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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 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, NICHD, Pfizer, March of Dimes and the Burroughs Wellcome Fund.

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

We are located in UCSF Mission Bay at 490 Illinois St, Floor 2, San Francisco, CA.

News

Data Science in Drug Discovery



UCSF Alumni Week 2020: Your Microbial Universe - Using Microbes as Medicine



Carry the One Radio: Women in Data Science - Dr. Marina Sirota



Drug Discovery in the Era of Precision Medicine



Research

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.

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.

People

Marina Sirota, PhD

Principal Investigator

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

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. She is a joint postdoc with Dr. Nuria Malats and her current research interests lie in the development of advanced statistical approaches to integrate omics and clinical data for pancreatic cancer.

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.

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 at Urbana-Champaign. He joined the Sirota Lab with the goal of learning more about data science applications to biology and medicine.

Jessica Neely, MD

Faculty

Jessica is an Assistant Professor of Pediatrics who earned her MD from the University of Kentucky, and completed her Pediatric Residency and Rheumatology Fellowship at UCSF. Her primary research interest is in precision medicine approaches to care, with a specific focus on Juvenile Dermatomyositis.

Gaia Andreoletti, PhD

Post Doctoral Scholar

Gaia obtained her PhD in Genomic Medicine from University of Southhampton. Following a postdoc at UC Berkley, she joined the Sirota Lab working on integrative projects in autoimmunity and leading the March of Dimes Data Repository efforts.

Stella Belonwu

PSPG Graduate Student

Stella is a PSPG Gradute student who is working on developing and applying computational methods to identify new treatments for Alzheimer's Disease.

Dimitri Abrahamsson, PhD

Post Doctoral Scholar

Dimitri is a postdoctoral scholar at the Program on Reproductive Health and the Environment and the Institute for Computational Health Sciences. He received his Ph.D. in Environmental Chemistry from Stockholm University in Sweden. His research at UCSF focuses on studying chemical exposures of pregnant women using non-target analysis.

Tomiko Oskotsky, MD

Research Scientist

Tomiko earned a BS in Biochemistry from UCLA and an MD from the Medical College of Wisconsin. She worked for over a decade at Stanford University in education and research groups within the Schools of Medicine and Engineering. She enjoys going for long walks and traveling with her husband.

Daniel Piqué, MD PhD

Post Doctoral Scholar / Pediatrics Resident

Daniel earned his BS in Genetics from the University of Georgia and his MD and PhD from the Albert Einstein College of Medicine. As part of his PhD, he developed software to identify new oncogene candidates with publicly available data. He is interested in leveraging genomics and clinical informatics to improve patient outcomes.

Caroline Warly Solsberg

PSPG Graduate Student

Caroline graduated from University of Colorado at Boulder with a BS in Chemical & Biological Engineering. She is interested in leveraging transcriptomic & genomic data to investigate heterogeneities in men and women with Alzheimer's Disease. She loves climbing, running, gardening, and just being outside. A fun fact about Caroline: she is a triplet.

Zachary Cutts

Bioinformatics Graduate Student

Zach graduated from California Polytechnic State University-San Luis Obispo with a BS in Wine and Viticulture as well as a MS in Biomedical Engineering. He is interested in Alzheimer's Disease research.

Alice Tang

Bioengineering Graduate Student

Alice is an MD/PhD Student at UCSF who graduated from UCLA with a BS in Bioengineering. She loves collecting and working with data, from omics to sensor data and so on, with the goal of using data to understand human diseases. Outside of lab, her hobbies include food, museums, cats, and games.

Yaqiao Li

PSPG Graduate Student

Yaqiao graduated from UC Berkeley and worked at UCSF as a research associate on studying molecular mechanism of neurodegenerative diseases. She is interested in developing a computational pipeline to find novel drug targets for Alzheimer's Disease.

You!

We are hiring!

Check out our open positions here.

