Lab lunch, Sep 2014. Missing: Dan Day, Nils Gehlenborg
Burak Alver, Ph.D. - Postdoctoral Fellow
Burak finished his Ph.D. in experimental heavy ion physics at MIT before joining the lab. He is interested in epigenetics.
Dan Day, B.S. - Graduate student
Dan is a graduate student in the MIT Health Sciences and Technology division, in the BIG (Bioinformatics and Integrative Genomics) program. He spent his summer after junior year in college working in the Park lab and has returned as a grad student. Dan is working on analysis of epigenomic data from next-generation sequencing.
Francesco Ferrari, Ph.D. - Postdoctoral Fellow
Francesco did his graduate work in molecular biology/bioinformatics at the University of Modena and Reggio Emilia in Italy and was a postdoc at the University of Padova before joining the lab.
Nils Gehlenborg, Ph.D. - Postdoctoral Fellow
Nils obtained his bioinformatics Ph.D. from the University of Cambridge and the European Bioinformatics Institute (EBML-EBI). Nils is interested in visualization of large data sets, with applications in cancer genomics.
Lucy Youngsook Jung, Ph.D. - Postdoctoral Fellow
Lucy finished her PhD in the Health Sciences and Technology division at MIT. She now works on analysis of chromatin modifications in Drosophila and other related projects.
Scott Kallgren, Ph.D. - Postdoctoral Fellow
Scott received his PhD in yeast chromatin biology at Columbia and joined the Bioinformatics Informatics Research Training (BIRT) program and the Park lab. He is working to gain expertise in computational biology to complement his wet-lab skills.
Alice Eunjung Lee, PhD - Instructor in Medicine
Alice finished her PhD in bioinformatics and was a research assistant professor at KAIST (Korean Advanced Institute of Science and Technology), where she worked on integrative network and pathway analysis.
Semin Lee, PhD - Postdoctoral Fellow
Semin received his PhD in biochemistry from the University of Cambridge, UK, working on properties of nucleic acid-binding proteins and structural bioinformatics.
Soohyun Lee, PhD - Postdoctoral Fellow
Soo received her bioinformatics Ph.D. from Boston University. She specializes in RNA-seq data analysis and likes anything related to RNA.
Joe Luquette, B.S. - Scientific Programmer
A recent graduate of Boston University, Joe comes up with cool algorithms, designs web servers, and helps out with everything else, when he is not taking algebra courses for fun.
Psalm Mizuki, M.S. - Scientific Programmer
Psalm studied bioinformatics at Rochester Institute of Technology and joined the lab in Dec 2010. She will work on a variety of projects in cancer genomics and epigenetics.
Peter J. Park, Ph.D. - Principal Investigator
More information here.
Andrew Wei Xu, Ph.D. - Postdoctoral Fellow
Andrew received his PhD from University of Ottawa with David Sankoff and did postdoctoral work at EPFL with Bernard Moret before joining the lab.
Lixing Yang, Ph.D. - Postdoctoral Fellow
As a PhD student in Genetics at the University of Georgia, Lixing performed bioinformatic analysis of transposable elements in plants. Now he is interested in cancer genomics.
