Genome Cafe

Expressionists Wednesday Seminar Schedule

Wednesdays at 2:30pm in room E3607 in the Johns Hopkins Bloomberg School of Public Health Building

Our weekly seminars cover diverse topics in gene expression analysis, genomics, and bioinformatics.

The one hour seminars are informal and very interactive, all are welcome.

Please email Carlo Colantuoni ( if you would like to be added to the emaill annoucement list for these seminars.

May 2009 Speaker Topic
May 6 Yu-yi Lin Starve A Yeast, Sweeten Its Lifespan
May 13 Su-In Lee Machine Learning for Gene Regulation and GWAS
May 20 Zhenqiu Liu ROC Based Methods for High Dimensional Genomic Data
May 27 Hannah Carter CHASM: cancer-specific high throughput annotation of somatic mutations

April 2009 Speaker Topic
April 1 - -
April 8 Sarah Wheelan The wacky world of transposable elements as they jump all over classical genetics
April 15 - -
April 22 Kwang Ho Choi Preliminary analysis on gene expression and SNP association
April 29 Ruth Heller Gene set analysis of observational microarray studies

March 2009 Speaker Topic
March 4 Rafael Irrizary CRLMM: A genotype calling algorithms for Affymetrix SNP chips
March 11 Carlo Colantuoni Exploration of the Genetic Control of Gene Expression (eQTL-ish)
March 18 Hector Corrada Bravo Statistical and computational challenges in second-generation sequencing data analysis
March 25 Hong Kai Ji Differential expression, transcription factor binding, and bivalent histone modification: an example in sonic hedgehog pathway

February 2009 Speaker Topic
February 4 no seminar -
February 11 Christopher Barr Identifying regions of differential methylation
February 18 Jeff Leek Some thoughts on batch effects in high-dimensional data
February 25 Rob Scharpf A copy number tool for high throughput genotyping arrays

January 2009 Speaker Topic
January 7 no seminar -
January 14 Carlo Colantuoni Paper: "Alternative isoform regulation in human tissue transcriptomes"
January 21 no seminar -
January 28 Panel Discussion On the Manipulation, Analysis, and Exploration of Large Matrices in R

December 2008 Speaker Topic
December 3 no seminar -
December 10 Stuart Ray Shifting sequences in human and virus, both happening in real time
December 17 Carlo Colantuoni Methods for visualizing BOTH global and local order in genome-wide correlations: is this possible?
December 24 no seminar -
December 31 no seminar -

November 2008 Speaker Topic
November 5 - -
November 12 Elana Fertig Predicting complex processes by integrating computational models and measurements
November 19 Alexander Favorov An evidence of role of the selection pressure in genome-wide CpG islands stability
November 26 - -

October 2008 Speaker Topic
October 1 - -
October 8 Mike Ochs Cancer Biomarkers - The Basics
October 15 Luigi Marchionni In-vitro culture imposes irreversible changes in gene expression
October 22 - -
October 29 Hector Corrada Bravo Towards an intensity model for next generation sequencing read alignment.

The 2nd Annual Junior Investigator Symposium on Genomics and Bioinformatics was be held on Friday, September 5th, 2008.
Slides from the presenters are available:
Introductory Speaker, Jonathan Pevsner: "Genomics, Bioinformatics and the Revolution in Biology"
Kathleen Burns: "Comprehensive transposon mapping in the human genome"
Rob Scharpf: "Genome-scale estimation of copy number and inference"
Bo Wen: "Heterochromatin blocks distinguish differentiated from embryonic stem cells" [unavailable]
Parminder Mankoo: "Somatic Mutations in PIK3CA"
Donald William Parsons: "Large-scale mutational analyses of human cancers: Lessons learned from sequencing cancer genomes"
Keynote Speaker, Steven Salzberg: "Assembling Genomes from Next-Generation Sequencers"

September 2008 Speaker Topic
September 3 NO SEMINAR All Day Symposium to be held Friday Sept 5th.
September 10 Silvano Piazza Characterization of Multipotent Adult Stem Cells (MASCs) from Epithelium Ovarian Cancer
September 17 Julia Engelmann Analyzing allele-specific methylation with Affymetrix SNP arrays
September 24 Matt Ritchie Analysis issues for Illumina BeadArrays

August 2008 Speaker Topic
August 6 NO SEMINAR -
August 13 Julia Engelmann Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species.
August 20 Valeria Edefonti Combinatorial mixtures of multiparameter distributions: an application to microarray data.
August 27 Rob Scharpf A hidden Markov model for trios using the Illumina genotyping platform.

