Genomes and Genes
Affiliation: McGill University
- Predicting site-specific human selective pressure using evolutionary signaturesJavad Sadri
School of Computer Science, McGill University, 3630 University, Montreal, QC, Canada H3A 2B2
Bioinformatics 27:i266-74. 2011..With the quickly increasing number of vertebrate genomes to compare with our own, this type of approach is set to become extremely powerful, provided the right analytical tools are available...
- Computational prediction of the localization of microRNAs within their pre-miRNAMickael Leclercq
School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada H3A2B2 and Laboratoire de bioinformatique du département informatique, Universite du Quebec a Montreal, Montreal, Quebec, Canada H2X3Y7
Nucleic Acids Res 41:7200-11. 2013..MiRdup is open source under the GPLv3 and available at http://www.cs.mcgill.ca/∼blanchem/mirdup/. ..
- Computational analysis of whole-genome differential allelic expression data in humanJames R Wagner
School of Computer Science, McGill University, Montreal, Quebec, Canada
PLoS Comput Biol 6:e1000849. 2010....
- FootPrinter3: phylogenetic footprinting in partially alignable sequencesFei Fang
McGill Centre for Bioinformatics, 3775 University St, Montreal, Quebec, Canada, H3A 2B4
Nucleic Acids Res 34:W617-20. 2006..g. chicken, zebrafish), as well as those of more closely related species (e.g. mammals). The FootPrinter3 web server is available at: http://www.mcb.mcgill.ca/~blanchem/FootPrinter3...
- Phylo: a citizen science approach for improving multiple sequence alignmentAlexander Kawrykow
School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
PLoS ONE 7:e31362. 2012..There, instances of hard computational problems are dispatched to a crowd of non-expert human game players and solutions are sent back to a central server...
- PReMod: a database of genome-wide mammalian cis-regulatory module predictionsVincent Ferretti
McGill University and Genome Quebec Innovation Center, 740 Dr Penfield, Montreal, QC, Canada H3A 1A4
Nucleic Acids Res 35:D122-6. 2007..It also provides a visual depiction of the chromosomal context of the selected pCRMs in terms of neighboring pCRMs and genes, all of which are linked to the UCSC Genome Browser and the NCBI. PReMod: http://genomequebec.mcgill.ca/PReMod...
- Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fishEmmanuel Mongin
McGill Centre for Bioinformatics, McGill University, Montreal, Canada
PLoS ONE 6:e19747. 2011..This pipeline represents a significant step towards the dissection of embryonic neuronal development in vertebrates...
- A flexible ancestral genome reconstruction method based on gapped adjacenciesYves Gagnon
Departement d informatique, DIRO, Universite de Montreal, Canada
BMC Bioinformatics 13:S4. 2012..The predicted CARs are likely to be more reliable as they are more directly deduced from observed conservations in extant species. However the challenge is to end up with a completely assembled genome...
- PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequencesSaurabh Sinha
Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021, USA
BMC Bioinformatics 5:170. 2004..This paper addresses the problem of discovering transcription factor binding sites in heterogeneous sequence data, which includes regulatory sequences of one or more genes, as well as their orthologs in other species...
- Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expressionMathieu Blanchette
McGill Centre for Bioinformatics, Montreal, Quebec, Canada, H3A 2B4
Genome Res 16:656-68. 2006..The set of predicted CRMs, which is made available as a public database called PReMod (http://genomequebec.mcgill.ca/PReMod), will help analyze regulatory mechanisms in specific biological systems...
- Reconstructing large regions of an ancestral mammalian genome in silicoMathieu Blanchette
Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
Genome Res 14:2412-23. 2004..In coming years, such reconstructions may help in identifying and understanding the genetic features common to eutherian mammals and may shed light on the evolution of human or primate-specific traits...
- Computation and analysis of genomic multi-sequence alignmentsMathieu Blanchette
McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada Email
Annu Rev Genomics Hum Genet 8:193-213. 2007..Finally, we describe the latest alignment-based approaches to identify and characterize various types of functional sequences. Key areas of research are identified and directions for future improvements are suggested...
- Predicting direct protein interactions from affinity purification mass spectrometry dataEthan Dh Kim
McGill Centre for Bioinformatics, McGill University, Quebec, Canada
Algorithms Mol Biol 5:34. 2010..One drawback of AP-MS, however, is that it is prone to detecting indirect interactions mixed with direct physical interactions. Therefore, the ability to distinguish direct interactions from indirect ones is of much interest...
- Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2Diane Forget
Institut de recherches cliniques de Montreal IRCM, Montreal, Quebec, Canada H2W 1R7, McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montreal, Quebec, Canada H3A 2B4
Nucleic Acids Res 41:6881-91. 2013....