Alumni

  • Idit Kosti, PhD, Postdoctoral Scholar (Computational Biologist, Alkahest)
  • Daniel Bunis, PhD, BMS Graduate Student (Senior Research Scientist, UCSF)
  • Arohee Bhoja, High School Student, The Harker School
  • Sachi Parikh, High School Student, Lynbrook High School
  • Tia Jain, High School Student, Saratoga High School
  • Christine Li, High School Student, Shanghai American School
  • Roman Kouznetsov, UCLA Undergraduate Student
  • Raghav Ganesh, High School Student, Lynbrook High School
  • Aarzu Gupta, High School Student, The Harker School
  • Irene Yang, High School Student, Dougherty Valley High School
  • Manish Paranjpe, Research Associate, UCSF (Medical Student, Harvard University)
  • Hongtai Huang, Postdoctoral Scholar, UCSF (Analyst II, Genentech)
  • Fawwad Khan, Research Associate, UCSF (Medical Student, UT Southwestern)
  • Alice Taubes, PhD, BMS Graduate Student, UCSF (Project Manager, Benevolent AI)
  • Shan Andrews, Postdoctoral Scholar, UCSF (Computational Biologist at Denali Therapeutics)
  • Aolin Wang, Postdoctoral Scholar, UCSF (Associate, Analysis Group)
  • Ishan Paranjpe, Research Associate, UCSF (Medical Student, Mt. Sinai)
  • Arabdha Biswas, High School Student, The Harker School (UC Santa Cruz Undergraduate)
  • Akshay Ravoor, High School Student, The Harker School (UC Berkeley Undergraduate)
  • Carolyn Wang, High School Student, Gunn High School (Columbia University Undergraduate)
  • Labanya Mukhopadhyay, High School Student, Evergreen Valley High School (UC Berkeley Undergraduate)
  • Anooshree Sengupta, High School Student, The Harker School (Stanford Undergraduate)
  • Grace Cho, BS, Stanford Medical Student (Dermatology Resident, Stanford)
  • Cindy Lin, Stanford Undergradaute Student (Software Engineer, Google)
  • Nishant Jain, Yale Undergraduate Student (Software Engineer, Google)
  • Charles Pei, High School Student (Harvard University Undergraduate)

Visiting Scholars

  • Karolin Froelich, PhD: Apr 2019 - Sept 2019 (Germany)
  • Isam Ben Soltane: Apr 2019 - Aug 2019 (France)
  • Ramy Karam Aziz: Aug 2018 (Egypt)

Rotation Students

  • Parker Grosjean, BMI
  • Harry Sun, BMS
  • Cuyler Luck, BMS
  • Maggie Tsui, BMI
  • Pooja Kathail, Computational Biology (Berkeley)
  • Ketrin Gjoni, PSPG
  • Brenda Miao, BMI
  • Jackie Roger, BMI
  • Whitney Tamaki, PSPG
  • Emily Connelly, PSPG
  • Michelle Wang, PSPG
  • Kirsten Chen, BMS
  • Bianca Vora, PSPG
  • Kennedy Agwamba, Computational Biology (Berkeley)

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)
  • 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)
  • 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)
  • Cristina Lanata, MD (Rheumatology, UCSF)
  • Chaz Langelier, MD, PhD (Infectious Diseases, UCSF)
  • Kathy Giacomini, PhD (Bioengineering, UCSF)
  • Benjamin Glicksberg, PhD (Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai)

Outreach Activities


Summer 2019-2020 | UCSF AI4ALL Program

UCSF AI4ALL is a partnership between UCSF and AI4ALL to teach AI to high school students from underrepresented groups, focusing on AI for biomedical applications. Founded and directed by Marina Sirota and co-directed by Tomiko Oskotsky, this tuition-free annual program involves hands-on experience with AI, hearing from a diverse set of role models in AI, and learning about how AI can be used to advance health. Please donate to UCSF AI4ALL!


PSPG DEI Outreach Committee – Faculty Co-Chair


IgEquity – Faculty Advisor

Teaching


Spring 2017-2020 | 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 provide a theoretical framework but focus on real applications.

