Students & Research

Daniel Gadala-Maria - Kleinstein lab (entered Fall 2009)
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Daniel is studying the antibody repertoire of humans. He is currently working on computational and graph-theoretic methods to sort into clonal lineages immunoglobulin data obtained from next-generation sequencing of blood samples. He also aims to study mutation patterns and track changes in the selection pressures acting upon these clones which may arise in response to antigen exposure.

 
Namita Gupta - Kleinstein lab (entered Fall 2011)
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Namita is developing computational methods to analyze large repertoires of immunoglobulin sequences generated by new sequencing technologies. She is interested in determining if the nucleotide sequence of an antibody can predict the virus or bacteria to which it binds.

 
Tingting Jiang - Kluger lab/ - Pusztai lab (entered Fall 2011)
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Tingting’s research is focused on analyzing and integrating multiple next generation sequencing data to identify driving mutation of breast cancer or other genomic markers that could help distinguish cancer subtypes. She’s also interested in finding proper measurement of cancer heterogeneity through genomics data.

 
Mate Nagy - Krauthammer lab/ - Cheung lab (entered Fall 2011)
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Mate is working in image mining. More specifically, he is using convolutional networks and other deep learning methods on images from PubMed publications to classify them and to find deeper information in them. He is also working on expanding the capabilities of Yale Image Finder by developing new tools for a variety of tasks by using semantic technologies.

Jason Vander Heiden - Kleinstein lab (entered Fall 2011)
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Jason is currently working on developing computational tools to analyze high-throughput sequencing data of lymphocyte receptors. He is applying these tools to studies characterizing B cell receptor diversity in influenza vaccination responses, West Nile virus infections, and multiple sclerosis.

 
Stefan Avey - Kleinsten lab (entered Fall 2012)
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Stefan’s research focuses on understanding the early innate immune response to influenza infection and vaccination. He is interested in discovering immune signatures of response as well as developing methods to more accurately model immunological systems.

Christopher Fragoso - Zhao lab/ - Dellaporta lab (entered Fall 2012)

Chris Fragoso is co-advised by Drs. Hongyu Zhao and Stephen Dellaporta. Chris is interested in statistical genomics. Specifically, he is interested in developing new methods to study genetic diversity in populations. Studying the genetic diversity of crop plants such as rice and maize offers insight into challenges surrounding food security.

Michael Klein - Zhao lab/ - Stern lab (entered Fall 2012)
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Michael’s research is in personal cancer genomics. He develops methods to identify what specific biological processes are perturbed in individual tumors based on the transcription profiles of those tumors. A major point of emphasis is that the methods are robust to choice of experimental platform and do not require any population level normalization.

Shantao Li - Gerstein lab (entered Fall 2012)
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Shantao’s research focuses on discovering and interpreting genetic variations in human populations as well as normal/cancer tissues. He develops his own algorithms and computational tools. He is also very interested in graphs and networks.

 
Cong Liang - Wagner lab (entered Fall 2012)
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Cong is investigating the phylogenetic tree-likeness in cell type evolution with their transcriptomic data. She is also interested in developing a model for cell type comparison with regulatory networks inferred from DNaseI footprints.

 
Ruijie Song - Acar lab (entered Fall 2012)

Ruijie’s research focuses on computational modeling of gene networks in yeast, generating predictions of network behavior to be experimentally tested by his fellow lab members. He is particularly interested in whether and how network dosage invariance affects other properties of the network.

Qian Wang - Zhao lab/ - Gelernter (entered Fall 2012)
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Qian is interested in integrating genomic data to get better understanding of biological mechanisms of some psychological disorders, such as substance abuse and depression disorders.

Vincent Zhao - Zucker lab (entered Fall 2012)
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Vincent is interested in understanding both low-level and high-level nervous system structures and functions. We build statistical models to model data encoding and decoding and the network structures of the nervous system. Currently, our research is focused on studying the connections among high-order statistics, edge and curvature detection in visual system, and the underlying nervous system structure.

Jennifer Gaines - O'Hern lab (entered Fall 2013)
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Jennifer focuses on modeling protein structure using a hard sphere model of atomic interactions. Specifically, she is developing the model to predict the effects of mutations on peptide-protein binding interactions.

Mengting Gu - Gerstein lab (entered Fall 2013)
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Mengting’s research involves processing next-generation sequencing data. She is interested in enhancer predictions and other functional annotations of the genome.

Mengting’s research involves processing next-generation sequencing data. She is interested in enhancer predictions and other functional annotations of the genome.

Alexandra Signoriello - O'Hern lab/ - Bosenburg lab (entered Fall 2013)
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Alexandra’s research seeks to understand how signaling and physical interactions between subsets of cancer stem cells regulate the function and spatiotemporal evolution of cancerous tumors. Her focus is on melanoma and other types of skin cancer.

 
Luan Chen - Steven Kleinstein (entered Fall 2014) (entered Fall 2012)
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Luan is currently working on large-scale characterization of B cell immunoglobulin (Ig) repertoires. She uses mostly statistical and machine learning methods that enable the extraction of useful information from raw data. Recent projects include a Myasthenia gravis specific antibody sequencing study. This research will help in understanding the physiological basis of the disease and the role of acetylcholine-receptor-specific antibodies, therefore providing a model for defining other antibody-mediated disorders as well.

 
Donghoon Lee - Gerstein lab (entered Fall 2014)
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Donghoon’s research has primarily focused on cancer genomics. He works on a computational method that combines genomic, transcriptomic, and epigenomic data from various next-generation sequencing technologies to study how post-transcriptional regulation and splicing machinery are affected in cancer.

Xiaotong Li - Gerstein lab/ - Pusztai lab (entered Fall 2014)
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Xiaotong is interested in next-generation sequencing data analysis, with a major focus on breast cancer. Currently she is working on whole genome sequencing analysis on inflammatory breast cancer, and heterogeneity analysis.

 
Ryan Powles - Zhao lab (entered Fall 2014)
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Ryan is interested in using statistical methods to better aggregate epigenetic annotation data in the human genome. To this end, he hopes to leverage this information to more effectively assess and characterize genetic variation and disease.

 
Jun Zhao - Kluger lab/ - Flavell lab (entered Fall 2014)
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Jun’s research focuses on the analysis of high-throughput sequencing data, RNA-seq, CRISPR, CLIP-Seq, etc. The goal is to help understand the genetic mechanisms of immune-related biological processes.

 
Dingjue Ji - Zhao lab (entered Fall 2015)

Frank is working on spatio-temporal transcriptomic data of brain. He is interested in developing new methods to identify the expression pattern of specific genes related to brain development. The new approaches are expected to help to understand the mechanisms of brain diseases like ASD.

Kevin Lopez - Krauthammer lab/ - Brandt lab (entered Fall 2015)
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Kevin works 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.

Quan Zhou - Kleinstein lab (entered Fall 2015)
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Julian works with high-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) data, especially in the context of B cell-mediated autoimmune diseases. He is interested in developing novel methods for inferring B cell lineages that help shed light on their developmental pathways.