Current Students and Research

Below are some of the current CBB students and their research.

Song Huang - Zhao lab (entered Fall 2004)

Song is studying how outbred stock mice with pedigree information contribute to admixture mapping.

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Kei-Hoi Cheung Web service technology to interoperate biological databases and analyze gene clustering
Mark Gerstein Statistical methods for preprocessing and scoring tiling microarray data
Hongyu Zhao Statistical issues in mapping quantitative trait loci for gene expression levels

Publications:

  • Huang S, Ballard D, Zhao H. The role of heritability in mapping expression quantitative trait loci. BMC Proc. 2007;1 Suppl 1:S86. Epub 2007 Dec 18.
  • Huang S, Wang S, Liu N, Chen L, Oh C, Zhao H. Whole-genome association analysis to identify markers associated with recombination rates using single-nucleotide polymorphisms and microsatellites. BMC Genet. 2005 Dec 30;6 Suppl 1:S51.
Kevin Keating - Pyle lab (entered Fall 2004)
Kevin Keating

Kevin is developing a method to accurately determine atomic coordinates for backbone atoms from low resolution RNA crystal structures. To do this, he is using both a reduced representation of RNA developed by the Pyle lab and RNA backbone rotamer library developed by the Richardson lab at Duke University. His goal is to get accurate information about the reduced representation from the electron density, and then determine the appropriate rotamer from this reduced representation data.

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Anna Pyle Comparing and analyzing two methods to examine RNA backbone structure: a reduced representation and a rotamer library
Mark Gerstein Analyzing protein hinges, or large inter-domain motions in proteins
Kevin White Attempting to develop microarray probes that could be used across multiple species of Drosophila

Publications:

  • Toor N, Keating KS, Pyle AM. Structural insights into RNA splicing. Curr Opin Struct Biol. 19 (2009) 260-266.
  • Keating KS, Flores SC, Gerstein MB, Kuhn LA. StoneHinge: Hinge prediction by network analysis of individual protein structures. Protein Science 18 (2009) 359-371.
  • Toor N, Rajashankar K, Keating KS, Pyle AM. Structural basis for exon recognition by a group II intron. Nat Struct Mol Biol. 15 (2008) 1221-1222.
  • Flores SC, Keating KS, Painter J, Morcos F, Nguyen K, Merritt EA, Kuhn LA, Gerstein MB. HingeMaster: normal mode hinge prediction approach and integration of complementary predictors. Proteins 73 (2008) 299-319.
  • Keating KS, Toor N, Pyle AM. The GANC Tetraloop: A Novel Motif in the Group IIC Intron Structure. JMB 383 (2008) 475-481.
  • Toor N, Keating KS, Taylor SD, Pyle AM. Crystal structure of a self-spliced group II intron. Science 320 (2008) 77-82.
  • Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA 14 (2008) 465-81.
  • Wadley LM, Keating KS, Duarte CM, Pyle AM. Evaluating and learning from RNA pseudotorsional space: Quantitative validation of a reduced representation for RNA structure. JMB 372 (2007) 942-57.
  • Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu EZ, Thorpe M, Gerstein M. The Database of Macromolecular Motions: New features added at the decade mark. NAR 34 (2006) D296-301.
Jill Rubinstein - Krauthammer lab/Lizardi lab (entered Fall 2004)
(now in MD-PhD program)
Jill Rubinstein

Jill's research focuses on the analysis and integration of multiple, large-scale datasets including epigenomic and genomic data from cancer tissues and cell lines. In particular, she is exploring the interplay between DNA methylation and gene expression, and the effect of demethylating chemotherapeutic agents on this relationship. She is interested in combining high-resolution, genome-wide molecular data with clinical information to ask questions with direct translational relevance.

