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Graduates PreDocs

Current Predoctoral Trainees

Ryan Powles

NLM Predoctoral Trainee: 9/1/16 –

Research Supervisor: Hongyu Zhao, PhD (Biostatistics, Genetics and Statistics and Data Science)

Research: Ryan Poweles is currently in the fourth year of graduate training. Ryan applies network level analysis tools and clonal evolution methods to sequencing data to characterize resistance in breast cancer to subtype-specific targeted therapies.

Q. Lu*, R. L. Powles*, S Abdallah, D. Ou, Q. Wang, Y. Hu, Y. Lu, W. Liu, B. Li, S. Mukherjee, P. K. Crane, H. Zhao. Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease. PLOS Genetics, 2017

Y. Hu*, Q. Lu*, R. Powles, X. Yao, C. Yang, F. Fang, X. Xu, H. Zhao. Leveraging functional annotations in genetic risk prediction for human complex diseases. PLoS Computational Biology, 2017

Q. Lu*, R. L. Powles*, Q. Wang, B. J. He, H. Zhao. Integrative tissue-specific functional annotations in the human genome provide novel insights on many complex traits and improve signal prioritization in genome wide association studies. PLoS Genetics, 2016

* indicates co-first authors

Jay Stanley

NLM Predoctoral Trainee: 9/1/17 –

Research Supervisor: Smita Krishnaswamy

Research: Jay Stanley is currently in the second year of graduate training. Jay is studying learned representations of biological data, in particular graph representations and their processing

Alexandra Signoriello

NLM Predoctoral Trainee: 9/1/15 –

Department: Interdepartmental Program in Computational Biology and Bioinformatics

Research Supervisor: Corey O’Hern, PhD (Mech Engineering, Physics, Applied Physics)

Research: Alexandra Signoriello is currently in the fifth year of graduate training. Alexandra's research is focused on computational modeling of the packing and collective motion of cells in monolayers, tissues, and tumors.  She has developed molecular dynamics simulations of interacting deformable cells (modeled in two dimensions as polygons with a large number of sides) and studied the structural and mechanical properties of cell monolayers near the confluent regime. She will compare the results from her simulations to experimental studies of growing keratinocyte monolayers.  Future work will involve developing a model of interacting deformable polyhedral cells in 3D. This work is performed in collaboration with Prof.  Marcus Bosenberg from the Departments of Pathology and Dermatology at Yale's School of Medicine.

Kevin Lopez

NLM Predoctoral Trainee: 9/1/15 –

Department: Interdepartmental Program in Computational Biology and Bioinformatics Research:

Research Supervisor: Michael Krauthammer, PhD (Pathology) and Cynthia Brandt, MD (Emergency Medicine and Anesthesiology)

Research: Kevin Lopez is currently in the third year of graduate training. Kevin is working on image classification using deep learning and convolutional neural networks. He is also working on expanding the capabilities of Yale Image Finder by applying deep learning methods to classify images from PubMed publications.

Mohammed Khan

NLM Predoctoral Trainee: 9/1/14 –

Department: Molecular, Cellular, and Developmental Biology

Research Supervisor: Michael Krauthammer

Research: Mohammed Khan is currently in the fourth year of graduate training. He is designing computational tools to further understand the role of different classes of RNA and how they may contribute to different diseases, especially cancer. The classes of RNAs he is investigating includes the protein-encoding mRNA and long non-coding RNA (lncRNA). Greater insight in the biological function of these RNA classes could help identify potential disease markers and targets to improve disease diagnosis & medical treatment.

*Peter Williams

NLM Predoctoral Trainee: 7/1/14 – 7/31/17

Department: Applied Physics

Research Supervisor: Corey O’Hern, PhD ( Mech Engineering, Physics, Applied Physics)

Research: Peter Williams is currently in the fifth year of graduate training. His research focuses on computational studies of crowding in the cytoplasm of bacterial cells. He has performed Langevin dynamics simulations to measure the growth of the structural relaxation time in model systems that mimic the dense environment of the cell.

