Alumni

UM Bioinformatics Alumni Information

Subramanian Shankar Ajay
Co-chairs: Brian Athey, Inhan Lee

Postdoctoral Fellow
Genome Informatics Section
NHGRI (National Human Genome Research Inst.)

Thesis Defense - Novel Bioinformatics Approaches for MicroRNA Detection and Target Prediction. MicroRNAs (miRNAs) are regulators of gene expression at the post-transcriptional level. Scientists have not been able to fully unlock their therapeutic potential because their functions and mechanisms of action have not been fully characterized. In this thesis we address shortcomings and provide solutions for detecting miRNAs in a high-throughput manner and for predicting miRNA targets - areas key to understanding miRNA function.

Mark Benson
Chair: Heather Carlson

Postdoctoral Associate
University of Florida

Current research: I am using ab initio quantum mechanics to model the enzymatic mechanism of LpxC and to discover novel inhibitors.

Stewart Chang
Chair: Denise Kirschner, Jennifer Linderman

Postdoctoral Fellow
University of British Columbia

Current research: My research concerns antigen presentation -- the process used by the immune system to identify pathogens as foreign -- and specifically how it occurs during tuberculosis. Mycobacterium tuberculosis, the causative agent of tuberculosis, has been shown to interfere with antigen presentation, and I use mathematical modeling to look at how this happens. In addition genetic differences exist among people that make some of us more or less susceptible to tuberculosis. A number of these differences affect antigen presentation, and I also use computational modeling to look at how these differences might be connected to disease.

Ji Chen
Chair: David States

Researcher
Microsoft, Inc.

Yili Chen
Co-chairs: Jessica Schwartz, David States

Postdoctoral Researcher
Delaware Biotechnology Institute

Current research: Project Develop novel methods or apply currently available algorithms to analyze gene expression data sets and infer genetic networks in order to understand the transcriptional regulation of cellular programs in clostridia and in megakaryocytes.

Yu Chen
Chair: Gordon Crippen

Research Scientist
Insightful, Corp.

Current research: Dr. Chen is currently working on multiple NIH phase II Small Business Innovative Research (SBIR) projects to develop analytical tools and modules for S-PLUS, including mass spectra processing / classification, and clustering algorithms on large data.

Chad Creighton
Co-chairs: Arul Chinnaiyan, Kerby Shedden

Asst. Prof. of Medicine
Baylor College of Medicine

Current research: I primarily work in collaboration with various investigators who want help understanding their data. Recent examples of these collaborative projects include the identification and characterization of the following:

Molecular changes associated with loss of progesterone receptor (PR) expression in human breast cancer (in collaboration with Adrian Lee, Rachel Schiff, and Kent Osborne)

Molecular changes at the microRNA, mRNA, and DNA levels associated with ovarian cancer (in collaboration with Martin Matzuk)

Gene transcription programs activated in the tumorigenic cell subpopulation within breast tumors (in collaboration with Jenny Chang, Jeff Rosen, and Michael Lewis)

insulin-like growth factor factor I (IGF-I) signaling (in collaboration with Adrian Lee) Gene transcription programs involved in the development of resistance of xenograft breast tumors to endocrine therapy (in collaboration with Rachel Schiff and Kent Osborne)

Jayson Falkner
Chair: Philip Andrews

Co-founder
Single Organism Software, Inc. (SOS)

Current research: SOS helps provide commercial services related to scientific data storage, sharing, and analysis.

Damian Fermin
Chair: Gil Omenn

Applications Programmer Intermediate
University of Michigan

Current research: I currently work as a Bioinformatician for the Pathology Department of the University of Michigan. My work involves developing user-friendly interfaces for open source programs for researchers unfamiliar with the linux/unix interface. The goal being to help researchers in the department to leverage these tools which they would otherwise not use. I also provide technical support for researchers who want to run compute-intensive programs on the department cluster.

In addition, I do research in Proteomics with Alexey Nesvizhskii. Currently my research focuses on developing ways to combine and analyze multiple proteomics replicates. Many experiments in proteomics involve control and treated samples often in replicate. However there is currently no software available to combine results from the individual data sets that address variations between replicates.