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David Tuck Using in silico modeling of tissue micro-heterogeneity to determine whether interaction between diverse clones of cells can lead to tumorigenesis
Paul Lizardi Studying the mechanisms of isothermal whole-genome amplification using in silico modeling
Michael Krauthammer Quantifying the strength of relationships between pathological terms and genes based on statistics of co-occurence in the literature

Publications:

  • Szpakowski S, Sun X, Lage JM, Dyer A, Rubinstein J, Kowalski D, Sasaki C, Costa J, Lizardi PM. Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements. Gene Epub 2009 Aug 20.
Hugo Lam - Gerstein lab (entered Fall 2005)
Hugo Lam

In one collaboration, Hugo is looking at the genetic variation effect between different strains of Saccharomyces cerevisiae that will lead to a quantitative difference in the binding of transcription factors. He is also surveying the pseudo genes in meta genomics by investigating their distribution by protein families in different geographical locations in prokaryotes. This project seeks to see how different environments and nutrition factors would affect the quantity of pseudo genes, categorized by their parent protein families. In a third project, he is developing a pipeline system for analyzing motifs from SH3 domains using comparative genomics, structural, and genomic approaches.

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Perry Miller Using Web Ontology Language (OWL) to integrate two neuronal database, CoCoDat and SenseLab
Mark Gerstein Working on microarray data optimization
Michael Snyder Analysis of transcription factors for pseudohyphal growth in different yeast strains

Publications:

  • Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB. Pseudofam: the pseudogene families database. Nucleic Acids Res. Epub 2008 Oct 28.
  • Kim PM, Lam HY, Urban AE, Korbel JO, Chen X, Snyder M, Gerstein MB. Analysis of copy number variants and segmental duplications in the human genome; Evidence for a change in the process of formation in recent evolutionary history. Genome Res. Epub 2008 Oct 8.
  • Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol. 2007;8(5):R81.
ThaiBinh Luong - Krauthammer lab (entered Fall 2005)
Thaibinh Luong

ThaiBinh's work involves mining through biomedical literature in order to map instances of gene strings and diseases to a repository of gene/disease identifiers. The aim of this process is to more easily classify research papers and identify relevant papers for researchers.

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Hongyu Zhao Establishing a database for a large microarray data set used to test the effects of drugs and toxicants on rat organs
Michael Krauthammer Analyzing several methods of term mapping in order to identify terms found in biological abstracts
David Tuck Classification of transcription factors in PubMed abstracts

Publications:

  • Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA Jr, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A. Introducing metaservices for biomedical information extraction. Genome Biology 2008, 9(Suppl 2):S6 (1 September 2008).
  • Tran N, Luong T, Krauthammer M. Mapping terms to UMLS concepts of the same semantic type. AMIA Annu Symp Proc. 2007 Oct 11:1136.
  • Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang CH, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, Schiller MR. Minimotif Miner: a tool for investigating protein function. Nat Methods. 2006 Mar;3(3):175-7.
Laura Mustavich - Kidd lab/Zhao lab (entered Fall 2005)
Laura Mustavich

Laura is using the complementary approaches of statistical methods and pharmacokinetic modeling to explore possible mechanisms underlying alcohol dependence.

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Hongyu Zhao Evaluating the performance of HapGraph, a program which determines the dependence among genetic loci, by testing it on SNP data from the International HapMap Project
Joe Chang Analyzing data from the Multiple Crime Study, which reports on an isolated population in Russia where individuals have committed multiple crimes. Laura used IDB analysis to determine if any of the genetic markers are linked to mental health or behavioral traits.
Kenneth Kidd Evaluation of markers to cluster people into ethnic populations
Pavithra Shivakumar - Krauthammer lab (entered Fall 2005)
Pavithra Shivakumar

Pavi uses microarray datasets from cancer patients to find patterns of drug sensitivity. She uses melanoma datasets to find genes playing an important role in the disease.

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Michael Krauthammer Analyzing protein interaction networks using graph theory algorithms to find subnetworks of disease genes
Mark Gerstein Building a web interface for Primer3, a program that designs primers for PCR
Michael Snyder Creating an abstract framework for tagging experimental data
Chong Shou - Gerstein lab/Snyder lab (entered Fall 2005)
Chong Shou

Chong currently works on mapping 5' UTR sequences in yeast by processing data from large-scale 5' RACE experiments. The project attempts to find annotation errors in gene translation start codon positions and original sequencing errors. It also works towards the development of a complete map of 5' UTR sequences in all yeast transcripts.

