Journal Club Presentations

Date: 01/20/2011
Presenter: Chen
Paper: Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
Presentation:

Date: 01/06/2011
Presenter: Maya
Paper: Global analysis of disease-related DNA sequence variation in 10 healthy individuals: Implications for whole genome-based clinical diagnostics
Presentation:

Date: 12/23/2011
Presenter: Lipika
Paper: Epistatic Selection between Coding and Regulatory Variation in Human Evolution and Disease continued
Presentation:

Date: 11/23/2011
Presenter: Lipika
Paper: Epistatic Selection between Coding and Regulatory Variation in Human Evolution and Disease
Presentation:

Date: 10/28/2011
Presenter: Nuttinee
Paper: Computational and statistical approaches to analyzing variants identified by exome sequencing, Exome sequencing supports a de novo mutational paradigm for schizophrenia
Presentation:

Date: 10/14/2011
Presenter: Yizhou
Paper: Bringing order to protein disorder through comparative genomics and genetic interactions
Presentation:

Date: 09/30/2011
Presenter: Albert
Paper: Genome-wide approaches for cancer gene discovery, Principles for the post-GWAS functional characterization of cancer risk loci
Presentation:

Date: 09/02/2011
Presenter: Chen
Paper: Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences
Presentation:

Date: 08/05/2011
Presenter: Maya
Paper: Gene-Disease Network Analysis Reveals Functional Modules in Mendelian, Complex and Environmental Diseases
Presentation:

Date: 07/22/2011
Presenter: Yizhou
Paper: Global quantification of mammalian gene expression control
Presentation:

Date: 06/29/2011
Presenter: Lipika
Paper: Molecular Reclassification of Crohn’s Disease by Cluster Analysis of Genetic Variants
Presentation:

Date: 06/17/2011
Presenter: Nuttinee
Paper: The rate of the molecular clock and the cost of gratuitous protein synthesis
Presentation:

Date: 05/27/2011
Presenter: Professor Arlin Stoltzfus
Paper: Non-adaptive origins of interactome complexity
Presentation:

Date: 05/13/2011
Presenter: Guoquin
Paper: Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
Presentation:

Date: 03/18/2011
Presenter: Albert
Paper: Identifying Causal Genes and Dysregulated Pathways in Complex Diseases
Presentation:

Date: 03/04/2011
Presenter: Chen
Paper: A Mathematical Framework for Protein Structure Comparison
Presentation:

Date: 02/18/2011
Presenter: Zhen
Paper: A biological solution to a fundamental distributed computing problem
Presentation:

Date: 02/04/2011
Presenter: Maya
Paper: The use of classification trees for bioinformatics, The example of how the algorithm can be used on real-life data:Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions
Presentation:

Date: 01/21/2011
Presenter: Lipika
Paper: Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology
Presentation:

Date: 01/07/2011
Presenter: Yizhou
Paper: Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments
Presentation:

Date: 12/03/2010
Presenter: Albert
Paper: Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components
Presentation:

Date: 11/12/2010
Presenter: Chen
Paper: Parasites lead to evolution of robustness against gene loss in host signaling networks, second paper: Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks
Presentation:

Date: 10/14/2010
Presenter: Zhen
Paper: An application of Random Forests to a genome-wide association dataset: Methodological considerations and new findings
Presentation:

Date: 10/01/2010
Presenter: Maya
Paper: Systematic discovery of nonobvious human disease models through orthologous phenotypes
Presentation:

Date: 09/17/2010
Presenter: Nuttinee
Paper: Classification and Determination of Possible Origins of ORFans through Analysis of Nucleocytoplasmic large DNA viruses from Intervirology, supplementary paper: Structure and functional insights into Mimivirus
Presentation:

Date: 09/03/2010
Presenter: Lipika
Paper: Pooled Association Tests for Rare Variants in Exon-Resequencing Studies
Presentation:

Date: 08/20/2010
Presenter: Yizhou
Paper: A novel approach to simulate gene-environment interactions in complex diseases
Presentation:

Date: 07/23/2010
Presenter: Professor Arlin Stoltzfus
Paper: On the Possibility of Constructive Neutral Evolution
Presentation: view

Date: 07/16/2010
Presenter: Chen
Paper: Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations?
Presentation:

Date: 07/02/2010
Presenter: Zhen
Paper: Edgetic perturbation models of human inherited disorders
Presentation: view

Date: 06/17/2010
Presenter: Maya
Paper: Cloud Technologies for Bioinformatics Applications, The case for cloud computing in genome informatics
Presentation: view

Date: 06/04/2010
Presenter: Lipika
Paper: Missing heritability and strategies for finding the underlying causes of complex disease
Presentation: view

Date: 05/14/2010
Presenter: Yizhou
Paper: Feature Space Resampling for Protein Conformational Search
Presentation: Supplemental material

