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About the Lab



The long-term research goal of the Sirota Lab is to develop integrative computational methods and apply these approaches in the context of disease diagnostics and therapeutics. We are specifically interested in leveraging and integrating different types of omics and clinical data to better understand the role of the immune system in disease. We are particularly interested in developing computational methods and using them to understand immune tolerance in the context of autoimmune disease and non-response (pregnancy, organ transplant, cancer). The laboratory is funded by several National Institutes of Health including NIA, NLM, NIAMS, Pfizer, March of Dimes and the Burroughs Wellcome Fund.

The Sirota Lab is part of the Department of Pediatrics and the Institute for Computational Health Sciences at UCSF.

We are located in Mission Hall on the 4th floor, 550 16th Street, San Francisco, CA.

News

  • On World Prematurity Day (November 17, 2017), we are proud to proud to announce the launch of the March of Dimes Database for Preterm Birth Research, a resource centralizing research efforts in preterm birth that we created in collaboration with the ImmPort team. Here is a blog post highlighting the work.
  • Marina Sirota was selected to receive the 2017 AMIA Young Investigator Award!
  • Congrats to Carolyn Wang for getting her project accepted as a talk to the AMIA 2017 High School Scholar Program in Washington DC, November 2017!!!
  • Our new study on the normal tissue adjacent to the tumor published in Nature Communications with UCSF and NCI press releases!
  • Congratulations to Ali for receiving the Hillblom Graduate Student Fellowship Award for 2017-2018!
  • Congratulations to Ali for being awarded the Alzheimer's Association Young Scientist Award!
  • We are very excited to apply computational drug repurposing to Alzheimer's Disease in collaboration with Yadong Huang at the Gladstone Institutes as part of a jointly funded R01 from NIA.
  • Congrats to Idit on getting her project accepted as a podium presentations to the Keystone Conference on Prematurity in October, 2017!
  • Very excited to embark on a new project funded by the Burroughs Wellcome Fund studying the immune system in pregancy and preterm birth with Dr. Tippi MacKenzie . Read about it more here!
  • Congrats to Silvia on getting her project accepted as a podium presentation to ASHG in October, 2017!
  • Congrats to Aolin and Hongtai on getting their projects accepted as podium presentations to ISES in October, 2017!
  • Congrats to Aolin and Hongtai on getting their projects accepted as podium presentations to ISEE in October, 2017!
  • Role Models in AI: Interview with Dr. Marina Sirota by AI4ALL in March 2017.
  • Congrats to Silvia and Anooshree on getting thier projects accepted as podium presentations to TBI AMIA in SF in March, 2017!
  • Grand Rounds Presentation at Santa Clara Valley Med Center, Santa Clara, CA, December 2016.
  • Congrats to Anooshree Sengupta for getting her project accepted as a talk to the AMIA 2016 High School Scholar Program in Chicago, November 2016!!!
  • Presentation at the Biomarkers and Precision Medicine USA Congress in San Diego, October 2016
  • Contrats to Aolin Wang on getting her paper published in Fertility and Sterilty, September 2016!
  • Presentation at the TTS Conference in Hong Kong, August 2016
  • Presentation at the PMSA Conference at UCSF, April 2016
  • Presentation at the CTOT Meeting at NIH, April 2016
  • Presentation at the AMIA Conference in SF, March 2016
  • Interview on Careers in Science, 2016
  • Presentation at the Festival of Genomics in SF, November 2015
  • Presentation at a Transplant Expert Summit Meeting in Vienna, October 2015
  • Presentation at ASHG in Baltimore, October 2015
  • Presentation at the Wrangle Conference in SF, September 2015
  • Presentation at the PAS in San Diego, April, 2015
  • Presentation at the World Transplant Congress in SF, July, 2014
  • Our drug repositioning work in Wall Street Journal, 2011
  • Our paper on genetic architecture of autommune disease, 2009

Data Science in Drug Discovery

Research

Integrative Genomics

With the advent of genotyping and whole genome sequencing technologies, more and more omics data is becoming available for integrative analysis and provides an opportunity to ask new questions about disease. We are interested in leveraging the genetic data across phenotypes to elucidate the;genetic architecture of disease with a special interest in autoimmune diseases (Plos Genetics 2009). Furthermore we are interested in leveraging and applying next-generation sequencing technologies in order to better understand the role of the immune system in disease (JCI 2012, STM 2014). This work is currently funded by National Institute of Arthritis and Musculoskeletal and Skin Diseases at NIH and Pfizer.