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Mark Gerstein Examined yeast regulatory networks to find the targets of essential transcription factors
Michael Snyder Performed ChIP-chip experiments on yeast Pol-2 transcription factor to find regulatory binding sites. Also produced 3 biological replicates and submitted data into the UCSC database.
Hongyu Zhao Inferred protein-protein interacting domains using high-throughput data from diverse organisms

Publications:

  • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscapes of the yeast genome defined by RNA sequencing. Science. 2008 Jun 6;320(5881):1344-9.
Sebastian Szpakowski - Krauthammer lab/Lizardi lab (entered Fall 2005)
Sebastian Szpakowski

The focus of Sebastian's research is the design of microarray chips that detect patterns of genomic methylation, e.g. in cancer versus normal tissues. He hopes that his analysis of the data derived from experiments using those chips will help to functionally annotate the uncharted genomic regions, known as the "junk" DNA.

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David Tuck Creating a simulation of the DNA damage response pathway in yeast using differential equations and agent-based frameworks
Paul Lizardi Developing and testing novel microarray normalization methods, analyzing methylation changes across the human genome, and determining the potential role of repetitive elements in the human genome
Michael Krauthammer Created custom gene ontologies based on preprocessed literature from PubMed

Publications:

  • Szpakowski S, McCusker J, Krauthammer M. Using Semantic Web Technologies to Annotate and Align Microarray Designs. Cancer Informatics 2009:8 65-73.
  • Szpakowski S, Sun X, Lage JM, Dyer A, Rubinstein J, Kowalski D, Sasaki C, Costa J, Lizardi PM. Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements. Gene Epub 2009 Aug 20.
Jamie Duke - Kleinstein lab (entered Fall 2006)

Jamie's research has been focused on understanding the targeting mechanisms of activation induced cytosine deaminase (AID), which is responsible for somatic hypermutation in germinal center B-cells. Her lab has recently been working to identify cis-regulatory modules which are responsible for recruiting AID to the immunoglobulin loci and other recently identified genes. The goal is to identify why some genes are targets of AID and others are not and additionally why some of the mutated genes are repaired in an error-free manner as opposed to other genes that are repaired in an error-prone manner.

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David Tuck Investigated the differences between breast cancer subtypes using microarray data
Annette Molinaro Began the initial setup of a data adaptive system for analysis of tissue microarrays
Steven Kleinstein Analyzed mutations occurring in non-immunoglobulin genes

Publications:

  • Liu M, Duke J, Richter L, Vinuesa DJ, Goodnow CG, Kleinstein SH, Schatz DG. Two levels of protection for the B cell genome during somatic hypermutation. Nature 451, 841-845.
Jia Kang - Zhao lab/Cho lab (entered Fall 2006)

Jia's research has been focused on genome wide association studies. One approach in obtaining a higher power in detecting the statistically significant associations between SNPs (single nucleotide polymorphisms) and disease status is to perform a summary analysis on several combined studies. This approach is referred to as meta-analysis. However, the challenge in meta-analysis is to achieve comparability between studies. Jia's current research involves exploring various possible approaches in performing meta-analysis on combined sets of Crohn's disease case-control studies while incorporating different imputation methods in expanding the sample size. In addition, as part of his research, he is also hoping to find solutions to account for the population structures when combining datasets.

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William Jorgensen 3D-docking a ligand library containing 24,000 ligands into the tautomerase site of Macrophage Migration Inhibitory Factor
Hongyu Zhao Analyzed the data and investigated the function of the p38 pathway at the molecular level
Kei Cheung Implemented a web interface that allows users to upload/convert a tab delimited text file
Karen Lostritto - Molinaro lab (entered Fall 2006)
Karen Lostritto

The aim of Karen's research is to develop methods for discovering patterns in high-dimensional data, specifically in survival data. She is studying non-parametric algorithms for partitioning observations based on their covariate values with the aim of minimizing the residual sum of squares for each partition. She has extended the partDSA (partitioning Deletion Substitution Addition algorithm) to accommodate censored survival data by implementing the Inverse Probability Censoring weighting scheme.

