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Welcome!

We are a bioinformatics research group and are part of the Center for Biomedical Informatics at Harvard Medical School, Children's Hospital Informatics Program, Harvard-MIT Division of Health, Science, & Technology, and Division of Genetics at Brigham and Women's Hospital. More information on the principal investigator is here.

News:

* Oct 31, 2013: This time, congratulations to Francesco, Andrew! Their papers came out (online) on the same day in Cell Reports and Cell. These are results of collaborations with the Mitzi Kuroda and Steve Elledge labs.

* May 9, 2013: Congratulations to Lixing and Francesco! Their papers came out on the same day in Cell and Cell Stem Cell.

* April, 2013: A "Technical comment" in Science by Ferrari & Jung et al, points out a problem with a Science article.

* Jan, 2013: Congratulations to Joshua Ho, who will begin his position as a faculty member at the Victor Chang Research Institute back at home in Sydney in the fall.

* July, 2012: Congratulations to Michael for his new faculty position in the Department of Molecular Biology at Massachusetts General Hospital. Well done! His lab page is here.

* June 2012: We welcome two visitors to the lab: Guidantonio Malagoli Tagliazucchi, a graduate student from Modena, Italy (May-Nov), and Dr. Marc Streit from Johannes Kepler University in Linz, Austria (Aug-Oct).

*June 2012: Congratulations to Alice and Michael for their forthcoming papers in Science and Molecular Cell, respectively.

*June 2012: Peter is a recipient of an HMS Young Mentor Award. (Seventeen in three categories were chosen from 481 nominees) link to HMS newsletter

*June 2012: Congratulations to Ruibin Xi, who will start a faculty position in the Center for Statistical Science at Peking University in the fall.

*Nov 2011: Students interested in a bioinformatics PhD should consider The Bioinformatics and Integrative Genomics PhD program at Harvard Medical School, co-directed by Isaac Kohane and Peter Park.

*Oct 2011: The Park lab team, led by Nils Gehlenborg, wins one of the two Integrated Biology Research Grants from Agilent Technologies. Press release from Agilent

*Jul 2011: Congratulations to Peter Kharchenko, who was offered an assistant professorship at Harvard! He will be starting his own lab at CBMI in the fall.

*Jun 2011: Richard Park is a finalist in the Illumina iDEA Challenge for his structural variation viewer for whole-genome sequenicng data.

* Dec 2010: The modENCODE papers are out! Congrats to Peter Khachenko and the team for the chromatin paper in Nature and the integrative paper in Science. For additional information, see the press release from NIH, Genome 'census' reveals hidden riches at NatureNews and Early Reports From the 'Dark Matter' of the Genome from wired.com. The figure on the right shows a snapshot from the chromatin state browser that Richard Park in the group implemented.

* Feb 2010: Peter wins the Sloan Research Fellowship.

Molecular Cell, volume 47, issue 4 (August 24, 2012). From the journal website: Composition and organization of chromatin greatly affects genome function. Histones--the major protein component of chromatin--undergo modifications and replacement with nonallelic variants in various biological processes. Incorporation of histone variants represents a significant change in local chromatin structure and therefore is likely to have important regulatory consequences. While histone variants were the focus of intensive research in recent years, their biology is still not completely understood, and their functions continue to emerge. In this issue, Tolstorukov et al. (pp. 596-607) characterize a rapidly evolving histone variant, H2A.Bbd. They demonstrate that in human cells H2A.Bbd nucleosomes form unconventional chromatin structures enriched within actively transcribed genes. Analysis of the transcriptome of the cells depleted for H2A.Bbd revealed widespread changes in transcriptional output and disruption of normal mRNA splicing patterns, revealing the role of this variant in diverse gene-expression pathways. Colored "gumballs" on the cover represent the nucleosomes bearing histone variants. Such nucleosomes constitute only a fraction of all nucleosomes in a cell, but play important roles in gene regulation. Cover design by Frank Hegyi with input from P.J.P. and M.Y.T.

Introduction

Recent technological developments have enabled researchers to generate experimental data in an unprecedented, genome-wide scale. Our aim is to gain biological insights through computational and statistical analysis of genomic data.

Epigenomics

We are interested in understanding chromatin structure and function in a variety of systems using high-throughput sequencing techniques. We specialize in analysis of ChIP-seq and nucleosome profiling data but also work with RNA-seq, whole-genome sequencing, and other data types. We collaborate with a number of experimental labs, both in the Harvard Medical area and around the world.

Integrative analysis of genomic data

We also engage in methodological research, developing new statistical and computational algorithms and tools for understanding next-generation sequencing data. We aim to address important problems and come up with efficient and statistically valid methods that will have practical impact on biological and clinical investigators.

 

Interested in joining the lab?

See the latest flyer for postdoctoral fellowship announcement!

NOTE: Please read the instructions on what to send. If you do not send the requested items, you will not receive a reply. Please note '[POSTDOC]' or '[GRAD]' in the subject line. If you do not hear back in one week, feel to send a reminder. Mass emails that do not meet basic requirements will not be acknowledged.

Postdoctoral Fellowship:

Multiple post-doctoral fellowships in bioinformatics are available immediately to work in the laboratory of Dr. Peter Park at Harvard Medical School.

The long-term goal of the group is to understand gene regulation through computational analysis of genomic data, with focus on epigenetic aspects. Positions: i) statistical methods for analysis of next-generation sequencing data, especially whole-genome sequencing data; ii) cancer genomics, combining data from expression, copy number, miRNA, SNP, methylation, and mutation sequencing; iii) chromatin structure and function using ChIP-seq data. In each position, the successful candidate will have an opportunity to work on new data sets from a fantastic group of experimental collaborators.

Ideal candidates will have a Ph.D. in a quantitative field and a substantial experience in analysis of genomic data. Excellent programming skills are essential and previous experience with R is a plus. The Harvard Medical area is one of the most exciting places in the world for biomedical research and our collaborators are among the top biologists.

Please send your CV, a brief statement of research interests, pdfs of your three best papers, and three letters of recommendations to peter_park@harvard.edu

Graduate Students

There are multiple openings for graduate students to work on the problems described above. The focus of the work will be computational; but, if desired, the student will have ample opportunity to carry out wet-lab work in one of the collaborating laboratories. Those with interest in epigenetics are particularly welcomed. NOTE: The student must already be enrolled in a graduate program at Harvard (Biophysics, Biological and Biomedical Sciences, or others) or at MIT (Health Sciences & Technology or others). Inquires regarding graduate student positions from those not already enrolled in one of these programs will go unanswered.

Undergraduate Research Assistants (MIT UROP or Harvard):

Multiple positions are open for undergraduates throughout the year. A 10-hour commitment during the term and full-time commitment during summer are required. Strong quantitative background and substantial programming experience are essential. Underclassmen with such experience are welcome to apply. You may also be interested in the Summer Institute in Bioinformatics and Integrative Genomics at Harvard-MIT Health, Science and Technology.