Cancer Informatics

We are interested in using publicly available gene expression and genetics data to identify novel biomarkers and therapeutic strategies for cancer. We are actively working on developing computational approaches for target identification, therapeutic prediction and selection of validation models (CPT 2015, BMC Med Genomics 2015, PSB 2015). We have a special interest in studying the tumor microenvironment and the interaction of immune cells in the context of cancer (Nature Communications, 2015).

Computational Drug Discovery

The identification of novel disease indications for approved drugs, or drug repositioning, offers several advantages over traditional drug development. The traditional paradigm of drug discovery is generally regarded as protracted and costly, with studies showing that it takes approximately 15 years and over $1 billion to develop and bring a novel drug to market. The repositioning of drugs already approved for human use mitigates the costs and risks associated with early stages of drug development, and offers shorter routes to approval for therapeutic indications. We are interested in leveraging publicly available data to carry out data-driven computational drug repositioning (STM 2011, JID 2016). This work is currently funded by the National Institue of Aging at NIH.

Integrative Methods for Preterm Birth Research

Each year, 15 million babies (representing 10% of the world’s births) are born preterm, defined as before the 37th week of gestation. Survival for most children born preterm has improved considerably, but surviving children remain at increased risk for a variety of serious complications, many of which contribute to lifelong challenges for individuals and their families, as well as to burdensome economic costs to society. The exact mechanism of spontaneous preterm birth is unknown, though a variety of social, environmental, and maternal factors have been implicated in its cause. We are in particular interested in applying computational integrative methods to investigate the role of the immune system in pregnancy and elucidating genetic, environmental and clinical determinants of preterm birth. This work is funded by the National Library of Medicine at NIH, March of Dimes and The Burroughs Wellcome Fund.

People

Marina Sirota, PhD

Principal Investigator

Marina is currently an Assistant Professor at the Institute for Computational Health Sciences at UCSF. Her research interests lie in developing computational integrative methods and applying these approaches in the context of disease diagnostics and therapeutics.

Aolin Wang, PhD

Post Doctoral Scholar

Aolin obtained her PhD in Epidemiology from UCLA in 2016. Her research interests lie in developing computational approaches to study the role of the environment in pregnancy outcomes.

Alice Taubes, BA

BMS Graduate Student

Ali's research interests include using applying transcriptomic meta-analysis and computational drug repositioning approaches to identify new therapeutics for late onset Alzheimer's disease.

Silvia Pineda, PhD

Post Doctoral Scholar

Silvia completed her PhD in Statistical Genetics at the Spanish National Cancer Research Centre jointly with the University of Liege. Her current research interests lie in the development of advanced statistical approaches to integrate omics and clinical data for organ transplantation.

Leandro Lima, PhD

Bioinformatics Scientist

Leandro is a Bioinformatics Scientist at the Gladstone Institutes. His research project is using integrative methods to identify novel therapeutic targets and diagnostic markers for Parkinson's Disease using omics data and is a collaboration with the Finkbeiner Lab.

Dmitry Rychkov, PhD

Post Doctoral Scholar

Dmitry obtained his PhD in Theoretical Physics from USC. His is developing applying computational approaches to genomic data in the context of autoimmunity.

Idit Kosti, PhD

Post Doctoral Scholar

Idit has a PhD in computational biology from the Technion, Haifa, Israel, where she studied epigenetics, trancription and splicing co-regulation in the human gene expression pathways. Her current focus is in meta anaylsis and computational integrative methods of human microbiome towards better understanding of preterm birth.

Hongtai Huang, PhD

Post Doctoral Scholar

Hongtai's main research interest lies in the interface between statistical analyses and health/environmental decision making. He is currently utilizing health and environmental data to assess and understand potential associations between adverse pregnancy outcomes and environmental exposures as part of PTBi.

Katharine Yu , BS

BMS Graduate Student

Kat is a BMS gradauate student at UCSF who is interested in developing and applying computational methods to understand cancer heterogeneity and experimental models.

Brian Le, PhD

Post Doctoral Scholar

Brian graduated Cum Laude from UCLA as a double major in physics and applied mathematics and went on to obtain his doctorate in physics from the University of Illinois. He joined the Sirota Lab with the goal of learning more about data science applications to biology and medicine.

Ishan Paranjpe, BS

Research Associate

Ishan obtined his BS in Chemical Biology from UC Berkeley in 2017. He is spending a year in the Sirota lab developing computational integrative approaches to study rheumatic disease before starting medical school at Mt. Sinai next year.

