Welcome

The ITMAT Bioinformatics Group is a bioinformatics research group that engages in collaborations on translational science to meet the needs of ITMAT investigators. We perform methods development for the statistical and computational analysis of high-throughput data, as well as solutions for "big data" management and deployment. We undertake all types of informatics projects both small and large, however our methods development is currently focused on RNA-Seq analysis, particularly low-level analysis starting with raw data and ending with quantified and normmalized spreadsheets. We are particularly focused on unbiased and rigorous benchmarking of the various stages of analysis. We offer RNA-Seq analysis as a primary service. We also offer consluting on study design and in the writing of bioinformatics methods for grants and publications.

Our services


RNA-Seq analysis

We provide basic low-level RNA-Seq analysis including alignment, quantification, normalization, differential expression analysis, pathway analysis and data annotation and management.
See our price list for specifics.


RNA-Seq workshops

The Institute for Translational Medicine and Therapeutics (ITMAT) in conjunction with the Institute of Biomedical Informatics (IBI) offer full day workshops on RNA-Seq analysis for bioinformaticians. Standard practices in RNA-Seq analysis do not tend to be the most effective methods. Most high profile reviews are based on impressions and not on hard data. In this workshop we present comparative analysis of existing methods to see what really works and what doesn't, as well as cover the most important issues and how to deal with them.

More info can be found on pages from previous workshops: Feb. 25th, 2014, June 11, 2014 - Milan, Italy, June 23, 2015 (for industry)

Sign up to get notified for the next workshop.

Our projects


RNA-Seq analysis

We develop methods for normalization, differential expression analysis, data simulation and benchmarking.


Proteomics

We perform mass spectometry data analysis for protein identification, spectra comparisons and visualization, multiple modifications identification, peptide and protein differential expression analysis, gene ontology and motif enrichment analysis, specific modifications site prediction, highest scored peptides and proteins identification.


Data management

We develop low overhead integrative genomics resources for managing the heterogeneous data and analyses generated by the typical academic lab.



Benchmarking

RNA-Seq analysis is a confusing landscape with dozens of published algorithms available for every step of the low-level analysis pipeline. We perform extensive benchmarking studies with both real and simulated data to evaluate and optimize the methods for each step.


eagle-i

eagle-i is an effort to make searching for resources like shopping on Amazon. We manage the UPenn local instance of this project and interface with the network.


Biobank

We have in-house systems for minimally tracking the whereabouts of biological samples and printing barcoded labels.

Our publications

(ITMAT Bioinformatics members indicated by bold)

Meet the team


Director

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Gregory Robert Grant, PhD

I'm the Director of the ITMAT Bioinformatics group, with primary appointment in the Department of Genetics. I have a PhD and B.S. in Mathematics, and a Masters in Computer Science. You may contact me at ggrant@ upenn.edu or (o) 215-573-3736, (c) 267-243-6111

Permanent members

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Dimitra Sarantopoulou, MSc

I’m a bioinformatician/application developer and joined the group in 2012. I have a Masters in Bioinformatics and a B.S in Computer Science. My interests are big data analysis, management and visualization, with specialization in proteomics. You may contact me at dimitras at upenn.edu

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Eun Ji Kim, MSc

I'm a bioinformatician and I joined the group in 2013. I have a Masters in Biotechnology (Bioinformatics) from the University of Pennsylvania and a B.A in Biological Science from Smith College. My interests include next generation sequencing data analysis and methods development. You may contact me at kimeunj at upenn.edu

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Nicholas Lahens, PhD

I'm a senior research coordinator and I joined the group in 2014. I have a PhD in Genomics and Computational Biology, and a B.S. in Bioinformatics and Computer Science. My research interests include circadian rhythms, analysis and visualization of big data, analysis of RNA-seq data, and assessing technical biases in sequencing data. You may contact me at nif at upenn.edu

Post-Doctoral members

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Qiwen Hu, PhD

I joined the group as a Postdoc in 2016. I finished my PhD training in Bioinformatics at North Carolina State University where I worked on identifying translated regions in Arabidopsis genome using machine learning and statistical approaches. Before coming to U.S., I received MSc in Biochemical and Molecular Biology and B.S. in Computer Science in China. I am interested in applying methods from computer science and statistics to solve biological problems. You may contact me at qiwenhu at upenn.edu

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Soumyashant (Soum) Nayak, PhD

I'm a Postdoc and joined the group in 2016. I completed my Ph.D. in Mathematics at UPenn and my B.Math.(Hons) in Mathematics at the Indian Statistical Institute, Bangalore Centre. You may contact me at nsoum at upenn.edu

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Peng Song, PhD

I obtained my PhD in physics from the University of Pennsylvania, and two honors B.S. degrees, one in physics and one in mathematics, from the University of Michigan, Ann Arbor. My current works include using mathematical models to solve problems in bioinformatics, and data analysis in genomics. You may contact me at songpeng at upenn.edu

Rotation students

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Rong Guo

I was a master's degree student at UPenn when I joined the group for a one semester rotation in Bioinformatics. During my rotation I performed a comparative benchmarking analysis of RNA-Seq alignment methods.

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Luna Frank-Fischer

I was working towards a BS in Mathematics and an MS in Computer Science in Stanford University when I joined the group for a summer internship in 2014. During my intern I developed a tool to identify circularized RNA in RNA-Seq data.

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Giacomo Baruzzo, PhD

I am a Ph.D. student in Bioinformatics and System Biology at University of Padova in Italy. I joined the group as an exchange student in 2015. I am a Software engineer, specialized in computational biology.

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Elio Scarci

I was a rotation student during the summer of 2016. I will graduate from high school in Rome, Italy in 2017.

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Thomas Campbell

I was working on my Ph.D at UPenn when I joined the group for a one semester rotation. During my rotation I studied False Discovery Rate corrections for p-values in highly parallel hypothesis testing such as in differential expression analysis of RNA-Seq.

Affiliated members

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Anand Srinivasan

I'm the PMACS Senior IT Project Leader and former member of the ITMAT Bioinformatics Group/PGFI. You may contact me at pmacshpc @ med.upenn.edu

Former members

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Angel Pizarro

Former Director of ITMAT Bioinformatics Group. Currently a Technical Business Development Manager at Scientific Computing at Amazon Web Services.

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Mike DeLaurentis

Application developer for bioinformatics tools.

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Katharina Hayer

Bioinformatician specialized in RNA-Seq data analysis.

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Faith Coldren, PhD

Physicist, specialized in data curation for eagle-i.





Contact us


E-mail Greg Grant at ggrant at upenn.edu
Call Greg Grant at (o) 215-573-3736, (c) 267-243-6111
Our address is Smilow Research Building, 10th Floor, 3400 Civic Center Blvd, Philadelphia, PA 19104-5158 (map)


Copyright © 2016 ITMAT Bioinformatics