July 2008 Speaker Topic
July 2 Giovanni Parmigiani Everything a clinical trials statistician needs to know about genomic data analysis, in one hour or less.
July 9 Les Cope Adapting gene signatures to novel experimental conditions.
July 16 NO SEMINAR -
July 23 Lieven Clement An introduction to state space models and Kalman filtering by example.
July 30 NO SEMINAR -

June 2008 Speaker Topic
June 4 Hongkai Ji CisGenome: An Integrated System for Analyzing ChIP-chip and ChIP-seq Data
June 11 Mahlet G Tadesse A stochastic partitioning method to associate high-dimensional datasets
June 18 Carlo Colantuoni MORE Exploratory Analysis of Human Cerebrocortical Transcriptional Change Across the Lifespan
June 25 John Goutsias Sensitivity Analysis of Biochemical Reaction Networks

May 2008 Speaker Topic
May 7 Simina Boca Statistical Issues in Gene-set analysis
May 14 Youfang Liu 1. Similarity-based association test using inferred ancestral haplotype, and 2. Association test incorporating genotyping uncertainty.
May 28 Fernando Pineda New ideas for computational detection of noncoding RNA: the case of P. falciparum

April 2008 Speaker Topic
April 2 Matt Mcall Cross-platform comparisons using microarray spike-in data
April 9 Stuart Ray Viral immune evasion and recombination: an opportunity to study evolution in the extreme
April 16 Chris Cheadle Simultaneous microarray measurement of nuclear and whole cell changes in gene expression reveals overlapping but distinct patterns of transcriptional regulation
April 23 Mike Ochs Transcribed or not transcribed: from signal to TF to microarray and back again
April 30 Rob Scharpf Estimating copy number from Affymetrix SNP arrays

March 2008 Speaker Topic
March 5 Jeff Leek Addressing dependence in high-throughput data with surrogate variable analysis
March 12 Diana Luca Genetic Matching for Optimal Use of Cases and Controls in Genome-Wide Association Studies
March 19 No Seminar Spring Break
March 26 Hao Wu Model Based Definitions of CpG Islands

February 2008 Speaker Topic
February 6 Steven L. Salzberg Computational Gene Finding in the Human Genome: How Many Genes Do We Have?
!! To be held in Owen's Auditorium in CRB2 (2:30PM Wed. Feb 6) !!
February 13 Svitlana Tyekucheva Analyzing large-scale genomic sequence data with old and new statistical methods
February 20 Rafael Irizarry Comprehensive High-throughput Array-based DNA Methylation Analysis
February 27 Yan Yuan Estimation of the prediction error for survival models

January 2008 Speaker Topic
January 2 - -
January 9 Carlo Colantuoni Exploratory Analysis of Transcriptional Change Across the Lifespan
January 16 Andrew Kossenkov ASAP: Automated Sequence Annotation Pipeline
January 23 Jonathan Pevsner SNP data analysis tools
January 30 Loris Mularoni Comparative genomics of amino acid tandem repeats

December 2007 Speaker Topic
December 5 Lixin Dai Distribution of group II introns in bacterial genomes
December 12 Alexander Favorov Allelic Pattern Sampler: Combinations of Genes Underlying Complex Disease
December 19 Kevin Becker, NIA Summary and analysis of published genetic association study information in common complex disease.
December 26 - -

Novermber 2007 Speaker Topic
Novermber 7 - -
Novermber 14 Laura Wood and Jimmy Lin The Genomic Landscapes of Human Breast and Colorectal Cancers
Novermber 21 - -
Novermber 28 Rob Scharpf A hidden Markov model for identifying regions of non-biparental inheritance in trios

