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.
Our services
RNA-Seq workshops
The Institute for Translational Medicine and Therapeutics (ITMAT) 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.
Circadian Analysis of Omics Data
The Institute for Translational Medicine and Therapeutics (ITMAT) offers full day workshops on Circadian Analysis for bioinformaticians. Focus is on RNA-Seq, but other omics also apply. Platforms utilized will be the Nitecap resource and also R.
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.
Nitecap
Nitecap is a method for identification of circadian or rhythmic patterns in massively-parallel measurements of biological entities; for example, finding circadian behavior in timecourse gene expression data from RNA-Seq or microarrays.
Teqila
Teqila is a tool that looks for enrichment of certain characteristics of differentially expressed genomic features.
RNA-Seq simulations
CAMPAREE is a member of the BEERS2 suite of tools that simulates the collection of RNA molecules in a biological sample, prior to RNA-seq library preparation.
BEERS2 is a modular RNA-Seq simulator (successor to the BEERS simulator), to generate realistic RNA-Seq data; by modeling each biochemical step in library preparation / sequencing and biological variability using empirical data.
Our publications
(ITMAT Bioinformatics members indicated by bold)
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Phenome-Wide Association Study of Actigraphy in the UK Biobank. Thomas G. Brooks, Nicholas F. Lahens, Gregory R. Grant, Yvette I. Sheline, Garret A. FitzGerald, Carsten Skarke. (Under Review)
- Time-Specific Associations of Wearable Sensor-Based Cardiovascular and Behavioral Readouts with Disease Phenotypes in the Outpatient Setting of the Chronic Renal Insufficiency Cohort (CRIC) Nicholas F. Lahens, Mahboob Rahman, Jordana B. Cohen, Debbie L. Cohen, Jing Chen, Matthew R. Weir, Harold I. Feldman, Gregory R. Grant, Raymond R. Townsend, Carsten Skarke Frontiers in Digital Health (in press)
2021
- Considerations for the Safe Operation of Schools During the Coronavirus Pandemic Ronan Lordan, Samantha Prior, Elizabeth Hennessy, Amruta Naik, ..., Antonijo Mrcela, Gregory R Grant, ..., Garret A. FitzGerald, Tilo Grosser Frontiers in Public Health (2021)
- Nitecap: an exploratory circadian analysis web application Thomas G. Brooks, Antonijo Mrcela, Nicholas F. Lahens, Georgios K. Paschos, Tilo Grosser, Carsten C. Skarke, Garret FitzGerald, Gregory R. Grant J Biol Rhythms. 2022 Feb;37(1):43-52
- CAMPAREE: A robust and configurable RNA expression simulator Nicholas Lahens, Thomas G Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Anand Srinivasan, Jonathan Schug, John B Hogenesch, Yoseph Barash, Gregory R Grant BMC Genomics (2021) Sep 25;22(1):692
- MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis Barry Slaff, Caleb M. Radens, Paul Jewell, Anupama Jha, Nicholas F. Lahens, Gregory R. Grant, Andrei Thomas-Tikhonenko, Kristen W. Lynch & Yoseph Barash. Nature Communications (2021) Jun 7;12(1):3353
- Sex Dependent Role of Atrial Natriuretic Peptide in the Regulation of Blood Pressure in Prostaglandin Deficient Mice. Tang SY, Anderson ST, Meng H, Sarantopoulou D, Ricciotti E, Hennessy E, Gregory R. Grant, FitzGerald GAJournal of Clinical Investigation (JCI). (2021) Jun 8;136310
- Comparative evaluation of full-length isoform quantification from RNA-Seq Dimitra Sarantopoulou*, Soumyashant Nayak*, Thomas G Brooks, Nicholas F Lahens, Gregory R Grant BMC Bioinformatics (2021) May 25;22(1):266
- Accounting for Time: Circadian Rhythms in the Time of COVID-19. Sengupta S, Thomas G. Brooks, Gregory R. Grant, FitzGerald GA J Biol Rhythms (2021) Feb;36(1):4-8
2020
- RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake Guo X, Gao X, Keenan BT, Zhu J, Sarantopoulou D, Lian J, Galante RJ, Gregory R. Grant, Pack AI. BMC Genomics (2020) Sep 14;21(1):633
2019
- Age Attenuates the Transcriptional Changes that Occur with Sleep in the Medial Prefrontal Cortex Xiaofeng Guo, Brendan T. Keenan, Dimitra Sarantopoulou, Diane C. Lim, Jie Lian, Gregory R. Grant, Allan I. Pack Aging Cell (2019) Dec;18(6):e13021
- Comparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input Dimitra Sarantopoulou, Soon Yew Tang, Emanuela Ricciotti, Nicholas F. Lahens, Damien Lekkas, Jonathan Schug, Xiaofeng S. Guo, Georgios K. Paschos, Garret A. FitzGerald, Allan I. Pack, Gregory R. Grant Scientific Reports (2019) Sep 17;9(1):13477.