The first hour of each session is in lecture format (livestreamed and archived) followed by an intimate disucssion session with the registered students.

  • Spring 2020 (COVID-19 focus): Co-directed by Gabi Fragiadakis and Matt Spitzer.
  • Spring 2019: Co-directed by Jill Hollenbach and Matt Spitzer.
  • Spring 2018: Co-directed by Jill Hollenbach and Matt Spitzer
  • Spring 2017: Co-directed by Matt Spitzer.


Summer 2016 | Computational Immunology Seminars

A Computational Immunology Seminar Series offered in collaboration with Stanford University. Seminars hosted at Stanford and interactively streamed at UCSF in Mission Hall. Subscribe to updates about lectures.

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.
    • 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.

Pre-Prints

Le BL, Sper R, Nielsen SCA, Pineda S, Nguyen, QH, Boyd SD, Mackenzie, TC and Sirota M. Maternal and Infant Immune Repertoire Sequencing Analysis Identifies Distinct Immunoglobulin and T Cell Receptor Development in Term and Preterm Infants. Cell Reports Sneak Peek. 2021. Available at SSRN: 3793962
Christenson SA, Mick E, DeVoe C, Deiss T, Pisco AO, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha BS, Serpa PH, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, COMET_Consortium, Hendrickson CM, Kangelaris KN, Krummel M, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and may be modified by dexamethasone. medRxiv 2020. DOI name: 10.21203/rs.3.rs-100914/v1
Sun M, Shankar R, Ko M, Chang CD, Yeh S, Li S, Liu K, Zhou G, Xing J, VanVelsen A, VanVelsen T, Paithankar S, Feng BY, Young K, Strug M, Turco L, Wang Z, Schadt E, Chen R, Li X, Oskotsky T, Sirota M, Glicksberg BS, Nadkarni GN, Moeser AJ, Li L, Kim S, Zhou J, Chen B. Sex differences in viral entry protein expression, host responses to SARS-CoV-2, and in vitro responses to sex steroid hormone treatment in COVID-19. Research Square. 2020. DOI name: 10.21203/rs.3.rs-100914/v2
Andreoletti G, Lanata CM, Paranjpe I, Jain TS, Nititham J, Taylor KE, Combes AJ, Maliskova L, Ye CJ, Katz P, Era MD, Yazdany J, Criswell LA, Sirota M. Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus. BioRxiv. 2020. DOI name: 10.1101/2020.10.30.362715
Le BL*, Andreoletti G*, Oskotsky T*, Vallejo-Gracia A, Rosales R, Yu KZ, Kosti I, Leon KE, Bunis DG, Li C, Kumar GR, White KM, García-Sastre AE, Ott M, Sirota M. Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19. BioRxiv. 2020. DOI name: 10.1101/2020.10.23.352666
Abrahamsson D, Wang A, Jiang T, Wang M, Siddharth A, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ. Comprehensive Non-Targeted Analysis of the Prenatal Exposome Reveals Significant Differences in Chemical Enrichment Between Maternal and Fetal Samples. ChemRxiv. 2020. DOI name: 10.26434/chemrxiv.13093457
Rychkov D, Neely J, Oskotsky T, Sirota M. Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis. bioRxiv. 2020. DOI name: 10.1101/2020.07.24.220483