October 2007 Speaker Topic
October 3 Ping Ye Predicting Temperature-sensitive Mutants through Integrating Structure and Sequence Information
October 10 Carlo Colantuoni The Human Cerebrocortical Transcriptome: Data Exploration Possibilities
October 17 Constantin Georgescu An enhanced test for pathway perturbation integrating topology information through multidimensional scaling
October 24 Luigi Marchionni "funcBox: an R package for the analysis of functional gene groups in expression data"
October 31 Dani Fallin A review of recent Whole Genome Association Meetings

September 2007 Speaker Topic
September 5 Rafael Irizarry A Gene Expression Barcode for Microarray Data
September 12 Cristina Battaglia Copy number alterations in renal cancer.
September 19 - -
September 26 - -

The 1st Annual Junior Investigator Symposium on Genomics and Bioinformatics. Was held on Tuesday, September 25th, 2007.

August 2007 Speaker Topic
August 1 - -
August 8 Giovanni Parmigianni Update on methods for mutational analysis projects.
August 15 Peter Cooper (NCBI) Gene Expression Omnibus (GEO)
August 22 Qing Li Logic Regression For Case-Parent Data: Searching for Gene-Gene interaction for Schizophrenia
August 29 Moonsu Kang Multiple Testing in Genome-Wide Studies

July 2007 Speaker Topic
July 4 - -
July 11 Rafael Irizarry Top Ten #7: SNP's and Tiling Arrays
NOTE: Seminar will be held in Darner Conference Room, Turner Concourse, SOM
July 18 Wensheng Zhang Predicting Cancer Subtypes in Presence of Misclassification among Training Samples Using Gene Expression Data
July 25 - -

June 2007 Speaker Topic
June 6 Luigi Marchionni Gene Set Enrichment: exploration across samples, platforms, and species
June 13 Carlo Colantuoni The Human Cerebral Transcriptome: Online From in Utero to in the Grave
June 20 - -
June 27 - -

May 2007 Speaker Topic
May 2 Benilton Carvalho Genotyping SNP's, Improving Calls - Thousands at a time
May 9 - -
May 16 Li Fan Bayesian Variable Selection in High Dimensional Structured Covariate Spaces.
May 23 - -
May 30 Carlo Colantuoni Top Ten #6: Experimental Design in Microarray Analysis
NOTE: Seminar will be held in BRB G-05, Broadway Res. Bldg, SOM

April 2007 Speaker Topic
April 4 Kung-Yee Liang Multipoint Linkage Mapping Using Sibpairs: Dealing with Complex Traits
April 11 Sang-Hoon Cho Penalties paid for ignoring the correlation between intensity channels in gene-expression analysis
April 18 Yoonhee Kim Problems with Pedigree Data in the Era of Highthroughput Genotyping
April 25 Carlo Colantuoni Top Ten #5: Microarray Quality Control
NOTE: Seminar will be held in Darner Conference Room, Turner Concourse, SOM

March 2007 Speaker Topic
March 7 Vasan Yegnasubramanian Analysis of protein-DNA interactions using tiling microarrays
March 14 - -
March 21 Ying Huang, University of Washington Evaluating predictive capacity of continuous biomarkers
March 28 Carlo Colantuoni Top Ten Talk #4: Clustering and Classification
NOTE: Seminar will be held in Darner Conference Room, Turner Concourse, SOM

February 2007 Speaker Topic
February 7 Rob Scharpf Combining high-throughput genomic data: methods and utility (Thesis Defense)
February 14 - -
February 21 Rafael Irizarry Top Ten Talk #3: Differential Gene Expression and Gene Set Enrichment Analysis
NOTE: Seminar will be held in Darner Conference Room, Turner Concourse, SOM
February 28 - -

January 2007 Speaker Topic
January 3 No Seminar No Seminar
January 10 Ingo Ruczinski Statistical approaches to assess gene copy number and loss of heterozygosity - a brief review of the recent literature
January 17 Michael Ochs The Impact of Multiple Gene Regulation and Signaling Processes on Microarray Analysis
January 24 Martin Meier-Schellersheim Multiscale modeling of cellular behavior: from molecular interactions to multicellular systems
January 31 Carlo Colantuoni Top Ten Talk #2: Gene Annotation in High-Throughput Genomics