Jennifer Gaines

NLM Predoctoral Trainee: 9/1/13 – 8/13/17

Department: Interdepartmental Program in Computational Biology and Bioinformatics

Research Supervisor: Corey O’Hern, PhD (Mech Engineering, Physics, Applied Physics)

Research: Jennifer Gaines is currently in the fifth year of graduate training. Jennifer's research focuses on computational modeling of protein structure.  In particular, she has studied the collective repacking of side chains in protein cores, determined the packing density of protein cores using an all-atom explicit hydrogren model, and compared these results to dense packings of non-spherical particles.  She is currently working on assessing the changes in protein structure that occur following mutations to residues in protein cores, with the goal of determining protein stability in response to mutations.  This work is done in collaboration with Prof. Lynne Regan in the Department of Molecular Biophysics & Biochemistry at Yale.

Michael Klein

NLM Predoctoral Trainee: 9/1/13 –

Department</>: Interdepartmental Program in Computational Biology and Bioinformatics

Research Supervisor: Hongyu Zhao, PhD (Biostatistics), David Stern, PhD (Pathology, Yale Cancer Center)

Research: Michael Klein is currently in the fifth year of graduate training. Michael’s current research focus is to understand the etiology of human cancers. Although much is known about individual oncogenes and how they contribute to cancer, very little is understood about how these individual oncogenes cooperate to cause malignancy. To this end Michael is developing computational approaches to infer the combinations of oncogenic events that are required for malignancy. He has also worked on developing GRAPE, a computational method for detecting abnormal pathway behavior from gene expression profiles. GRAPE is a template-based method and is robust to batch effects.

Klein MI, Stern DF, and Zhao H. GRAPE: A pathway template method to characterize tissue-specific functionality from gene expression profiles. BMC Bioinformatics, 18:317 (June 2017).

Langdon CG, Platt JT, Means RE, Iyidogan P, Mamillapalli R, Klein MI, Held, MA, Lee JW, Koo JS, Hatzis C, Hochster HS, and Stern DF. Combinatorial Screen of Pancreatic Adenocarcinoma Reveals Sensitivity to Drug Combinations Including Bromodomain Inhibitor plus Neddylation Inhibitor. Molecular Cancer Ther. 16(6); 1041-53, 2017.

Langdon CG, Held MA, Platt JT, Meeth K, Iyidogan P, Mamillapalli R, Koo AB, Klein M, Liu Z, Bosenberg MW, and Stern DF: The broad-spectrum receptor tyrosine kinase inhibitor dovitinib suppresses growth of BRAF-mutant melanoma cells in combination with other signaling pathway inhibitors. Pigment Cell Melanoma Res. 2015 Jul; 2015 May 6. PMID: 25854919.

Recent Predoctoral Students

Stefan Avey

NLM Predoctoral Trainee: 9/1/13 - 8/31/15

Current position: Sr. Statistician Position @ Johnson & Johnson

Avey, S., ... Kleinstein, S. H. (2017). Multiple network-constrained regressions expand insights into influenza vaccination responses. Bioinformatics, 33(14), pp. i208-i216. doi: 10.1093/bioinformatics/btx260.

The HIPC-CHI Signatures Project Team, HIPC-I Consortium. (2017). Multi-cohort analysis reveals baseline transcriptional predictors of influenza vaccination responses. Science Immunology, 2(eaal4656), pp. 113. doi: 10.1126/sciimmunol.aal4656.

Paul Baranay

NLM Predoctoral Trainee: 9/1/12 - 5/31/14

Department: Interdepartmental Program in Computational Biology and Bioinformatics

Research: Paul Baranay studied ChIP-seq data from hematopoietic stem cells to identify differential expression of transcription factors. He completed the requirements for the MS degree in Computational Biology and Bioinformatics, receiving the degree in December. 2014.

Current Position: Lead Data Engineer, Wiser

Christopher Bolen (Mentor: Steven Kleinstein)

NLM Predoctoral Trainee: 9/1/08 - 6/30/13

Research: Christopher Bolen studied the rates of response to treatment of HCV in different individuals by using a combination of pretreatment gene expression data and patient demographic data to predict the patient's response. He designed a method to be used to predict the specific cell subset responsible for the upregulation of a set of genes in a mixed cell population.

Current position: Associate Scientist, Genentech, Inc.