- Mapping association between long-range cis-regulatory regions and their target genes using syntenyEmmanuel Mongin
McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
J Comput Biol 18:1115-30. 2011....
- Hox in motion: tracking HoxA cluster conformation during differentiationMathieu Rousseau
Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, H3A 0E9, Canada
Nucleic Acids Res 42:1524-40. 2014....
- Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometryMathieu Lavallée-Adam
McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montreal, Quebec H3A 2B4, Canada
J Proteome Res 12:272-81. 2013..Finally, we demonstrate that this improvement in sensitivity leads to the discovery of novel interactions of RNAP II carboxyl-terminal domain (CTD) interacting domain (CID) proteins with POLR2A...
- Computing chromosome conformationJames Fraser
Department of Biochemistry, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
Methods Mol Biol 674:251-68. 2010..This chapter explains how 5C studies are performed and describes stepwise how to use currently available bioinformatics tools for experimental design, data analysis, and interpretation...
- StructMiner: a tool for alignment and detection of conserved secondary structureQian Yang
McGill Center for Bioinformatics, McGill University, Montreal, Quebec, H3A 2B4, Canada
Genome Inform 15:102-11. 2004..In addition, StructMiner is efficient in terms of CPU time and memory usage, making it suitable for structural analysis of very long sequences...
- Exact and heuristic algorithms for the Indel Maximum Likelihood ProblemAbdoulaye Banire Diallo
McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montreal, Quebec, Canada
J Comput Biol 14:446-61. 2007..A heuristic is presented to make the method practical for large data sets, while retaining an extremely high degree of accuracy. The methods are illustrated on a 1-Mb alignment of the CFTR regions from 12 mammals...
- Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI)Benoit Coulombe
Gene Transcription and Proteomics Laboratory and Proteomics Discovery Platform, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada
Biochem Cell Biol 86:149-56. 2008..The process governing the evolution of HuPI towards becoming a repository of accurate and complete protein interaction maps is described...
- SPARCS: a web server to analyze (un)structured regions in coding RNA sequencesYang Zhang
School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, H3A 0C6 QC, Canada
Nucleic Acids Res 41:W480-5. 2013..A web server implementing this discovery pipeline is available at http://csb.cs.mcgill.ca/sparcs together with the source code of the sampling algorithm. ..
- Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo samplingMathieu Rousseau
McGill Centre for Bioinformatics, Bellini Building, Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, Quebec, H3G 0B1, Canada
BMC Bioinformatics 12:414. 2011..Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization...
- The three-dimensional architecture of Hox cluster silencingMaria A Ferraiuolo
Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada
Nucleic Acids Res 38:7472-84. 2010..Our data suggest that Hox cluster looping may represent an evolutionarily conserved structural mechanism of transcription regulation...
- A probabilistic approach for SNP discovery in high-throughput human resequencing dataRose Hoberman
McGill Centre for Bioinformatics, McGill University, Montréal H36 0B1, Canada
Genome Res 19:1542-52. 2009....
- Long-range regulation is a major driving force in maintaining genome integrityEmmanuel Mongin
McGill Centre for Bioinformatics, McGill University, Montreal, Canada
BMC Evol Biol 9:203. 2009..The cause of the non-uniformity of breakpoints that occurred during vertebrate evolution is poorly understood...
- Aligning multiple genomic sequences with the threaded blockset alignerMathieu Blanchette
Howard Hughes Medical Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA
Genome Res 14:708-15. 2004..We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser...
- A probabilistic model for sequence alignment with context-sensitive indelsGlenn Hickey
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
J Comput Biol 18:1449-64. 2011..Fine-grained studies of small functional regions or disease markers, for example, could be significantly improved by our method. The implementation is available at www.mcb.mcgill.ca/~blanchem/software.html...
- Detecting non-coding selective pressure in coding regionsHui Chen
McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada H3A 2B4
BMC Evol Biol 7:S9. 2007..Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches...
- Modeling contaminants in AP-MS/MS experimentsMathieu Lavallée-Adam
McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Canada
J Proteome Res 10:886-95. 2011..Our approach will thus allow improved accuracy in PPI identification while reducing the number of control experiments required...
- Ancestors 1.0: a web server for ancestral sequence reconstructionAbdoulaye Banire Diallo
Department of Computer Science, Universite du Quebec a Montreal, PO Box 8888 Downtown Station, Montreal, QC H3C3P8, Canada
Bioinformatics 26:130-1. 2010..The results presented by the server include the posterior probabilities for the last two steps of the ancestral genome reconstruction and the expected error rate of each ancestral base prediction...