You!

We are hiring!

Check out our open positions here.

Alumni

  • Akshay Ravoor, High School Student, The Harkar School
  • Carolyn Wang, High School Student, Gunn High School
  • Labanya Mukhopadhyay, High School Student, Evergreen Valley High School
  • Anooshree Sengupta, High School Student, The Harkar School
  • Grace Cho, BS, Stanford Medical Student
  • Cindy Lin, Stanford Undergradaute Student
  • Nishant Jain, Yale Undergraduate Student
  • Charles Pei, High School Student (Harvard Undergraduate Student)

Close Collaborators

  • Atul Butte, MD, PhD (Institute for Computational Health Sciences, UCSF)
  • Dexter Hadley, MD, PhD (Institute for Computational Health Sciences, UCSF)
  • Bin Chen, PhD (Institute for Computational Health Sciences, UCSF)
  • Dvir Aran, PhD (Institute for Computational Health Sciences, UCSF)
  • Idit Kosti, PhD (Institute for Computational Health Sciences, UCSF)
  • Hanna Paik, PhD (Institute for Computational Health Sciences, UCSF)
  • Nadav Rappoport, PhD (Institute for Computational Health Sciences, UCSF)
  • David Stevenson, MD, Gary Shaw, PhD (Stanford MOD Prematurity Center, Stanford University)
  • David Relman, PhD, Steven Quake, PhD, Martin Angst, MD (Stanford MOD Prematurity Center, Stanford University)
  • Laura Jelliffe-Pawlowski, PhD, Larry Rand, MD (Preterm Birth Initiative, UCSF)
  • Tippi McKenzie, MD, PhD (Fetal Maternal Medicine, UCSF)
  • Linda Guidice, MD, PhD (Obstetrics, Gynecology and Reproductive Sciences, UCSF)
  • Minnie Sarwal, MD, PhD (Nephrology, UCSF)
  • Tracey Woodruff, PhD (Environmental Science, UCSF)
  • Jinoos Yazdany, MD (Rheumatology, UCSF)
  • Lindsey Criswell, MD, MPH (Rheumatology, UCSF)
  • Esteban Burchard, MD, MPH (Pulmonology, UCSF)
  • Gaia Skibinski, PhD and Steven Finkbeiner, MD, PhD (Neurology, Gladstone/UCSF)
  • Yadong Huang, MD, PhD (Neurology, Gladstone/UCSF)
  • Christian von Buedingen, MD (Neurology, UCSF)
  • Steven Bagley, PhD and Russ Altman, MD, PhD (Biomedical Informatics, Stanford University)

Teaching

Spring 2017 | Computational Immunology Mini Course

This course provides an overview of computational methods used in the analysis of immunological data, including transcriptomics, next generation sequencing, cytometry and CyTOF. We will provide a theoretical framework but focus on real applications.

The first hour of each session was a lecture format that was livestreamed and archived here, followed by an intimate disucssion session with the registered students. This course was co-directed with Matt Spitzer.

Summer 2016 | Computational Immunology Seminars

In collaboration with Stanford University, would like to invite you to join us for a Computational Immunology Seminar Series this summer. The seminars will be hosted at Stanford and interactively streamed at UCSF in Mission Hall. Click here to subscribe to our updates about the lectures. We have an array of exciting speakers lined up and hope you will join us!

Open Positions

Post-doctoral opportunities in Translational Bioinformatics at UCSF

The laboratory of Dr. Marina Sirota at UCSF is seeking highly motivated investigators to develop and study novel approaches in translational bioinformatics, or the application of analytic and interpretive methods to optimize the transformation of genomic and clinical data into precision medicine. We are currently recruiting investigators interested in focusing on using omics and integrative approaches to study pregnancy outcomes with a focus on preterm birth.

Ideal candidates will have an M.D. and/or Ph.D. with a strong background in bioinformatics, computational biology, biostatistics, and genomics, and a great publication record.

Strong problem-solving skills, creative thinking, and the ability to build new software tools as needed are required. Applicants must possess good communication skills and be fluent in both spoken and written English. A background in molecular biology or medicine or pharmacology will be a strong plus. Prior experience with genetic, microarray, drug, or clinical databases, text-mining, knowledge representation, or parallel computing platforms is a plus. This exciting work will be guided by multidisciplinary collaborations with top scientists in neonatology, genetics, environmental science, immunology and microbiome research at UCSF.