- Variability in the Analgesic Response to Ibuprofen Is Associated With Cyclooxygenase Activation in Inflammatory Pain. Theken KN, Hersh EV, Lahens NF, Lee HM, Li X, Granquist EJ, Giannakopoulos HE, Levin LM, Secreto SA, Gregory R. Grant, Detre JA, FitzGerald GA, Grosser T, Farrar JT Clin Pharmacol Ther. (2019) Mar 31
- A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes. Sun Y, Kim EJ, Felt SA, Taylor LJ, Agarwal D, Gregory R. Grant, López CB. PLoS Pathog. (2019) Apr 17;15(4):e1007707
- Distinct vascular genomic response of proton and gamma radiation-A pilot investigation. Ricciotti E*, Sarantopoulou D*, Gregory R .Grant, Sanzari JK, Krigsfeld GS, Kiliti AJ, Kennedy AR, Grosser T PLoS One (2019) Feb 11;14(2):e0207503. doi: 10.1371/journal.pone.0207503
2018
- Spliceosome factors target timeless (tim) mRNA to control clock protein accumulation and circadian behavior in Drosophila. Shakhmantsir I, Nayak S, Gregory R. Grant, Sehgal A Elife. (2018) Dec 5;7. pii: e39821
- Lipocalin-Like Prostaglandin D Synthase but Not Hemopoietic Prostaglandin D Synthase Deletion Causes Hypertension and Accelerates Thrombogenesis in Mice. Song WL, Ricciotti E, Liang X, Grosser T, Gregory R. Grant, FitzGerald GA J Pharmacol Exp Ther. (2018) Dec;367(3):425-432
- SAP97 regulates behavior and expression of schizophrenia risk enriched gene sets in mouse hippocampus. Gupta P, Uner OE, Nayak S, Gregory R. Grant, Kalb RG PLoS One. (2018) Jul 11;13(7):e0200477
- Overlap in signaling between Smoothened and the α subunit of the heterotrimeric G protein G13. Guo X, Riobo-Del Galdo NA, Kim EJ, Gregory R. Grant, Manning DR PLoS One. (2018) May 15;13(5):e0197442
- Complete Transcriptome Profiling of Normal and Age-Related Macular Degeneration Eye Tissues Reveals Dysregulation of Anti-Sense Transcription. Kim EJ, Gregory R. Grant, Bowman AS, Haider N, Gudiseva HV, Chavali VRM Sci Rep. (2018) Feb 14;8(1):3040
- Iso-relevance Functions - A Systematic Approach to Ranking Genomic Features by Differential Effect Size Soumyashant Nayak, Nicholas Lahens, Eun Ji Kim, Emanuela Ricciotti, George Paschos, Sarah Tiskoff, Dimitra Sarantopoulou, Shaon Sengupta, Barry Cooperman, Tilo Grosser, Gregory Grant BioRxiv (2018) doi: https://doi.org/10.1101/381814
- Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. Norton SS, Vaquero-Garcia J, Lahens NF, Gregory R. Grant, Barash Y. Bioinformatics. (2018) May 1;34(9):1488-1497
- Analysis of hydroxyeicosatetraenoic acids (HETEs) in human whole blood by chiral ultrahigh performance liquid chromatography (UHPLC)-electron capture atmospheric pressure chemical ionization/high resolution mass spectrometry (ECAPCI/HRMS) Liudmila L Mazaleuskaya, Ashkan Salamatipour, Dimitra Sarantopoulou, Liwei Weng, Garret A FitzGerald, Ian A Blair, and Clementina Mesaros. J. Lipid Res. (2018) Jan 4. pii: jlr.D081414
2017
- A Pilot Characterization of the Human Chronobiome. Skarke C, Lahens NF, Rhoades SD, Campbell A, Bittinger K, Bailey A, Hoffmann C, Olson RS, Chen L, Yang G, Price TS, Moore JH, Bushman FD, Greene CS, Gregory R. Grant, Weljie AM, FitzGerald GA Sci Rep. (2017) Dec 7;7(1):17141
- Mitotic Transcription and Waves of Gene Reactivation During Mitotic Exit. Katherine C. Palozola, Greg Donahue, Gregory R. Grant, Justin S. Becker, Allison Cote, Hong Liu, Hongtao Yu, Arjun Raj, Kenneth S. Zaret. Science (2017) Oct 6;358(6359):119-122
