Karl Keat
Graduate Student
A301 Richards Building
3700 Hamilton Walk, Philadelphia, PA 19104
Twitter
ORCID
GitHub
LinkedIn
Current Projects
- Using genomics, machine learning, and multi-omics data to improve drug response prediction and precision medicine.
Education
Work Experience
- Harvard Summer Institute in Biomedical Informatics (Sunyaev Lab) - Summer 2019
- Broad Summer Research Program (Regev Lab) - Summer 2018
- TecBio REU at The University of Pittsburgh (Cooper Lab) - Summer 2017
- NIH Summer Internship Program (Baxevanis Lab) - Summer 2015, 2016
Publications:
For the list of my publications please visit Google Scholar
Rachit Kumar
Graduate Student
A301 Richards Building
3700 Hamilton Walk, Philadelphia, PA 19104
Github
Website
Google Scholar
Current Projects
- Incorporation of domain knowledge in a domain-agnostic way using network representations of data and known relationships
- Developing methods of representing patients that allow us to identify treatment plans for individual patients
- Using machine learning and deep learning to improve clinical and basic science understanding through rigorous hypothesis generation from preexisting data
Education
- MD-PhD, University of Pennsylvania, 08/2020-Present
Doctor of Medicine, Perelman School of Medicine, University of Pennsylvania, 08/2020-Present
Doctor of Philosophy, Genomics and Computational Biology, University of Pennsylvania, 08/2022-Present
- B.S. in Biomedical Engineering, Georgia Institute of Technology, 08/2016-05/2020
Work Experience
Publications
For the list of my publications please visit Google Scholar
Daniel Hui
Graduate Student
A301 Richards Building
3700 Hamilton Walk, Philadelphia, PA 19104
Current Projects
I am interested in the genetic basis for human traits and diseases, with a focus on cardiometabolic diseases and related anthropometric traits. I am especially interested in using individuals from diverse ancestry and environment in order to facilitate discovering and quantifying the effects of different genetic loci. I hope the research I conduct will improve human health for populations all around the world, especially for conditions that have a large healthcare burden and are significantly genetic in their etiology.
Education
- University of Pennsylvania, PhD Genomics and Computational Biology, 2019-Present
- University of Pittsburgh, B.S. Computer Science, 2013-2017
Research Experience
- Graduate Research Assistant, University of Pennsylvania, Perelman School of Medicine, Fall 2019 - Present. Advisors: Drs. Marylyn Ritchie and Sarah Tishkoff
- Bioinformatician, Brigham and Women's Hospital, Harvard Medical School, The Broad Institute, September 2019-May 2019
- Undergraduate Research Assistant, Children's Hospital of University of Pittsburgh Medical Center, University of Pittsburgh, May 2014-May 2017
Publications:
For the list of my publications please visit Google Scholar
William Bone
Graduate Student
A301 Richards Building
3700 Hamilton Walk, Philadelphia, PA 19104
Current Projects
Using multi-trait genetic association methods to better understand the genetic etiology of cardiometabolic diseases.
Education
Work Experience
- Recursion Pharmaceuticals 2022
- Data Science InternAgilent Technologies 2015-2017
- Bioinformatics EngineerNational Institutes of Health Undiagnosed Diseases Program 2012 – 2015
- Post-baccalaureate Intramural Research Trainee
Publications:
For the list of my publications please visit Google Scholar
Joseph Park
Graduate Student
A301 Richards Building
3700 Hamilton Walk, Philadelphia, PA 19104
Current Projects
- Understanding how genetic variants predispose to or protect from human disease by cross-referencing DNA sequencing data with phenotype data derived from electronic health records (EHR), with specific interests in rare coding variants and cardiovascular+metabolic diseases
Education
Work Experience
- Chan Laboratory, Harvard Medical School, Brigham and Women's Hospital
2012-2015 - Hofstra University, Department of Mathematics, Dr. Dan Ismailescu
2008-2011 - Beth Israel Medical Center, Department of Surgery, Dr. I Michael Leitman
2008-2011
Publications:
For the list of my publications please visit Google Scholar
Pankhuri Singhal
Graduate Student
A301 Richards Building
3700 Hamilton Walk, Philadelphia, PA 19104
Current Projects
Temporal modeling of patient health trajectories in electronic health records + omic data to
- identify disease comorbidity patterns over time and
- predict next clinical event based on disease path insights
Education
- University of Pennsylvania (Philadelphia, PA) | 2017 – Present
Ph.D. candidate in Genetics - Northeastern University (Boston, MA) | 2017
B.S. in Neuroscience
Work Experience
- Monaghan Laboratory | 2014-2017
Northeastern University, Dept. of Biology
Undergraduate researcher - Editas Medicine | 2015 & 2016
Molecular biology co-op (full time jan-aug)
Publications
For the list of my publications please visit Google Scholar.