- A whole genome study and identification of specific carcinogenic regions of the human papilloma virusesAbdoulaye Banire Diallo
Departement d informatique, Universite du Quebec a Montreal, Succursale Centre Ville, Montreal, Quebec, Canada
J Comput Biol 16:1461-73. 2009..Supplementary Material is provided (see online Supplementary Material at www.libertonline.com )...
- On the inference of parsimonious indel evolutionary scenariosLeonid Chindelevitch
School of Computer Science, McGill University, 3480 University Street, Montreal, Quebec, H3A 2A7, Canada
J Bioinform Comput Biol 4:721-44. 2006..Our algorithms are tested and shown efficient and accurate on a set of 1.8 Mb mammalian orthologous sequences in the CFTR region...
- FootPrinter: A program designed for phylogenetic footprintingMathieu Blanchette
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA
Nucleic Acids Res 31:3840-2. 2003..The software is called FootPrinter and is available at http://bio.cs.washington.edu/software.html...
- Into the heart of darkness: large-scale clustering of human non-coding DNAGill Bejerano
Center for Biomolecular Science and Engineering, Baskin School of Engineering University of California in Santa Cruz, Santa Cruz, CA 95064, USA
Bioinformatics 20:i40-8. 2004..It is currently believed that the human genome contains about twice as much non-coding functional regions as it does protein-coding genes, yet our understanding of these regions is very limited...
- Seeder: discriminative seeding DNA motif discoveryFrançois Fauteux
Department of Plant Science, McGill University, Ste Anne de Bellevue, Quebec, Canada
Bioinformatics 24:2303-7. 2008..The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches...
- The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase IIDiane Forget
Institut de Recherches Cliniques de Montreal, Montreal, Québec H2W1R7, Canada
Mol Cell Proteomics 9:2827-39. 2010..A model for RNAPII biogenesis is presented...
- A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activityPhilippe Cloutier
Institut de recherches cliniques de Montreal IRCM, Montreal, Quebec, Canada
PLoS Genet 9:e1003210. 2013....
- Detection of locally over-represented GO terms in protein-protein interaction networksMathieu Lavallée-Adam
McGill Centre for Bioinformatics and School of Computer Science, Montreal, Quebec, Canada
J Comput Biol 17:443-57. 2010..When applied to these two biological networks, our approach recovers many known complexes and pathways, but also suggests potential functions for many subnetworks. Online Supplementary Material is available at www.liebertonline.com...
- Genetic map refinement using a comparative genomic approachDenis Bertrand
DIRO, Universite de Montreal, Montreal, Quebec, Canada
J Comput Biol 16:1475-86. 2009..We apply our algorithms to the plant species represented in the Gramene database, and we evaluate the simplified maps we obtained...
- Global patterns of cis variation in human cells revealed by high-density allelic expression analysisBing Ge
McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
Nat Genet 41:1216-22. 2009..The dense collection of associations will facilitate large-scale isolation of cis-regulatory SNPs...
- Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatinPhilippe Cloutier
Institut de recherches cliniques de Montreal IRCM, Montreal, Quebec H2W 1R7, Canada
J Proteomics 100:115-24. 2014..These results are discussed in view of the putative cellular function of Kin17...
- Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gammaCatherine R Dufour
Molecular Oncology Group, McGill University Health Centre, Montreal, Quebec H3A 1A1, Canada
Cell Metab 5:345-56. 2007..Our study thus reveals that the ERRs orchestrate a comprehensive cardiac transcriptional program and further suggests that modulation of ERR activities could be used to manage cardiomyopathies...
- Chromatin conformation signatures of cellular differentiationJames Fraser
Department of Biochemistry and McGill Cancer Center, McGill University, 3655 Promenade Sir William Osler, Montreal, H3G1Y6, Canada
Genome Biol 10:R37. 2009..Genome-wide chromatin conformation signature identification might uniquely identify disease-associated states and represent an entirely novel class of human disease biomarkers...
- Positional mapping and candidate gene analysis of the mouse Ccs3 locus that regulates differential susceptibility to carcinogen-induced colorectal cancerCharles Meunier
Department of Biochemistry, McGill University, Montreal, Quebec, Canada
PLoS ONE 8:e58733. 2013..The interval contains another positional candidate Slc39a8 that is differentially expressed in A vs B6 colons, and that has recently been associated in CRC tumor aggressiveness in humans...
- Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sitesMathieu Blanchette
McGill Centre for Bioinformatics and School of Computer Science, McGill University, H3C 2B4 Québec, Canada
BMC Bioinformatics 13:S2. 2012..In parallel to this development, an increasing number of mammalian genomes are now sequenced and it is becoming possible to infer, to a surprisingly high degree of accuracy, ancestral mammalian sequences...