December 2006 Speaker Topic
December 6 Rafael Irizarry Top Ten Talk #1: Introduction to Microarray Technology and Data Analysis.
NOTE: Seminar Held in West 1 Conference Room, off Turner Concourse in the School of Medicine.
December 13 Yu Chuan Tai Modeling cancer risk variation by mutational spectra
December 20 - -
December 27 No Seminar No Seminar

November 2006 Speaker Topic
November 1 Karl Broman The X chromosome in QTL mapping: What a pain in the @$$!
November 8 Ani Manichaikul Binary trait mapping in experimental crosses with genotypes on all, some or no unaffecteds
November 15 Giovanni Parmigiani The transcriptome of Clostridium Novyi NT
November 22 No Seminar No Seminar
November 29 Dr. Greg Alvord A Microarray Analysis of Differential Gene Expression in the Soybean Genome.

October 2006 Speaker Topic
October 4 Yen-YI Ho Statistical Methods for Identifying Differentially Expressed Gene Combinations
October 11 Gang Wu, UMBC What contributes to the variations in the correlation between mRNA concentration and protein abundance?
October 18 Luigi Ferrucci, NIA BLSA - Baltimore Longitudinal Study of Aging
October 25    

September 2006 Speaker Topic
September 6 Rafael Irizarry Preprocessing Affymetrix SNP Chips: Improving Genotype Calling and Copy Number Estimation - 1
September 13 Rafael Irizarry Preprocessing Affymetrix SNP Chips: Improving Genotype Calling and Copy Number Estimation - 2
September 20 - -
September 27 Sean Davis, NHGRI Cancer Applications of Array CGH

August 2006 Speaker Topic
August 2 Giovanni Parmigianni FDR and Bayesian Multiple Comparisons Rules
August 9 Ernest Kawasaki, NCI Review & Update of the ERCC & MAQC Microarray Consortia & Applications of Their Findings
August 16 Yen-YI Ho An integrative genomic approach to infer causal associations between gene expression and disease
August 23 Joseph Lee, NIDDK Analysis of alternative splicing's effect on microarray platform concordance  
August 30 Shan Zhao, NIDDK Microarray Data Processing with Stream Lined Gene Ontology

July 2006 Speaker Topic
July 5 Dani Fallin How to weight statistical evidence for a gene: our story of schizophrenia and chromosome 10.
July 12 Michael McDevitt Genomic Investigations in Myeloid Malignancies: The Hunt for Tumor Suppressors
July 19 Ingo Ruczinski On Missing Genotype Data
July 26 Yen-YI Ho Identification of QTLS controlling gene expression networks defined a priori.

June 2006 Speaker Topic
June 7 Ainong Zhou Bayes Factors Comparing Two Multi-Normal Covariance Matrices and Their Application to Microarray Data Analysis
June 14 James Balow & Ivona Aksentijevich, NIAMS Gene Expression Studies in NOMID patients before and after anakinra treatment
June 21 Rafael Irizarry A Gene Expression Barcode for Human and Mouse Organs
June 28 Yen-YI Ho Genetic Analysis of Genome-Wide Variation in Human Gene Expression

May 2006 Speaker Topic
May 3 - -
May 10 Danielle & Jean Thierry-Mieg, NCBI, NLM AceView:
May 17 Fernando Pineda Searching for nonclassical RNA in Plasmodium falciparum
May 24 - -
May 31 Les Cope & Raghu Reddy Peesari Peptide Microarrays for Understanding Kinase Function

April 2006 Speaker Topic
April 5 Chris Cheadle Microarray Platform Comparison Through Gene Group Analysis
April 12 Carlo Colantuoni Artifacts and Effects in Gene Expression Data
April 19 Rafael Irizarry Gene Annotaion Tools - BioConductor
April 26 Byungwoo Ryu Gene expression profiles for melanoma marker discovery