Date: 05/30/2010
Presenter: Albert
Papers: 1. Understanding mechanisms underlying human gene expression variation with RNA sequencing
2. Transcriptome genetics using second generation sequencing in a Caucasian population
Presentation:

Date: 02/26/2010
Presenter: Nuttinee
Paper: A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archael and bacterial genomes
Presentation: view

Date: 01/22/2010
Presenter: Professor Arlin Stoltzfus
Paper: Recent de novo origin of human protein-coding genes
Presentation:

Date: 11/20/2009
Presenter: Chen
Paper: Information theory, multivariate dependence, and genetic network inference
Presentation: view

Date: 11/6/2009
Presenter: Zhen
Paper: Identification of rare cancer driver mutations by network reconstruction
Presentation: view, Supplemental material

Date: 10/7/2009
Presenter: Lipika
Paper: Chromatin organization marks exon-intron structure
Presentation: view

Date: 9/23/2009
Presenter: Yizhou
Paper: Protein sectors evolutionary units of three dimensional structure 2009 Cell
Presentation: view

Date: 9/2/2009
Presenter: Albert
Paper: Domain shuffling and the evolution of vertebrates
Presentation:

Date: 8/7/2009
Presenter: Chen
Paper: Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome
Presentation:

Date: 7/17/2009
Presenter: Nuttinee
Paper: The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes
Presentation:

Date: 6/17/2009
Presenter: Zhen
Paper: Models from experiments: combinatorial drug perturbations of cancer cells
Presentation: view

Date: 6/5/2009
Presenter: Maya
Paper: A survey of visualization tools for biological network analysis
Presentation: view

Date: 5/15/2009
Presenter: Nuttinee
Paper: Microbial co-habitation and lateral gene transfer: what transposases can tell us
Presentation:

Date: 4/22/2009
Presenter: Lipika
Paper: Using biological networks to search for interacting loci in genome-wide association studies
Presentation: view

Date: 3/6/2009
Presenter: Yizhou
Paper: Computational structure based redesign of enzyme activity
Presentation: view

Date: 2/18/2009
Presenter: Albert
Paper: Gene Expression Levels Are a Target of Recent Natural Selection in the Human Genome
Presentation: view

Date: 2/6/2009
Presenter: Chen
Paper: Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
Presentation:

Date: 1/23/2008
Presenter: Zhen
Paper: Network-based classification of breast cancer metastasis
Presentation: dowload, Supplemental material

Date: 1/9/2009
Presenter: Maya
Paper: Neural networks for genetic epidemiology: past, present, and future
Presentation: view

Date: 12/12/2008
Presenter: Nuttinee
Paper: An ancient evolutionary origin of genes associated with human genetic diseases
Presentation:

Date: 11/21/2008
Presenter: Lipika
Paper: Gene prioritization through genomic data fusion
Presentation:view

Date: 10/3/2008
Presenter: Chen
Paper: Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
Presentation:

Date: 9/25/2008
Presenter: Maya
Paper: A human phenome-interactome network of protein complexes implicated in genetic disorders
Presentation: view

Date: 8/8/2008
Presenter: Zhen
Paper: Assembly reflects evolution of protein complexes, paper supplemental material
Presentation: view
Supplemental Material: 3D Complex: A structural classification of protein complexes

Date: 7/25/2008
Presenter: Lipika
Paper: Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
Presentation: view

Date: 6/27/2008
Presenter: Albert
Paper: Detecting non-coding selective pressure in coding regions
Presentation: view part 1, part 2

Date: 6/05/2008
Presenter: Zhen
Paper: A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans Paper supplemental material
Presentation: view
Supplemental Material: A map of human protein interactions derived from co-expression of human mRNAs and their orthologs,
Genome-Wide Prediction of C. elegans Genetic Interactions, Analysis of the human protein interactome and comparison with yeast, worm, and fly interaction datasests, A Probabilistic Functional Network of Yeast Genes, Lethality and centrality in protein networks, Scale-free Networks

Date: 5/16/2008
Presenter: Maya
Paper: Network-based prediction of protein function
Presentation: view

Date: 4/16/2008
Presenter: Albert
Paper: Modular epistasis in yeast metabolism
Presentation: view part 1, part 2

Date: 3/14/2008
Presenter: Albert
Paper: On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer
Presentation: view

Date: 2/15/2008
Presenter: Nuttinee
Papers: 1. Genomic clocks and evolutionary timescales.
2. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land
Presentation: view

Date: 12/21/2007
Presenter: Lipika
Paper: Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis
Presentation:view

Date: 12/07/2007
Presenter: Albert
Paper: 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
Presentation: view

Date: 11/9/2007
Presenter: Nuttinee
Paper: "Elevated rates of protein secretion, evolution, and disease among tissue-specific genes" Genome Res. 14:54-61, 2004
Presentation:


	Journal Club Presentations Presentations are organized by years. Clicking on a year in the following menu will open all the presentations of the respective year. + 2012 Date: 01/20/2011 Presenter: Chen Paper: Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome Presentation: Date: 01/06/2011 Presenter: Maya Paper: Global analysis of disease-related DNA sequence variation in 10 healthy individuals: Implications for whole genome-based clinical diagnostics Presentation: + 2011 Date: 12/23/2011 Presenter: Lipika Paper: Epistatic Selection between Coding and Regulatory Variation in Human Evolution and Disease continued Presentation: Date: 11/23/2011 Presenter: Lipika Paper: Epistatic Selection between Coding and Regulatory Variation in Human Evolution and Disease Presentation: Date: 10/28/2011 Presenter: Nuttinee Paper: Computational and statistical approaches to analyzing variants identified by exome sequencing, Exome sequencing supports a de novo mutational paradigm for schizophrenia Presentation: Date: 10/14/2011 Presenter: Yizhou Paper: Bringing order to protein disorder through comparative genomics and genetic interactions Presentation: Date: 09/30/2011 Presenter: Albert Paper: Genome-wide approaches for cancer gene discovery, Principles for the post-GWAS functional characterization of cancer risk loci Presentation: Date: 09/02/2011 Presenter: Chen Paper: Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences Presentation: Date: 08/05/2011 Presenter: Maya Paper: Gene-Disease Network Analysis Reveals Functional Modules in Mendelian, Complex and Environmental Diseases Presentation: Date: 07/22/2011 Presenter: Yizhou Paper: Global quantification of mammalian gene expression control Presentation: Date: 07/22/2011 Presenter: Yizhou Paper: Global quantification of mammalian gene expression control Presentation: Date: 06/29/2011 Presenter: Lipika Paper: Molecular Reclassification of Crohn’s Disease by Cluster Analysis of Genetic Variants Presentation: Date: 06/17/2011 Presenter: Nuttinee Paper: The rate of the molecular clock and the cost of gratuitous protein synthesis Presentation: Date: 05/27/2011 Presenter: Professor Arlin Stoltzfus Paper: Non-adaptive origins of interactome complexity Presentation: Date: 05/13/2011 Presenter: Guoquin Paper: Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths Presentation: Date: 03/18/2011 Presenter: Albert Paper: Identifying Causal Genes and Dysregulated Pathways in Complex Diseases Presentation: Date: 03/04/2011 Presenter: Chen Paper: A Mathematical Framework for Protein Structure Comparison Presentation: Date: 02/18/2011 Presenter: Zhen Paper: A biological solution to a fundamental distributed computing problem Presentation: Date: 02/04/2011 Presenter: Maya Paper: The use of classification trees for bioinformatics, The example of how the algorithm can be used on real-life data:Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions Presentation: Date: 01/21/2011 Presenter: Lipika Paper: Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology Presentation: Date: 01/07/2011 Presenter: Yizhou Paper: Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments Presentation: + 2010 Date: 12/03/2010 Presenter: Albert Paper: Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components Presentation: Date: 11/12/2010 Presenter: Chen Paper: Parasites lead to evolution of robustness against gene loss in host signaling networks, second paper: Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks Presentation: Date: 10/14/2010 Presenter: Zhen Paper: An application of Random Forests to a genome-wide association dataset: Methodological considerations and new findings Presentation: Date: 10/01/2010 Presenter: Maya Paper: Systematic discovery of nonobvious human disease models through orthologous phenotypes Presentation: Date: 09/17/2010 Presenter: Nuttinee Paper: Classification and Determination of Possible Origins of ORFans through Analysis of Nucleocytoplasmic large DNA viruses from Intervirology, supplementary paper: Structure and functional insights into Mimivirus Presentation: Date: 09/03/2010 Presenter: Lipika Paper: Pooled Association Tests for Rare Variants in Exon-Resequencing Studies Presentation: Date: 08/20/2010 Presenter: Yizhou Paper: A novel approach to simulate gene-environment interactions in complex diseases Presentation: Date: 07/23/2010 Presenter: Professor Arlin Stoltzfus Paper: On the Possibility of Constructive Neutral Evolution Presentation: view Date: 07/16/2010 Presenter: Chen Paper: Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations? Presentation: Date: 07/02/2010 Presenter: Zhen Paper: Edgetic perturbation models of human inherited disorders Presentation: view Date: 06/17/2010 Presenter: Maya Paper: Cloud Technologies for Bioinformatics Applications, The case for cloud computing in genome informatics Presentation: view Date: 06/04/2010 Presenter: Lipika Paper: Missing heritability and strategies for finding the underlying causes of complex disease Presentation: view Date: 05/14/2010 Presenter: Yizhou Paper: Feature Space Resampling for Protein