Xing Li
Chair: Deborah Gumucio

Postdoctoral Fellow
Windber Research Institute

Thesis Defense: Bioinformatic Analysis of Epithlial:Mesenchymal Crosstalk during Mouse Gut Development and Patterning. Microarray technology together with bioinformatics techniques makes it possible to study holistic gene expression profiles during organ and tissue development. This can teach us new lessons about signaling pathways and transcription factors that are responsible for tissue organogenesis.

Arvind Rao
Co-chairs: Doug Engel, Alfred O. Hero III, David States

Lane Fellow
Center for Computational Biology, Carnegie Mellon

Thesis defense: Eukaryotic Transcription is regulated by transcription factor (TF) proteins that are recruited at the proximal promoter as well as distal genomic elements (like enhancers). In this work we present a generalizable in-silico strategy to locate these functional regulatory elements, some of which might lie hundreds of kilobases from the gene, using genomic-sequence, gene expression, and protein-interaction modalities. As a case study, I will examine the previously reported urogenital enhancers of the Gata2 gene from various perspectives (sequence features, annotated expression data and protein interaction). Additionally, recent results from the ENCODE project (http://genome.gov/ENCODE) have made several new observations, some of which will be examined in the context of this problem.

Daniel Rhodes
Chair: Eric Fearon

Co-founder
Compendia Bioscience

Current research: Dan Rhodes received a Ph.D. in Bioinformatics and Cancer Biology from the University of Michigan in 2006. He has six years of experience in the cancer genomics field, having authored more than 20 publications, including several important advances in cancer bioinformatics. He led the development of Oncomine™ and has received several awards for his work including consecutive American Association of Cancer Research Scholar-in-Training Awards, the Harold M. Weintraub Award, and the Team Science Award from AACR.

Carlos Santos
Co-chairs: Brian Athey, David States

CEO
Retinapharma Technologies, Inc.

Thesis defense: This dissertation discusses the use of automated natural language processing for characterization of biomolecular events in signal transduction pathway databases and for summarization and annotation of genomic data within large document collections. An application is presented where natural language processing software, beginning with genomic expression data, automatically identifies and joins disparate experimental observations supporting biochemical interaction relationships between candidate genes. We discuss the need for accurate named entity resolution to the biological sequence databases and how sequence-based approaches can unambigously link automatically extracted assertions to their respective biomolecules in a high-speed manner.

We also demonstrate a system for large-corpus summarization by hierarchical document clustering and conversion into a mapped image. The image allows easy visualization and browsing of large document collections for topics of interest. An initial application of the system explores the prostate cancer literature and compares the performance of the document summarization images in relation to expert human review articles. In a second application, we explore the use of a literature-based system for context-specific functional annotation engine of cancer-related gene signatures.

Peter Ulintz
Chair: Philip Andrews

Postdoctoral Fellow
University of Michigan

Thesis defense: The proteomics field is driven by the need to develop increasingly high-throughput methods for the identification and characterization of proteins. The overall goal of this research is to improve the success rate of modern high-throughput proteomics studies in identifying new proteins. The focus is on developing computational strategies for increasing the number of identifications as well as improving the ability to distinguish new forms of proteins and peptides. Several studies are presented, addressing different points in the proteomics analysis pipeline. Most fundamentally, methods are discussed which aim to improve the final results generated by mass spectrometry database search algorithms. Methods for using modern machine learning algorithms to improve the ability to distinguish correct from incorrect peptide identifications are presented. These techniques have the potential to minimize the need for manual curation of results, providing a significant increase in throughput in addition to increased confidence in identification.

Jianjun Yu
Chair: Arul Chinnaiyan

Bioinformatician
Novartis Oncology, Inc.

Dongxiao Zhu
Chair: Alfred O. Hero, III

Asst. Prof.
University of New Orleans, Dept. of Computer Science

Dr. Zhu's bioinformatics research interest area includes: computational and statistical methods for analyzing genome-wide data, biological network inference, comparative genomics and biological sequence analysis. His applied statistics research interest area includes: applied multivariate analysis, statistical inference and computing, machine learning. In addition, he actively collaborates with biomedical researchers to apply appropriate computational and statistical techniques to solve real-world biomedical problems.