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 (ccolantu@jhsph.edu) if you would like to be added to the emaill annoucement list for these seminars.
| May 2009 | Speaker | Topic |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 21 | NO SEMINAR | GRADUATION DAY | |
| May 28 | Fernando Pineda | New ideas for computational detection of noncoding RNA: the case of P. falciparum |
| April 2008 | Speaker | Topic |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| 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 |
Slides |
|---|---|---|---|
| May 3 | - | - | |
| May 10 | Danielle & Jean Thierry-Mieg, NCBI, NLM | AceView: www.ncbi.nlm.nih.gov/IEB/Research/Acembly/ | |
| 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 |
Slides |
|---|---|---|---|
| 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 |
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