- Sleep restriction induced energy, methylation and lipogenesis metabolic switches in rat liver. Arjun Sengupta, Seth D Rhoades, Eun Ji Kim, Soumyashant Nayak, Gregory R Grant, Peter Meerlo, Aalim M Weljie. Int J Biochem Cell Biol. (2017) Dec;93:129-135
- A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression. Nicholas F. Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens, Eun Ji Kim, Giacomo Baruzzo, Katharina E. Hayer, Tapan Ganguly, Jonathan Schug, Gregory R. Grant. BMC Genomics (2017) Aug 10;18(1):602
- Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain. Qiwen Hu, Eun Ji Kim, Jian Feng, Gregory R. Grant, Elizabeth A. Heller. PLoS Comput Biol. (2017) Jun 13;13(6)
- The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression Paul L. Babb, Nicholas F. Lahens, Sandra M. Correa-Garhwal, David N. Nicholson, Eun Ji Kim, John B. Hogenesch, Matjaž Kuntner, Linden Higgins, Cheryl Y. Hayashi, Ingi Agnarsson, Benjamin F. Voight Nature (2017)
- Characterizing the 'POAGome': a bioinformatics-driven approach to primary open-angle glaucoma Ian D. Danford, Lana D. Verkuil, Daniel J. Choi, David W. Collins, Harini V. Gudiseva, Katherine E. Uyhazi, Marisa K. Lau, Levi N. Kanu, Gregory R. Grant, Venkata R.M. Chavali, Joan M. O'Brien Progress in Retinal and Eye Research (2017) Feb 18
- Transcriptional and Cell Cycle Alterations Mark Aging of Primary Human Adipose-Derived Stem Cells Xiaoyin Shan, Cleresa Roberts, Eun Ji Kim, Arianna Brenner, Gregory Grant, Ivona Percec Stem Cells (2017) Feb 17
- Simulation-Based Comprehensive Benchmarking of RNA-Seq Aligners Giacomo Baruzzo, Katharina E. Hayer, Eun Ji Kim, Barbara Di Camillo, Garret A. FitzGerald, Gregory Grant. Nature Methods (2017) Feb;14(2):135-139
2016
- A broad-spectrum lipidomics screen of anti-inflammatory drug combinations in human blood. Liudmila Mazaleuskaya, John Lawson, Xuanwen Li, Gregory Grant, Clementina Mesaros, Tilo Grosser, Ian Blair, Emanuela Ricciotti, Garret Fitzgerald. JCI Insight. (2016) Aug 4;1(12)
- Investigation of the functional role of human Interleukin-8 gene haplotypes by CRISPR/Cas9 mediated genome editing Manjunatha R. Benakanakere, Livia S. Finoti, Urara Tanaka, Gregory R. Grant, Raquel M. Scarel-Caminaga, Denis F. Kinane. Scientific Reports (2016) Aug 8;6:31180
- Cardiovascular Consequences of Prostanoid I Receptor Deletion in Microsomal Prostaglandin E Synthase-1 Deficient Hyperlipidemic Mice Soon Yew Tang, James Monslow, Gregory R. Grant, Leslie Todd, Sven-Christian Pawelzik, Lihong Chen, John Lawson, Ellen Pure, Garret A. FitzGerald Circulation. (2016) Jul 26;134(4)
- Timing of expression of the core clock gene Bmal1 influences its effects on aging and survival. Guangrui Yang, Lihong Chen, Gregory R. Grant, Georgios Paschos, Wenliang Song, Erik S. Musiek, Vivian Lee, Sarah C. McLoughlin, Tilo Grosser, George Cotsarelis, and Garret A. FitzGerald. Science Translational Medicine (2016) Feb 3;8(324)
2015
- Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Gregory R. Grant. Bioinformatics (Oxford, England). (2015);
- Considerations for RNA-seq analysis of circadian rhythms. Li J, Gregory R. Grant, Hogenesch JB, Hughes ME. Methods in enzymology. (2015); 551:349-67.