- Improving the prediction of mRNA extremities in the parasitic protozoan LeishmaniaMartin Smith
Research Centre in Infectious Diseases, CHUL Research Centre, 2705 Laurier Blvd, Quebec, QC G1V 4G2, Canada
BMC Bioinformatics 9:158. 2008..Trans-splicing signals are often U-rich polypyrimidine (poly(Y)) tracts, which precede AG splice acceptor sites. However, as opposed to higher eukaryotes there is no consensus polyadenylation signal in trypanosomatid mRNAs...
- Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression treesXiaoyu Chen
McGill Centre for Bioinformatics, 3775 University Street, Room 332, Montreal, Quebec, Canada, H3A 2B4
BMC Bioinformatics 8:S2. 2007..In vertebrates, a large part of gene transcriptional regulation is operated by cis-regulatory modules. These modules are believed to be regulating much of the tissue-specificity of gene expression...
- Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioningBenoit Guillemette
Centre de recherche sur les mécanismes du fonctionnement cellulaire, Departement de Biologie, Faculte des Sciences, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
PLoS Biol 3:e384. 2005..Our data suggest that the incorporation of H2A.Z into specific promoter-bound nucleosomes configures chromatin structure to poise genes for transcriptional activation. The relevance of these findings to higher eukaryotes is discussed...
- An approximation algorithm for the Noah's Ark problem with random feature lossGlenn Hickey
School of Computer Science, McGill University, 3480 University Street, McConnell Engineering Building, Room 318, Montreal, QC H3A 2A7, Canada
IEEE/ACM Trans Comput Biol Bioinform 8:551-6. 2011..In this paper, we present a pseudopolynomial time approximation scheme for NAPL...
- An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malariaSilayuv E Bongfen
Department of Biochemistry, McGill University, Montreal, Canada
PLoS ONE 7:e31012. 2012..CM resistance in Jak3(W81R/+) heterozygotes occurs in presence of normal T, B and NK cell numbers. These findings highlight the pathological role of CD8(+) T cells and Jak3-dependent IFN-γ-mediated Th1 responses in CM pathogenesis...
- Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzymeCélia Jeronimo
Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de Recherches Cliniques de Montreal, Montreal, QC, Canada
Mol Cell 27:262-74. 2007..Our results define a high-density protein interaction network for the mammalian transcription machinery and uncover multiple regulatory factors that target the transcription machinery...
- Genome-wide mouse mutagenesis reveals CD45-mediated T cell function as critical in protective immunity to HSV-1Gregory Caignard
Departments of Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada
PLoS Pathog 9:e1003637. 2013..Altogether, these results revealed the CD45-mediated T cell function as potentially critical for infection and viral spread to the brain, and also for subsequent HSE development. ..
- BH3-ligand regulates access of MCL-1 to its E3 ligaseMatthew R Warr
Department of Biochemistry, McIntyre Medical Sciences Building, McGill University, Montreal, Que, Canada
FEBS Lett 579:5603-8. 2005..This suggests that the unliganded form of Mcl-1 is sensitive to LASU1-mediated degradation of Mcl-1...
- Gene maps linearization using genomic rearrangement distancesGuillaume Blin
IGM LabInfo, UMR CNRS 8049, Universite Paris Est, Marne la Vallee, France
J Comput Biol 14:394-407. 2007..A time-efficient greedy heuristic is then given for the general case and is empirically shown to produce solutions within 10% of the optimal solution, on simulated data. Applications to the analysis of grass genomes are presented...
- Algorithms for phylogenetic footprintingMathieu Blanchette
Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, WA 98195 2350, USA
J Comput Biol 9:211-23. 2002..Each technique is implemented and successfully identifies a number of known binding sites, as well as several highly conserved but uncharacterized regions. The program is available at http://bio.cs.washington.edu/software.html...
- Identification and characterization of multi-species conserved sequencesElliott H Margulies
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Genome Res 13:2507-18. 2003....
- Reconstructing contiguous regions of an ancestral genomeJian Ma
Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA
Genome Res 16:1557-65. 2006..Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals...
- Discovery of regulatory elements by a computational method for phylogenetic footprintingMathieu Blanchette
Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195 2350, USA
Genome Res 12:739-48. 2002..We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known...
- Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cellsMaria Shnyreva
Department of Immunology, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 101:12622-7. 2004..Like IFN-gamma expression, these histone modifications were T-bet-dependent in CD4+ cells, but not CD8+ T cells. These findings define two distal regulatory elements associated with T cell subset-specific IFN-gamma expression...