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Paul Lizardi Studied the basis for hypermethylation and hypomethylation in CpG islands
Steven Kleinstein Model mutations of B-cells using a discrete stochastic model so that the number of mutations in each B-cell could be tracked
Annette Molinaro Focused on the challenge of missing data imputation when employing non parametric search algorithms

Publications:

  • Molinaro A, Lostritto K. Book Chapter: "Statistical Resampling Techniques for Large Biological Data Analysis." Statistical Bioinformatics. Jae K. Lee. John Wiley & Sons, 2009.
Michael Sneddon - Emonet lab (entered Fall 2006)
Michael Sneddon

Michael works on developing new techniques, algorithms, and software to efficiently handle the complexity of modeling large and multiscale biological systems. His particular emphasis is on stochastically simulating biochemical reaction networks that are generally intractable using traditional simulation methods. He is applying his new techniques to model the bacterial chemotaxis system in order to study how single cells and populations of cells process information and communicate as they navigate complex environments.

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Steven Kleinstein Developed new computational techniques and software to statistically characterize white blood cell trafficking that was imaged in lymph nodes of live mice
Michael Snyder Worked on microarray based experiments to study how differences in transcription factor binding between several strains of yeast affect observed phenotype
Thierry Emonet Created a stochastic model of the bacterial flagellar motor and used it to study how slow fluctuations in the chemotaxis signaling system affect the swimming behavior of single cells

Publications:

  • Hauser AE, Junt T, Mempel TR, Sneddon MW, Kleinstein SH, Henrickson SE, von Andrian UH, Shlomchik MJ, Haberman AM. Definition of germinal-center B cell migration in vivo reveals predominant intrazonal circulation patterns. Immunity. 2007 May;26(5):655-67.
Emmett Sprecher - Tuck lab (entered Fall 2006)
Emmett Sprecher

Emmett works on creating system models of breast cancer pathology, with a focus on HER2+ breast cancers. He is currently investigating copy number variations in different patients, as well as HER2+ breast cancer cell lines.

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Mark Gerstein Investigated the related network features of bottlenecks
David Tuck Developed a software tool to help with network analysis
Steven Kleinstein Investigated the combined effects of IFN-Lambda with IFN-alpha or IFN-gamma on IFN-stimulated gene expression and Hepatitis C Virus replication in hepatocytes

Publications:

  • Yu K, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol. 2007 Apr 20;3(4):E59.
Mohamed Uduman - Kleinstein lab (entered Fall 2006)
Mohammed Uduman

Mohamed's research involves computational analysis of the immune system. Specifically, he is studying Immunoglobulin (Ig) receptor sequences and lineage trees.

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Kenneth Kidd Created interactive simulations to model several population genetics principles
Steven Kleinstein Investigated lineage trees of the B-cell populations for various selection values
Perry Miller/Hongyu Zhao Identified significant genes associated with Age-related Macular Degeneration using a simple GWAS analysis

Publications:

  • Hershberg U, Uduman M, Shlomchik MJ, Kleinstein SH. Improved methods for detecting selection by mutation analysis of Ig V region sequences. Int Immunol. 2008 May;20(5):683-94.
Pedro Alves - Gerstein lab (entered Fall 2007)

Pedro is studying yeast genes that are essential to its quiescent state by integrating various data sources, such as gene expression studies, sub-cellular protein localization, and protein-protein interaction networks. He is also working on demonstrating the important relationships between quiescence and human neurodegenerative diseases.