2014
- Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing. Toung JM, Lahens N, Hogenesch JB, Grant G. PLoS One. (2014) Nov 14;9(11)
- IVT-seq reveals extreme bias in RNA-sequencing. Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Gregory R. Grant, Hogenesch JB. Genome Biol (2014) June 30; 15(6)
- Erythropoietin upregulation in pulmonary arterial hypertension. Karamanian VA, Harhay M, Gregory R. Grant, Palevsky HI, Grizzle WE, et al. Pulmonary circulation. (2014); 4(2):269-79.
- Myeloid cell microsomal prostaglandin E synthase-1 fosters atherogenesis in mice. Chen L, Yang G, Monslow J, Todd L, Cormode DP, Tang J, Gregory R. Grant, Delong JH, Tang SY, Lawson JA, Pure E, Fitzgerald GA. PNAS (2014) May 6;111(18):6828-33
- Myeloid COX-2 deletion reduces mammary tumor growth through enhanced cytotoxic T lymphocyte function Edward P. Chen, Nune Markosyan, Emma Connolly, John A. Lawson, Xuanwen Li, Gregory R. Grant, Tilo Grosser, Garret A. FitzGerald and Emer M. Smyth Carcinogenesis (2014) published online March 3rd.
2013
- Systematic evaluation of spliced aligners for RNA-Seq. Par G. Engstron, Tamara Stejger, Botond Sipos, Gregory R Grant, RGASP Consortium, Nick Goldman, Tim J. Hubbard, Jennifer Harrow, Roderic Guigo, Paul Bertone. Nature Methods (2013) 10, 1185-1191.
- Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. Michael H Farkas, Gregory R Grant, Joseph A White, Maria E Sousa, Mark B Consugar and Eric A Pierce. BMC Genomics (2013), 14:486
- Cell Selective Cardiovascular Biology of Microsomal Prostaglandin E Synthase-1. Lihong Chen, Guangrui Yang, Xiufeng Xu, Gregory Grant, John A. Lawson, Mohammad Bohlooly-Y, and Garret A. FitzGerald. Circulation (2013), 127: 233-243
- Drug Resistance and pseudoresistance; and unintended consequence of Enteric Coated Aspirin. Tilo Grosser, Susanne Fries, John Lawson, Shiv Kapoor, Gregory Grant, Garret A. FitzGerald. Circulation (2013), 127: 377-385
2012
- Obesity in mice with adipocyte-specific deletion of clock component Bmal1. Georgios K. Paschos, Salam Ibrahim, Wen-Liang Song, Takeshige Kunieda, Gregory Grant, Teresa M. Reyes, Christopher A. Bradfield, Cheryl H. Vaughan, Michael Eiden, Mojgan Masoodi, Julian L. Griffin, Fenfen Wang, John A. Lawson and Garret A. FitzGerald. Nature Medicine (2012) Nov 11
- Transcriptome Analyses to Investigate the Pathogenesis of RNA Splicing Factor Retinitis Pigmentosa. Michael H. Farkas, Greg R. Grant, Eric A. Pierce. Advances in Experimental Medicine and Biology (2012), Volume 723, pp 519-525
- Transcriptional Pausing Controls. A Rapid Antiviral Innate Immune Response In Drosophila Jie Xu, Gregory Grant, Leah R. Sabin, Beth Gordesky-Gold, Ari Yasunaga, Mathew Tudor, Sara Cherry. Cell: Host & Microbe (2012) Oct 18;12(4):531-43.
- Deep sequencing the circadian and diurnal transcriptome of Drosophila brain Hughes ME, Gregory R. Grant, Paquin C, Qian J, Nitabach MN. Genome Research (2012) Jul;22(7):1266-81.