Mitzi Kuroda, Ph.D. (website) - Brigham and Women's Hospital/Department of Genetics, Harvard Medical School
Robert Kingston, Ph.D. (website) - Chief, Dept of Molecular Biology, Massachusetts General Hospital/Department of Genetics, Harvard Medical School
Isaac S. Kohane, M.D./Ph.D. Lawrence J. Henderson Professor of Pediatrics and Health Sciences and Technology, Harvard Medical School
Mark Johnson, M.D./Ph.D. (website) - Neurosurgery,
Brigham and Women's Hospital & Harvard Medical School
modENCODE chromatin group: Gary Karpen, Ph.D. (Lawrence Berkeley labs), Vince Pirrotta, Ph.D. (Rutgers), and Sally Elgin, Ph.D. (WashU)
Charlie Roberts, M.D./Ph.D. - Dana-Farber Cancer Institute/Harvard Medical School
Jon Seidman, Ph.D. - Department of Genetics, Harvard Medical School
Raju Kucherlapati, Ph.D. - Brigham and Women's Hospital/Department of Genetics, Harvard Medical School
Lynda Chin, M.D. - Dana-Farber Cancer Institute/Department of Genetics, Harvard Medical School
Robert Klose, Ph.D. - Department of Biochemistry, Oxford
Carla Kim, Ph.D. - Children's Hospital Boston/Harvard Medical School
George Daley, M.D./Ph.D. - Children's Hospital Boston/Harvard Medical School
David Scadden, M.D. - Massachusetts General Hospital/Harvard Medical School
Nabeel Bardeesy, Ph.D. - Massachusetts General Hospital/Harvard Medical School
Yang Shi, Ph.D. - Children's Hospital Boston/Harvard Medical School
Erica Larschan, Ph.D. - Molecular Biology, Cell Biology, & Biochemistry, Brown University
Konrad Hochedlinger, Ph.D. - Massachusetts General Hospital/Harvard Medical School
Fred Winston, Ph.D. - Department of Genetics, Harvard Medical School
Stephen Elledge, Ph.D. - Brigham and Women's Hospital/Department of Genetics, Harvard Medical School
Steven A. Greenberg, M.D. (website) - Dept of Neurology, Brigham and Women's Hospital/Harvard Medical School
Simon Kasif, Ph.D. - Boston University
Previous Members and Visitors
(The member's position immediately after leaving the group is listed)
Mattia Forcato, Ph.D. - Visitor (2014). Mattia was a postdoc at the Center for Genome Research, University of Modena and Reggio Emilia. He worked on Hi-C data for higher-order chromatin interactions.
Luca Petiti, B.S. - Visiting graduate student (2013-2014). Luca was a PhD student in the School of Molecular Medicine at Università degli Studi di Milano in Italy when he came to visit us for a year. He worked on large-scale analysis of epigenetic data.
Richard Park, B.S. - Graduate student (2009-2014). Richard received his PhD from Boston University in May 2014 with a thesis entitled "Visualization and analysis of cancer genome sequencing studies". An expert in data visualization, Richard worked on several projects related to visualization of structural variation as well as germline variants in cancer data. With his visualization work, he was a finalist in the Illumina iDEA Challenge in 2011.
Joshua Ho, Ph.D. - Postdoctoral Fellow (2010-2013). Joshua finished his PhD at the University of Sydney in Australia, working on microarray analysis and its clinical applications. In the Park lab, he worked on various genomics and epigenomic studies related to the SysCODE project. He now leads the Bioinformatics and Systems Medicine Laboratory at Victor Chang Cardiac Research Institute and Senior Lecturer at the University of New South Wales, back in Sydney.
Huiling Xue, Ph.D. - Postdoctoral Fellow (2012-2013). Huiling received her Ph.D. in bioinformatics from the Chinese Academy of Sciences and joined the lab to work on epigenetics after working in the Giraldez lab at Yale. She worked on analysis of model organism ENCODE data and copy number data.
Tae-Min Kim, M.D./Ph.D. - Postdoctoral Fellow (2008-2012). Tae-Min received his MD/PhD from The Catholic University of Korea in 2008. He worked on analysis of DNA copy number in tumor genomes as well as several other collaborations. He runs his own lab at his alma mater.
Guidantonio Malagoli Tagliazucchi - Visiting graduate student (2012). Guidantonio visited us from the Department of Biomedical Sciences at the University of Modena and Reggio Emilia in Italy to work on epigenetic data analysis.
Eric Bishop, B.S. - Graduate student (2008-2012). Eric was a graduate student in the bioinformatics program at Boston University and worked on analysis of next-generation sequencing data from ChIP-seq and GRO-seq experiments. After his PhD, he is working as a programmer/consultant.