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Mark Gerstein The study of neurodegenerative diseases
Michael Krauthammer Focused on the use of text mining to find related articles
Michael Snyder Validated the predictor for identifying genes in yeast that were essential to its G0 (quiescent) state

Publications:

  • Alves P, Arnold RJ, Clemmer DE, Li Y, Reilly JP, Sheng Q, Tang H, Xun Z, Zeng R, Radivojac P. Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. Bioinformatics. 2008 Jan 1; 24(1):102-109.
  • Alves P, Arnold RJ, Novotny MV, Radivojac P, Reilly JP, Tang H. Advancement in protein inference from shotgun proteomics using peptide detectability. Pac Symp Biocomput, 409-420 (2007).
  • Tang H, Arnold RJ, Alves P, Xun Z, Clemmer DE, Novotny MV, Reilly JP, Radivojac P. A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics. 2006 Jul 15;22(14):e481-488.
Raymond Auerbach - Gerstein lab/Snyder lab (entered Fall 2007)

Ray is working on several projects including: 1) Analyzing results from ChIP-Sequencing experiments to locate novel transcription factor binding site patterns in the human and worm genomes, 2) developing new methods to analyze large datasets inherent in next-generation sequencing and metagenomics experiments, and 3) applying existing biological information/annotations to the results of ChIP-Seq experiments. He has also helped develop a new scoring method for ChIP-Seq data as well as a method to analyze data from barcoded libraries on the Illumina next-generation sequencing platform.

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Mark Gerstein Examined transcription factor binding site patterns in yeast
Michael Snyder Analyzed the data produced by chIP-Seq experiments
Perry Miller/Kei Cheung Explored possible data representation methods/structures for high-throughput, next-generation sequencing data

Publications:

  • Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrancois P, Struhl K, Gerstein M, Snyder M. Mapping Accessible Chromatin Regions Using Sono-Seq. PNAS. August 18,2009.
  • Vogler AJ, Birdsell D, Price LB, Bowers JR, Beckstrom-Strernberg SM, Auerbach RK, Beckstrom-Sternberg JS, Johansson A, Clare A, Buchhagen JL, Petersen JM, Pearson T, Vaissaire J, Dempsey MP, Foxall P, Engelthaler DM, Wagner DM, Keim P. Phylogeography of Francisella Tularensis: Global Expansion of a Highly Fit Clone. Journal of Bacteriology. 191 (2009) 2474-84.
  • Lefrancois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M. Efficient Yeast ChIP-Seq Using Multiplex Short-Read DNA Sequencing. BMC Genomics. 10 (2009) 37.
  • Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnology. 2009 Jan;27(1):66-75.
  • Tuanyok A, Leadem BR, Auerbach RK, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, Mayo M, Wuthiekanun V, Brettin TS, Nierman WC, Peacock SJ, Currie BJ, Wagner DM, Keim P. Genomic islands from five strains of Burkholderia pseudomallei. BMC Genomics. 2008 Nov 27;9:566.
  • Vogler AJ, Driebe EM, Lee J, Auerbach RK, Allender CJ, Stanley M, Kubota K, Andersen GL, Radnedge L, Worsham PL, Keim P, Wagner DM. Assays for the rapid and specific identification of North American Yersinia pestis and the common laboratory strain CO92. Biotechniques. 2008 Feb;44(2):201, 203-4, 207.
  • Tuanyok A, Auerbach RK, Brettin TS, Bruce DC, Munk AC, Detter JC, Pearson T, Hornstra H, Sermswan RW, Wuthiekanun V, Peacock SJ, Currie BJ, Keim P, Wagner DM. A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. J Bacteriol. 2007 Dec;189(24):9044-9.
  • Beckstrom-Sternberg SM, Auerbach RK, Godbole S, Pearson JV, Beckstrom-Sternberg JS, Deng Z, Munk C, Kubota K, Zhou Y, Bruce D, Noronha J, Scheuermann RH, Wang A, Wei X, Wang J, Hao J, Wagner DM, Brettin TS, Brown N, Gilna P, Keim PS. Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS ONE. 2007 Sep 26;2(9):e947.
  • Auerbach RK, Tuanyok A, Probert WS, Kenefic L, Vogler AJ, Bruce DC, Munk C, Brettin TS, Eppinger M, Ravel J, Wagner DM, Keim P. Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. PLoS ONE. 2007 Aug 22;2(1):e770.
  • Lee K, Costerton JW, Ravel J, Auerbach RK, Wagner DM, Keim P, Leid JG. Phenotypic and functional characterization of Bacillus anthracis biofilms. Microbiology. 2007 Jun;153(Pt 6):1693-701.
  • Touchman JW, Wagner DM, Hao J, Mastrian SD, Shah MK, Vogler AJ, Allender CJ, Clark EA, Benitez DS, Youngkin DJ, Girard JM, Auerbach RK, Beckstrom-Sternberg SM, Keim P. A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis. PLoS ONE. 2007 Feb 21;2(2):e220.
Lukas Habegger - Gerstein lab/Snyder lab (entered Fall 2007)
Lukas Habegger