Xinyuan (Blair) Zhang
Graduate Student
A301 Richards Building
3700 Hamilton Walk, Philadelphia, PA 19104
Current Projects
Identify pleiotropy across cardiovascular and neurological diseases in electronic health record data using multivariate approaches.
Education
B.S Biotechnology
Northwest A&F University, Xianyang, China
2014
Work Experience
Research Assistant
Internship Agricultural Genomes Institute at Shenzhen
Chinese Academy of Agricultural Sciences
2014-2015
Publications
For the list of my publications please visit Google Scholar
Binglan (Victoria) Li
Graduate Student
A301 Richards Building
3700 Hamilton Walk, Philadelphia, PA 19104
Current Projects
Data integration approach to identify disease status indicating factors, including genetic factors and features from electronic heath records.
Education
B.S Life Sciences
Fudan University, Shanghai, China
2015
Anna Okula Basile
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Graduate Student
Pennsylvania State University
328 Innovation Blvd. Suite 210
Current Projects
Phenome-wide association studies
Education
M.A. Biochemistry
City University of New York: Hunter College
2013
B.S Forensic Toxicology
John Jay College of Criminal Justice
2008
Work Experience
Adjunct Lecturer
City University of New York: Hunter College
2011-2013
Formulation Chemist: Research and Development Laboratory
E.T. Browne Drug Company Inc.
2007-2011
Will Bush
Graduate Student
Center for Human Genetics Research
Vanderbilt University
Current Contact Information
Todd Edwards
Graduate Student
Vanderbilt University
Current Contact Information
Neerja Katiyar
Master's Bioinformatics and Genomics
The Pennsylvania State University
University Park, PA
Emily Holzinger
Graduate Student (Human Genetics)
Vanderbilt University
Nashville, TN
Currently Post-Doctoral fellow at NIH
Carrie Moore
Graduate Student (MD/PhD)
Vanderbilt University
Nashville, TN
Ben Grady
Graduate Student (Human Genetics)
Vanderbilt University
Nashville, TN
Ruowang Li
Graduate Student
512 Wartik Laboratory
Pennsylvania State University
Current Projects
B.S Biology and Biotechnology
Minor in Computer Science
Worcester Polytechnic Institute
2011
Publications
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Dokyoon Kim, Ruowang Li, Scott M. Dudek, Marylyn D. Ritchie. ATHENA: Identifying interactions between different levels of genomic data using grammatical evolution neural network. Translational Bioinformatics Conference (submitted)
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Ruowang Li, E.R. Holzinger, S.M. Dudek, M.D. Ritchie. (2013). Evaluation of parameter contribution to neural network size and fitness in ATHENA for genetic analysis. Genetic Programming Theory And Practice (accepted)
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Marylyn Ritchie, Emily Holzinger, Ruowang Li, Sarah Pendergrass. Next-generation analyses for exploring the genetic architecture of complex traits: meta-dimensional approaches. Nature Reviews Genetics (submitted)
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Marylyn Ritchie, Sarah Pendergrass, Ruowang Li, Emily Holzinger. Meta-dimensional analysis to dissect the architecture of complex traits. Trends in Genetics (submitted)
- Ozlem Yildirim, Ruowang Li, Jui-Hung Hung,Poshen B. Chen,Xianjun Dong,Ly-Sha Ee, Zhiping Weng,Oliver J. Rando, and Thomas G. Fazzio (2011) Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells. Cell 147, 1498–1510 (2011).
- Benjamin R. Carone, Lucas Fauquier, Naomi Habib, Jeremy M. Shea, Caroline E.Hart, Ruowang Li, Christoph Bock, Chengjian Li, Phillip D. Zamore, Alexander Meissner, Zhiping Weng, Hans A. Hofmann, Nir Friedman, and Oliver J. Rando. (2010) Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell (1084-1096, 23 December 2010)
- Quanqin Dai, Yingnan Wang, Yu Zhang, Xinbi Li, Ruowang Li, Bo Zou, JaeTae Seo, Yiding Wang, Manhong Liu, William W. Yu. (2009) Stability Study of PbSe Semiconductor Nanocrystals over Concentration, Size, Atmosphere, and Light Exposure. Langmuir 25 (20), 12320-12324