Conformational Search Presentation: Supplemental material Date: 05/30/2010 Presenter: Albert Papers: 1. Understanding mechanisms underlying human gene expression variation with RNA sequencing 2. Transcriptome genetics using second generation sequencing in a Caucasian population Presentation: Date: 02/26/2010 Presenter: Nuttinee Paper: A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archael and bacterial genomes Presentation: view Date: 01/22/2010 Presenter: Professor Arlin Stoltzfus Paper: Recent de novo origin of human protein-coding genes Presentation: + 2009 Date: 11/20/2009 Presenter: Chen Paper: Information theory, multivariate dependence, and genetic network inference Presentation: view Date: 11/6/2009 Presenter: Zhen Paper: Identification of rare cancer driver mutations by network reconstruction Presentation: view, Supplemental material Date: 10/7/2009 Presenter: Lipika Paper: Chromatin organization marks exon-intron structure Presentation: view Date: 9/23/2009 Presenter: Yizhou Paper: Protein sectors evolutionary units of three dimensional structure 2009 Cell Presentation: view Date: 9/2/2009 Presenter: Albert Paper: Domain shuffling and the evolution of vertebrates Presentation: Date: 8/7/2009 Presenter: Chen Paper: Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome Presentation: Date: 7/17/2009 Presenter: Nuttinee Paper: The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes Presentation: Date: 6/17/2009 Presenter: Zhen Paper: Models from experiments: combinatorial drug perturbations of cancer cells Presentation: view Date: 6/5/2009 Presenter: Maya Paper: A survey of visualization tools for biological network analysis Presentation: view Date: 5/15/2009 Presenter: Nuttinee Paper: Microbial co-habitation and lateral gene transfer: what transposases can tell us Presentation: Date: 4/22/2009 Presenter: Lipika Paper: Using biological networks to search for interacting loci in genome-wide association studies Presentation: view Date: 3/6/2009 Presenter: Yizhou Paper: Computational structure based redesign of enzyme activity Presentation: view Date: 2/18/2009 Presenter: Albert Paper: Gene Expression Levels Are a Target of Recent Natural Selection in the Human Genome Presentation: view Date: 2/6/2009 Presenter: Chen Paper: Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence Presentation: Date: 1/23/2008 Presenter: Zhen Paper: Network-based classification of breast cancer metastasis Presentation: dowload, Supplemental material Date: 1/9/2009 Presenter: Maya Paper: Neural networks for genetic epidemiology: past, present, and future Presentation: view + 2008 Date: 12/12/2008 Presenter: Nuttinee Paper: An ancient evolutionary origin of genes associated with human genetic diseases Presentation: Date: 11/21/2008 Presenter: Lipika Paper: Gene prioritization through genomic data fusion Presentation:view Date: 10/3/2008 Presenter: Chen Paper: Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes Presentation: Date: 9/25/2008 Presenter: Maya Paper: A human phenome-interactome network of protein complexes implicated in genetic disorders Presentation: view Date: 8/8/2008 Presenter: Zhen Paper: Assembly reflects evolution of protein complexes, paper supplemental material Presentation: view Supplemental Material: 3D Complex: A structural classification of protein complexes Date: 7/25/2008 Presenter: Lipika Paper: Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network Presentation: view Date: 6/27/2008 Presenter: Albert Paper: Detecting non-coding selective pressure in coding regions Presentation: view part 1, part 2 Date: 6/05/2008 Presenter: Zhen Paper: A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans Paper supplemental material Presentation: view Supplemental Material: A map of human protein interactions derived from co-expression of human mRNAs and their orthologs, Genome-Wide Prediction of C. elegans Genetic Interactions, Analysis of the human protein interactome and comparison with yeast, worm, and fly interaction datasests, A Probabilistic Functional Network of Yeast Genes, Lethality and centrality in protein networks, Scale-free Networks Date: 5/16/2008 Presenter: Maya Paper: Network-based prediction of protein function Presentation: view Date: 4/16/2008 Presenter: Albert Paper: Modular epistasis in yeast metabolism Presentation: view part 1, part 2 Date: 3/14/2008 Presenter: Albert Paper: On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer Presentation: view Date: 2/15/2008 Presenter: Nuttinee Papers: 1. Genomic clocks and evolutionary timescales. 2. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land Presentation: view + 2007 Date: 12/21/2007 Presenter: Lipika Paper: Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis Presentation:view Date: 12/07/2007 Presenter: Albert Paper: 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser Presentation: view Date: 11/9/2007 Presenter: Nuttinee Paper: "Elevated rates of protein secretion, evolution, and disease among tissue-specific genes" Genome Res. 14:54-61, 2004 Presentation:
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