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Michael Snyder Established three single-stranded cDNA libraries from different human cell lines for high-throughput 454 sequencing
Steven Kleinstein Investigated the migration patterns of B-cells that are entering and existing the germinal center during affinity maturation
Mark Gerstein Mapped the tanscriptome of the human genome using high-throughout sequencing
Rebecca Robilotto - Gerstein lab (entered Fall 2007)
Rebecca Robilotto

Becky is studying comparative genomics among multiple species, including worm, fly, human and yeast. She is reviewing different ortholog resources that are available to help determine a final gene pair list. She is also looking at available tandem mass spectrometry data to try to determine a new way to confirm possible genome annotations.

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Michael Krauthammer Investigated detailed relationships between a gene and disease
Mark Gerstein Examined comparative genomics of functional elements in C. elegans and C. briggsae
Michael Snyder Used the ChIP-seq experimental method in order to identify transcription factor binding sites in C. elegans

Publications:

  • Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biology 2009, 10:R2.
Taiwo Togun - Molinaro lab/Tuck lab (entered Fall 2007)
Taiwo Togun

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Hongyu Zhao Employed a method that uses both gene expression data and pathway information
Michael Snyder Performed the ChIP procedure for the precipitation of binding sites of RNA polymerase II (pol II), and acetylated Histone IV (Ac-H4)
Paul Lizardi Classified each known SVA sequence in the genome into the consensus sub-family to which it is best aligned
Annette Molinaro Analyzed the lung cancer survival dataset to determine predictors (combination of variables) that determine life expectancy of patients
Christopher Bolen - Kleinstein lab (entered Fall 2008)

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Kenneth Kidd Expanded upon the work by McQuillan et al. by using their method on the large genotyping dataset
Mark Gerstein Examined the change in the numbers of ABC transporters among bacteria under various environmental conditions
Steven Kleinstein Examined the process of affinity maturation of antibodies
Xiaowei Chen - Zhao lab/Slack lab (entered Fall 2008)
Taiwo Togun

Xiaowei's research focus is genome wide association studies and analysis of next generation sequencing data. She is currently working on a cancer resequencing project to identify the ovarian-cancer-related variations in 3' UTRs and microRNAs. She is also working with Clip-seq data to find the RNAs interacting with protein Lin-28.

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Frank Slack Identification of novel microRNAs and their targets in life span regulation
Tae Hoon Kim Cross species analysis of CTCF-binding sites and CTCF purification
Hongyu Zhao Crohn's disease genome wide association study based on single SNP and haplotype analysis
Mark Gerstein Metagenomic bacteria identification by characteristic 16s rRNA oligonucleotides
Jing (Jane) Leng - Gerstein lab/Noonan lab (entered Fall 2008)

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James Noonan Investigated the regulators to identify enhancers regulating microRNAs
David Tuck Identified RIDGEs in breast cancer using microarray expression data
Mark Gerstein Identified translocations in the human genome with paired-end (PE) sequencing data
Lucas Lochovsky - Gerstein lab (entered Fall 2008)

Lucas' current research involves investigating the saturation of human transcription factor binding sites (TFBSes) with chromatin immunoprecipitation sequencing (ChIP-seq) of human cell lines used in the ENCODE project. He has also worked on using expression levels of interacting gene networks to predict prostate cancer phenotypes.