- Vascular COX-2 modulates blood pressure and thrombosis in mice. Yu Y, Ricciotti E, Scalia R, Tang SY, Grant G, Yu Z, Landesberg G, Crichton I, Wu W, Puri E, Funk CD, FitzGerald GA. Sci Transl Med (2012) May 2;4(132)
2011
- Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM) Gregory R. Grant, Michael H. Farkas, Angel Pizarro, Nicholas Lahens, Jonathan Schug, Brian Brunk, Christian J. Stoeckert Jr, John B. Hogenesch and Eric A. Pierce. Bioinformatics (2011) 2011 Sep 15;27(18):2518-28.
- Side-Specific Expression of Activated Leukocyte Adhesion Molecule (ALCAM; CD166) in Pathosusceptible Regions of Swine Aortic Valve Endothelium Marie A. Guerraty, Gregory R. Grant, John W. Karanian, Oscar A. Chiesa, William F. Pritchard, Peter F. Davies. The Journal of Heart Valve Disease (2011);20:165-167
- Microsomal Prostaglandin E2Synthase-1 Modulates the Response to Vascular Injury. Miao Wang, Kaori Ihida-Stansbury, Devashish Kothapalli, Mathieu C. Tamby, Zhou Yu, Lihong Chen, Gregory Grant, Yan Cheng, John A. Lawson, Richard K. Assoian, Peter L. Jones, PhD; Garret A. FitzGerald, MD Cicrulation (2011) (123:631-639)
- Time-Specific Associations of Wearable Sensor-Based Cardiovascular and Behavioral Readouts with Disease Phenotypes in the Outpatient Setting of the Chronic Renal Insufficiency Cohort (CRIC) Nicholas F. Lahens, Mahboob Rahman, Jordana B. Cohen, Debbie L. Cohen, Jing Chen, Matthew R. Weir, Harold I. Feldman, Gregory R. Grant, Raymond R. Townsend, Carsten Skarke Frontiers in Digital Health (in press)
2022
Teaching
Meet the team
Permanent members
Gregory Robert Grant, PhD
Director of the ITMAT Bioinformatics Laboratory, with primary appointment in the Department of Genetics. B.S. and PhD in Mathematics, Masters in Computer Science. You may contact me at ggrant@upenn.edu or (o) 215-573-3736, (c) 267-243-6111
Nicholas Lahens, PhD
Senior Bioinformatician, research coordinator and project manager. Joined the group in 2014, PhD in Genomics and Computational Biology, B.S. in Bioinformatics and Computer Science. 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 @ upenn.edu
Neetu Rajpal, PhD
Eagle-i project manager. Neetu.Rajpal@ pennmedicine.upenn.edu
Post-Doctoral members
Thomas G. Brooks, PhD
Postdoc, joined the group in 2018. I completed my Ph.D. in Riemannian Geometry at the Department of Mathematics at UPenn. You may contact me at thobr at upenn.edu
Antonijo Mrcela, PhD
Postdoc and joined the group in 2020. I completed my Ph.D. at the Department of Mathematics at UPenn. You may contact me at Antonijo.Mrcela@Pennmedicine.upenn.edu
Past Rotation students
Aditi Manjrekar
Neuroscience major at The University of Texas at Dallas. During my rotation I performed a meta-analysis of circadian transcriptomics.
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.
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.
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. For my rotation we wrote and published this paper in Nature Methods.
Elio Scarci
I was a rotation student during the summer of 2016. I will graduate from high school in Rome, Italy in 2017.
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
Anand Srinivasan
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
Dimitra Sarantopoulou, MSc
Bioinformatician 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 and visualization, with specialization in proteomics and RNA-Seq. You may contact me at dimitras at upenn.edu
Soumyashant (Soum) Nayak, PhD
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
Cris Lawrence, PhD
Senior Application Developer and I joined the group in 2018. I have a PhD in Chemistry and a Masters in Information Systems. You may contact me at criswlawrence at gmail.com
Angel Pizarro
Former Director of ITMAT Bioinformatics Group. Currently a Technical Business Development Manager at Scientific Computing at Amazon Web Services.
Mike DeLaurentis
Application developer for bioinformatics tools.
Katharina Hayer
Bioinformatician specialized in RNA-Seq data analysis.
Faith Coldren, PhD
Physicist, specialized in data curation for eagle-i.
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.
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.
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.
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)