To apply, please send your CV, a brief statement of research interests, and contact information for three references in one PDF document to marina.sirota@ucsf.edu.

Rotation Students

The Sirota Lab has openings each quarter for rotating students.

Expecations:

  • You will be expected to spend close to the theoretical 50% working in the lab, and spend that 50% in our office-space in Mission Hall.
  • You will meet with the PI on a bi-weekly basis.
  • You will need to interact with the Post-doctoral Fellows and graduate students.
  • You are expected to attend the weekly laboratory meetings.
  • You will be expected to present to the laboratory in the presentation rotation.
  • You are strongly encouraged to submit a paper on your work, even though it is just a rotation project.

What you will learn:

  • R is the open-source statistical software package we preferentially use.
  • Perl is the scripting/programming language we preferentially use, because most of our programs are quite small. We use Python for larger programs.
  • MySQL is the open-source database software package we preferentially use.

High School Students

We strongly recommend you apply through the UCSF high school research summer program . Exceptional applicants outside this program will be considered.

College Students

We accept students through the UCSF Summer Internship Program. Exceptional candidates outside the program will be considered, especially if the applicants have fellowship funding and a track-record of publications in biomedical informatics.

Publications

2017

Pineda S, Sigdel T, Chen J, Jackson A, Sirota M*, Sarwal M*. Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant. Fronteirs Immunology, 2017.
Van Blarcom T, Lindquist K, Melton Z, Cheung WL, Wagstrom C, McDonough D, Oseguera CV, Ding S, Rossi A, Potluri S, Sundar P, Pitts S, Sirota M, Casas MG, Yan Y, Jones J, Roe-Zurz Z, Srinivasan SS, Zhai W, Pons J, Rajpal A, Chaparro-Riggers J. Productive common light chain libraries yield diverse panels of high affinity bispecific antibodies. MAbs. 2017. PubMed PMID: 29227213.
Mirza AN, Fry MA, Urman NM, Atwood SX, Roffey J, Ott GR, Chen B, Lee A, Brown AS, Aasi SZ, Hollmig T, Ator MA, Dorsey BD, Ruggeri BR, Zificsak CA, Sirota M, Tang JY, Butte A, Epstein E, Sarin KY, Oro AE. Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment. JCI Insight. 2017. PubMed PMID: 29093271.
Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ. Comprehensive analysis of normal adjacent to tumor transcriptomes. Nat Commun. 2017. PubMed PMID: 29057876.
Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, Chen B, Paik H, Aran D, Spatz J, Himmelstein D, Panahiazar M, Bhattacharya S, Sirota M, Musen MA, Butte AJ. Precision annotation of digital samples in NCBI's gene expression omnibus. Sci Data. 2017. PubMed PMID: 28925997.
Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Adams Dudley R, Yazdany J. Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety. Rheumatol Int. 2017.PubMed PMID:28748425.
Apeltsin L, Wang S, von Büdingen HC, Sirota M. A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data. Sci Rep. 2017. PubMed PMID: 28706301.
Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nat Commun. 2017. PubMed PMID: 28699633.
Schmajuk G, Tonner C, Trupin L, Li J, Sarkar U, Ludwig D, Shiboski S, Sirota M, Dudley RA, Murray S, Yazdany J. Using health-system-wide data to understand hepatitis B virus prophylaxis and reactivation outcomes in patients receiving rituximab. Medicine (Baltimore), 2017.PubMed PMID: 28353614.
Sirota M, Sarwal M. Transplantomics: Towards Precision Medicine in Transplantation Research. Transplantation, 2017. PubMed PMID: 28121910.