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Kei Cheung Investigated the benefits and challenges involved in producing and maintaining a wiki for high-throughput sequencing (HTS) data
Michael Snyder Performed RNA-Seq on two strains of yeast: Saccharomyces bayanus and Saccharomyces mikitae
Mark Gerstein Investigated gene networks that allow discernment between prostate cancer patients
Haisu Ma - Zhao lab (entered Fall 2008)

Haisu is interested in the analysis of human gene coexpression networks using microarray data. She is also involved in the DREAM4 project to reconstruct gene regulatory networks from simulated steady-state and time–series data.

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Steven Kleinstein Worked on a differential equation model to identify top regulators of IRF2 using time continuous expression data
Mark Gerstein Analyzed pesudogene evolution using a maximum likelihood method
Hongyou Zhao Worked on the construction of gene coexpression networks using GENEVAR data of HapMap samples
Kelly Stanton - Tuck lab (entered Fall 2008)

Kelly is looking for micro RNA targets in invasive micropapillary breast cancer. He is developing a new method for gene regulatory network reconstruction to find novel interactions in primitive erythropoesis.

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Mark Gerstein Examined an Alzheimer gene expression set
David Tuck Studied the dynamic bayesian analysis of primitive erythrocyte gene expression
Thierry Emonet The goal was to add functionality for modeling systems with discrete physical compartments
Jing (Crystal) Wang - Gerstein lab/Noonan lab (entered Fall 2008)

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Michael Snyder Worked on RNA sequencing technology, and applied this technology in yeast mating mechanisms study and compared transcriptomes among different yeast species
James Noonan Identified conserved elements with primate specific substitutions
Mark Gerstein Studied allele-specific expression by RNA-Seq

CBB Graduates

Valentin Dinu - PhD, May 2007 (entered 2003)
Assistant Professor, Biomedical Informatics, Arizona State University

Dissertation: "Informatics Approaches to Translational Research: Management and Analysis of Clinical and High Density Genomic Data"

Yin Liu - PhD, December 2007 (entered 2002)
Assistant Professor, Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston
Adjunct Assistant Professor, Department of Biomedical Engineering, The University of Texas at Austin

Dissertation: "Statistical Modeling of Biological Interactions in Eukaryotes using Genomics and Proteomics Data"

Tom Royce - PhD, December 2007 (entered 2002)
Bioinformatics Scientist, Illumina, San Diego, California

Dissertation: "Tiling Microarray Informatics"

Xiaowei Zhu - PhD, December 2008 (entered 2002)

Dissertation: "Mapping Regulatory Networks Using Genomic and Proteomic Approaches"

Sujun Hua - PhD, May 2009 (entered 2002)
Postdoctoral Fellow, DePinho Lab, Dana-Farber Cancer Institute

Dissertation: "Genomic Studies on Nuclear Receptor-Mediated Transcriptional Networks in Breast Cancer Cells"

Tara Gianoulis - PhD, May 2009 (entered 2003)
Postdoctoral Fellow, Church Lab, Harvard Medical School

Dissertation: "Mining Biological Complexity: Cross Integration of Large-Scale Metagenomics, Environmental, and Chemical Datasets"

David Ballard - PhD, May 2009 (entered 2004)
Assistant Investigator, Feinstein Institute for Medical Research

Dissertation: "Integration of Genomic Data to Identify Genes and Pathways Associated with Disease"

Sara Nichols - PhD, December 2009 (expected) (entered 2003)
Postdoctoral Fellow, McCammon Group, University of California, San Diego

Dissertation: "High-throughput Methods in Computer-aided Drug Design Pertaining to Flexibility, Selectivity and Lipophilicity"