Abraham A, Le BL, Kosti I, Straub P, Velez Edwards DR, Davis LK, Muglia L, Rokas A, Bejan A, Sirota M, Capra JA. Dense phenotyping from electronic health records enables machine-learning-based prediction of preterm birth. bioRxiv. 2020. DOI name: 10.1101/2020.07.15.20154864
Tarca AL, Pataki BA, Romero R, Sirota M, Guan Y, Kutum R, Gomez-Lopez N, Done B, Bhatti G, Yu T, Andreoletti G, Chaiworapongsa T, The DREAM Preterm Birth Prediction Challenge Consortium, Hassan SS, Hsu CD, Aghaeepour N, Stolovitzky G, Csabai I, Costello JC. Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. bioRxiv. 2020. DOI name: 10.1101/2020.06.05.130971
Paranjpe MD, Belonwu S, Wang JK, Oskotsky T, Gupta A, Taubes A, Zalocusky K, Paranjpe I, Glicksberg BS, Huang Y, Sirota M. Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women with Alzheimer's Disease. bioRxiv. 2020. DOI name: 10.1101/2020.04.24.060558
Rahmioglu N, Banasik K, Christofidou P, Danning R, Galarneau G, Giri A, MacGregor S, Mortlock S, Sapkota Y, Schork AJ, Sobalska-Kwapis M, Stefansdottir L, Turman C, Uimari O, Adachi S, Andrews S, Arnadottir R, Burgdorf KS, Campbell A, Cheuk CS, Clementi C, Cook J, De IV, DiVasta A, O D, Edwards T, Fontanillas P, Fung JN, Geirsson RT, Girling J, Harris HR, Holdsworth-Carson S, Houshdaran S, Hu-Seliger T, Jaqrvelin M, Kepka E, Kulig B, Laufer MR, Law M, Low S, Mangino M, Marciniak B, Matalliotaki C, Matalliotakis M, Murray AD, Nezhat C, Nõukas M, Olsen C, Padmanabhan S, Paranjpe M, Parfitt D, Peters M, Polak G, Porteous DJ, Romanowicz H, Saare M, Shafrir A, Siewierska-Górska A, Skarp S, Slomka M, Smith BH, Smolarz B, Szaflik T, Szyllo K, Terry K, Thorleifsson G, Tomassetti C, Vanhie A, Vincent K, Vitonis A, Werge T, DBDS Genetic Consortium Andersen S, Banasik K, Brunak S, Burgdorf KS, Erikstrup C, Hansen TF, Hjalgrim H, Jemec G, Jennum P, Nielsen KR, Nyegaard M, Paarup HM, Pedersen OB, Petersen M, Sorensen E, Ullum H, Werge T, Gudbjartsson D, Stefansson K, Stefansson H, Þorsteinsdottir U, iPSYCH-Broad Consortium Mortensen PB, Hougaard DM, Borglum AD, the Celmatix Research Team the 23andMe Research Team Chasman DI, D’Hooghe T, Giudice LC, Goulielmos GN, Hapangama DK, Hayward C, Horne AW, Kamatani Y, Kubo M, Martikainen H, Rogers PA, Saunders PT, Sirota M, Spector T, Strapagiel D, Tung JY, Whiteman D, Becker CM, Salumets A, Magi R, Kraft P, Nyegaard M, Nyholt DR, Steinthorsdottir V, Stefansson K, Velez-Edwards DR, Yurttas PB, Missmer SA, Montgomery GW, Morris AP, Zondervan KT. Large-scale genome-wide association meta-analysis of endometriosis reveals 13 novel loci and genetically-associated comorbidity with other pain conditions. bioRxiv. 2018. DOI name: 10.1101/406967
Daugherty AC, Farrington C, Hakim I, Mujahid S, Noblin ES, Radin AM, Chua MS, Rabe M, Fernald G, Ford D, Sirota M, Schaevitz L, Radin AA. Rapid Identification and Validation of Novel Rheumatoid Arthritis Drug Treatments using an Integrative Bioinformatics Platform. bioRxiv. 2018. DOI name: 10.1101/243998