Marc Streit, Ph.D. - Visitor (2012). Marc is an assistant professor in the Institute of Computer Graphics at Johannes Kepler University in Linz. He worked on development of StratomeX, a visualization tool for cancer genomics data.
Michael Tolstorukov, Ph.D. - Postdoctoral Fellow/Instructor (2007-2012). Michael received his Ph.D. and was a faculty member at V. Karazin Kharkov National University, Kharkov, Ukraine. He is an expert in the biophysics of nucleosome positioning. He is a special Departmental Fellow in the Molecular Biology Department at the Massachusetts General Hospital.
Ruibin Xi, Ph.D. - Postdoctoral Fellow (2009-2012). Ruibin is a statistician with a PhD from Washington University in St. Louis. He developed new methods for analysis of copy number and structural variations from sequencing data. He is now an assistant professor in the School of Mathematical Sciences and the Center for Statistical Science at Peking University in China.
Alexander Lex, PhD. - Visiting graduate student (2011). Alex is at the Institute for Computer Graphics and Vision in Graz University of Technology, Austria. He worked on development of StratomeX, a visualization tool for cancer genomics data.
Peter Kharchenko, Ph.D. - Postdoctoral Fellow/Instructor (2006-2011). Peter finished his biophysics PhD in George Church's lab at Harvard Medical School in 2005 and joined the Park lab in 2006. He now runs his own lab at CBMI, after earning the top spot in a national faculty search.
Shouyong Peng, Ph.D. - Postdoctoral Fellow (2005-2010). Shouyong joined the Park lab after obtaining his physics PhD at Boston University in 2005.
He is now a staff scientist at the Broad Institute/Dana-Farber Cancer Institute.
Mikaela Keller, Ph.D. - Postdoctoral Fellow (2009-2010, joint with John Brownstein). Mika is a computer scientist specialized in statistical machine learning, with a PhD from Ecole Polytechnique Fédérale de Lausanne (EPFL) in Switzerland. She worked mainly in the HealthMap project at Children's Hospital but explored challenges in bioinformatics as part of this lab.
Geehoon Hong, B.S. - Research Assistant (2009-2010), a recent MIT graduate in mathematics, now a combinatorics graduate student at George Tech
Nathan Clement - Summer student (2009), undergraduate at Brigham Young University
Matthew Salesi - Summer student (2009), undergraduate at Princeton
Dan Day, B.S. - Summer student (2008), currently graduate student, MIT
Hyunsoo Kim, Ph.D. - Postdoctoral Fellow (2007-2009), Wistar Institute
Vidhu Choudhary, M.A. - Bioinformatics Programmer (2007-2008), Programmer, Marshfield Clinic, Wisconsin
Jonathan Dreyfuss, M.S. - Bioinformatics Analyst (2006-2008), graduate student, Boston University
Julie Yoo, B.S. - MS/MBA Student (2007-2008), MBA student
Weil Lai, B.S. - HPCGG Bioinformatics Analyst (2004-2007), medical student, Tufts University
Hyun-Ju Lee, Ph.D. - Postdoctoral Fellow (2006-2007), assistant professor, Gwangju Inst of Science & Technology, Korea
Kyu-Baek Hwang, Ph.D. - visiting doctoral student from Seoul
National University (2004-2005), assistant professor, Soongsil Univ, Korea
Richard Kim, B.S. - HPCGG Bioinformatics Analyst (2003-2005), medical student, Univ of California at San Francisco
Summer interns (MIT UROP, 2005-2006): Songzi Du, Kathy Ye, Daon Ha, Fan Yang, MinJeong Ahn, Christopher Palmer
From an annual hiking trip to the Whilte Mountains in New Hampshire (October 2011):
Photos by PJP and NG
A group lunch at the Harvard Faculty Club (2011):