Bolen CR, Robek MD, Brodsky L, Schulz V, Lim JK, Taylor MW, Kleinstein SH, (2013), The blood transcriptional signature of chronic hepatitis C virus is consistent with an ongoing interferon-mediated antiviral response. Journal of Interferon & Cytokine Research: The Official Journal of The International Society for Interferon and Cytokine Research. 33(1): 15-23. PMCID: PMC3539252.

Bolen CR, Ding S, Robek MD, Kleinstein SH, (2013), Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes reveals a stable hierarchy of gene expression. Hepatology (Baltimore, Md.). 59(4): 1262-72. PMCID: PMC3938553.

Christopher Fragoso

NLM Predoctoral Trainee: 9/1/13 - 6/30/17

Current position: Postdoc @ UC Berkeley

Christopher A. Fragoso, Maria Moreno, Zuoheng Wang, Christopher Heffelfinger, Lady J. Arbelaez, John A. Aguirre, Natalia Franco, Luz E. Romero, Karine Labadie, Hongyu Zhao, Stephen L. Dellaporta, and Mathias Lorieux. Genetic architecture of a rice nested association mapping population. G3: Genes, Genomes, Genetics 7.6 (2017): 1913-1926.

Christopher Heffelfinger, Christopher A. Fragoso, Mathias Lorieux. Constructing linkage maps in the genomics era with MapDisto 2.0. Bioinformatics (2017): btx177.

Christopher A. Fragoso, Christopher Heffelfinger, Hongyu Zhao and Stephen L. Dellaporta. Imputing Genotypes in Biallelic Populations from Low-Coverage Sequence Data. Genetics 115 (2016). Publicly available:

Christopher Heffelfinger, Christopher A. Fragoso, Maria A. Moreno, John D. Overton, John P. Mottinger, Hongyu Zhao, Joe Tohme and Stephen L. Dellaporta. Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC genomics 15.1 (2014):979.

Thomas P. Howard III, Andrew P. Hayward, Anthony Tordillos, Christopher A. Fragoso, Maria A. Moreno, Joe Tohme, Albert P. Kausch, John P. Mottinger, Stephen L. Dellaporta. Identification of the maize gravitropism gene lazy plant1 by a transposon-tagging genome resequencing strategy. PloS one 9.1 (2014).

Namita Gupta

NLM Predoctoral Trainee: 9/1/11 - 7/31/15

Current position: Associate Bioinformatics Scientist, Regeneron Pharmaceuticals

Matthew Holford (Mentors: Michael Krauthammer and Kei Cheung)

NLM Predoctoral Trainee: 9/1/09 - 4/15/14

Research: Matt Holford built an integrative data warehouse containing different types of data related to cancer from different sources. He is used this database to explore research issues related to semantic data mining using Semantic Web technologies.

Current position: Senior Consulting Engineer, Attivio

Mate Nagy

NLM Predoctoral Trainee: 9/1/11 - 8/31/16

Current position: Computational Biology Scientist, NeoGenomics

Rebecca Robilotto (Mentor: Mark Gerstein)

Research: Rebecca Robilotto studied comparative genomics among multiple species, including worm, fly, human, and yeast. This work included identification of pseudogenes in the multiple organisms, as well as comparing them to other functional elements in the genome. One goal was to determine whether pseudogenes may have a type of regulatory role.

Current position: Data Scientist,True&Co

Kelly Stanton (Mentors: Yuval Kluger and David Tuck)

NLM Predoctoral Trainee: 7/21/08 - 7/20/13

Research: Kelly Stanton is studying erythrocytes and leukemia and particularly a cohort of RNA-sequence data. He is trying to identify alternative splice events and fusion proteins and determine their role in pathogenesis. He is also exploring techniques for non-linear dimensionality reduction of point cloud data and signal processing. Finally he is continuing work on an invasive micropapillary data set, and has determined leads for characteristic genes of the disease that are currently in experimental validation.

Current position: PostDoc Associate, Yale University

Mohamed Uduman (Mentor: Steven Kleinstein)

Research: Mohamed Uduman’s research involved computational analysis of the immune system. Specifically, he studied Immunoglobulin (Ig) receptor sequences and lineage trees.

Current position: Self Employed

Jason Vander Heiden

NLM Predoctoral Trainee: 9/1/11 - 6/30/16

Current position: Postdoctoral, Yale University