Suppl 1:S14. Epub 2007 Feb 8.

Banting & Best Department of Medical Research, Donnelly CCBR, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1186/1471-2148-7-S1-S14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1796608PMC
February 2007

Accounting for structural properties and nucleotide co-variations in the quantitative prediction of binding affinities of protein-DNA interactions.

Pac Symp Biocomput 2006 :379-90

Charles H. Best Institute, University of Toronto, 112 College Street, Toronto, Ontario, M5G 1L6, Canada.

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January 2007

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.

Nucleic Acids Res 2007 Jan 11;35(Database issue):D55-60. Epub 2006 Nov 11.

Center for Comparative Genomics and Bioinformatics, 506B Wartik, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1093/nar/gkl851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669708PMC
January 2007

PseudoPipe: an automated pseudogene identification pipeline.

Bioinformatics 2006 Jun 30;22(12):1437-9. Epub 2006 Mar 30.

Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto 160 College Street, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btl116DOI Listing
June 2006

Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations.

J Comput Biol 2006 May;13(4):929-45

Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto, Ontario, Canada.

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http://dx.doi.org/10.1089/cmb.2006.13.929DOI Listing
May 2006

Alternative signaling pathways: when, where and why?

FEBS Lett 2005 Oct;579(24):5265-74

Banting and Best Department of Medical Research, University of Toronto 112 College, Canada.

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http://dx.doi.org/10.1016/j.febslet.2005.08.062DOI Listing
October 2005

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.

Nucleic Acids Res 2005 28;33(8):2374-83. Epub 2005 Apr 28.

Department of Biology, McGill University Stewart Biology Building, 1205 Dr. Penfield Avenue, Montreal, Quebec, Canada H3A 1B1.

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http://dx.doi.org/10.1093/nar/gki531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087782PMC
May 2005

Integrated pseudogene annotation for human chromosome 22: evidence for transcription.

J Mol Biol 2005 May 2;349(1):27-45. Epub 2005 Apr 2.

Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1016/j.jmb.2005.02.072DOI Listing
May 2005

Large-scale analysis of pseudogenes in the human genome.

Curr Opin Genet Dev 2004 Aug;14(4):328-35

Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520-8114, USA.

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http://dx.doi.org/10.1016/j.gde.2004.06.003DOI Listing
August 2004

Comparative analysis of processed pseudogenes in the mouse and human genomes.

Trends Genet 2004 Feb;20(2):62-7

Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S01689525030034
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http://dx.doi.org/10.1016/j.tig.2003.12.005DOI Listing
February 2004

Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.

Genome Res 2003 Dec;13(12):2541-58

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.

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http://dx.doi.org/10.1101/gr.1429003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403796PMC
December 2003

Reconstructing genetic networks in yeast.

Nat Biotechnol 2003 Nov;21(11):1295-7

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http://dx.doi.org/10.1038/nbt1103-1295DOI Listing
November 2003

Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes.

Nucleic Acids Res 2003 Sep;31(18):5338-48

Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC203328PMC
http://dx.doi.org/10.1093/nar/gkg745DOI Listing
September 2003