2016

Low YS, Daugherty AC, Schroeder EA, Chen W, Seto T, Weber S, Lim M, Hastie T, Mathur M, Desai M, Farrington C, Radin AA, Sirota M, Kenkare P, Thompson CA, Yu PP, Gomez SL, Sledge GW Jr, Kurian AW, Shah NH. Synergistic drug combinations from electronic health records and gene expression. J Am Med Inform Assoc, 2016. PubMed PMID: 27940607.
Yeung YA, Foletti D, Deng X, Abdiche Y, Strop P, Glanville J, Pitts S, Lindquist K, Sundar PD, Sirota M, Hasa-Moreno A, Pham A, Melton Witt J, Ni I, Pons J, Shelton D, Rajpal A, Chaparro-Riggers J. Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire. Nat Commun, 2016. PubMed PMID: 27857134.
Paik H, Chen B, Sirota M, Hadley D, Butte AJ. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. CPT Pharmacometrics Syst Pharmacol, 2016. PubMed PMID: 27860440.
Wang A, Padula A, Sirota M, Woodruff TJ. Environmental influences on reproductive health: the importance of chemical exposures. Fertil Steril, 2016. Review. PubMed PMID: 27513554.
Kosti I, Jain N, Aran D, Butte AJ, Sirota M. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Sci Rep, 2016. PubMed PMID: 27142790.
Bagley SC*, Sirota M*, Chen R, Butte AJ, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput Biol, 2016. PubMed PMID: 27115429.
Cho HG, Fiorentino D, Lewis M, Sirota M*, Sarin KY*. Identification of alpha-adrenergic agonists as potential therapeutic agents for dermatomyositis through drug-repurposing using public expression datasets. J Invest Dermatol, 2016. PubMed PMID: 26975725.

2015

Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015 Dec 4;6:8971. doi: 10.1038/ncomms9971. PubMed PMID: 26634437.
Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. CPT Pharmacometrics Syst Pharmacol, 2015. PubMed PMID: 26535158.
Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. BMC Med Genomics, 2015. PubMed PMID: 26043652.
Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, Plon SE, Ramos EM, Sherry ST, Watson MS; ClinGen. ClinGen--the Clinical Genome Resource. N Engl J Med, 2015. PubMed PMID: 26014595.
Sirota M, Willemsen G, Sundar P, Pitts SJ, Potluri S, Prifti E, Kennedy S, Ehrlich SD, Neuteboom J, Kluft C, Malone KE, Cox DR, de Geus EJ, Boomsma DI. Effect of genome and environment on metabolic and inflammatory profiles. PLoS One, 2015.PubMed PMID: 25853885.
Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte AJ. A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets. Pac Symp Biocomput, 2015. PubMed PMID: 25592598.
Wu M, Sirota M, Butte AJ, Chen B. Characteristics of drug combination therapy in oncology by analyzing clinical trial data on ClinicalTrials.gov. Pac Symp Biocomput, 2015.PubMed PMID: 25592569.

2014

Palanichamy A*, Apeltsin L*, Kuo TC*, Sirota M*, Wang S, Pitts SJ, Sundar PD, Telman D, Zhao LZ, Derstine M, Abounasr A, Hauser SL, von Büdingen HC. Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis. Sci Transl Med, 2014. ubMed PMID: 25100740.
von Büdingen HC, Kuo TC, Sirota M, van Belle CJ, Apeltsin L, Glanville J, Cree BA, Gourraud PA, Schwartzburg A, Huerta G, Telman D, Sundar PD, Casey T, Cox DR, Hauser SL. B cell exchange across the blood-brain barrier in multiple sclerosis. J Clin Invest, 2012. PubMed PMID: 23160197.
Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, Sirota M, Morgan AA, Chen R, Ohtsu H, Maeda S, Kadowaki T, Butte AJ. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A, 2012. PubMed PMID: 22499789.

2012

Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol, 2012. PubMed PMID: 22383865.
Liu LY, Schaub MA, Sirota M, Butte AJ. Sex differences in disease risk from reported genome-wide association study findings. Hum Genet, 2012. PubMed PMID: 21858542.
Liu LY, Schaub MA, Sirota M, Butte AJ. Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. Inflamm Bowel Dis, 2012. PubMed PMID: 21618365.

2011

Sirota M*, Dudley JT*, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med, 2011. PubMed PMID: 21849665.
Dudley JT*, Sirota M*, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med, 2011. PubMed PMID: 21849664.
Sirota M, Butte AJ. The role of bioinformatics in studying rheumatic and autoimmune disorders. Nat Rev Rheumatol, 2011. PubMed PMID: 21691330.

2010

Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol, 2010. PubMed PMID: 21152010.
Chen R, Davydov EV, Sirota M, Butte AJ. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One, 2010. PubMed PMID: 21042586.
Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E. Drug discovery in a multidimensional world: systems, patterns, and networks. J Cardiovasc Transl Res, 2010. PubMed PMID: 20677029.

2009

Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune disease classification by inverse association with SNP alleles. PLoS Genet, 2009. PubMed PMID: 20041220.
Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics, 2009. PubMed PMID: 19477990.

2007

Gross SS, Do CB, Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol, 2007. PubMed PMID: 18096039.

Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature, 2007. PubMed PMID: 17994087.