Publications

2021

Maric I*, Oskotsky T*, Kosti I, Le B, Wong RJ, Shaw GM, Sirota M**, Stevenson DK**. Decreased Mortality Rate Among COVID-19 Patients Prescribed Statins: Data From Electronic Health Records In The US. Frontiers in Medicine. 2021. DOI: 10.3389/fmed.2021.639804
Rychkov D, Sur S, Sirota M, Sarwal MM. Molecular Diversity of Clinically Stable Human Kidney Allografts. JAMA Network Open. 2021. PMID: 33492376
Bunis D, Bronevetsky Y, Krow-Lucal E, Bhakta NR, Kim CC, Nerella S, Jones N, Mendoza VF, Bryson YJ, Gern JE, Rutishauser RL, Ye CJ, Sirota M, McCune JM, Burt TD. Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Hematopoiesis. Cell Reports. 2021. Pubmed PMID: 33406429


2020

Zinter MS, Lindemans C, Versluys B, Mayday MY, Sunshine S, Reyes G, Sirota M, Sapru A, Matthay MA, Kharbanda S, Dvorak CC, Jan Boelens JJ, DeRisi JL. The Pulmonary Metatranscriptome Prior to Pediatric Hematopoietic Cell Transplantation Identifies Post-HCT Lung Injury. Blood. 2020. DOI name: 10.1182/blood.2020009246
Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M. dittoSeq: Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit. Bioinformatics. 2020. DOI name: 10.1093/bioinformatics/btaa1011
Pineda S, Sur S, Sigdel T, Nguyen M, Crespo E, Torija A, Meneghini M, Gomà M, Sirota M, Bestard O, Sarwal MM. Peripheral Blood RNA Sequencing Unravels a Differential Signature of Coding and Noncoding Genes by Types of Kidney Allograft Rejection. Kidney International Reports. 2020. DOI name: 10.1016/j.ekir.2020.07.023
Kober KM, Lee M-C, Olshen A, Conley YP, Sirota M, Keiser M, Hammer MJ, Abrams G, Schumacher M, Levine JD, Miaskowski C. Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain. Molecular Pain. 2020. Pubmed PMID: 32586194
Pineda S, Bunis D, Kosti I, Sirota M. Data Integration for Immunology. Annual Review of Biomedical Data Science. 2020. DOI name: 10.1146/annurev-biodatasci-012420-122454
Abrahamsson D, Park JS, Singh R, Sirota M, Woodruff T. Applications of Machine Learning to in silico Quantification of Chemicals without Analytical Standards. Journal of Chemical Information and Modeling. 2020. DOI name: 10.1021/acs.jcim.9b01096
Stevenson DK, Wong RJ, Aghaeepour N, Maric I, Angst MS, Contrepois K, Darmstadt GL, Druzin ML, Eisenberg ML, Gaudilliere B, Gibbs RS, Gotlib IH, Gould JB, Lee HC, Ling XB, Mayo JA, Moufarrej MN, Quaintance CC, Quake SR, Relman DA, Sirota M, Snyder MP, Sylvester KG, Hao S, Wise PH, Shaw GM, Katz M. Towards personalized medicine in maternal and child health: integrating biologic and social determinants. Pediatr Res. 2020. DOI name: 10.1038/s41390-020-0981-8
Norgeot B, Muenzen K, Peterson TA, Fan X, Glicksberg B, Schenk G, Rutenberg E, Oskotsky B, Sirota M, Yazdany J, Schmajuk G, Ludwig D, Goldstein T, Butte AJ. Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes. Nature Partner Journals Digital Medicine. 2020. DOI name: 10.1038/s41746-020-0258-y
Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M. Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Frontiers in Microbiology. 2020. DOI name: 10.3389/fmicb.2020.00476
Sarin V, Yu K, Ferguson ID, Gugliemini O, Nix MA, Hann B, Sirota M, Wiita AP . Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis. Leukemia. 2020. PubMed PMID: 32123307
Le BL, Iwatani S, Wong RJ, Stevenson DK, Sirota M. Computational discovery of therapeutic candidates for preventing preterm birth. JCI Insight. 2020. PubMed PMID: 32051340
Garg A, Fazio S, Duell PB, Baass A, Udata C, Joh T, Riel T, Sirota M, Dettling D, Liang H, Garzone PD, Gumbiner B, Wan H. Molecular Characterization of Familial Hypercholesterolemia in a North American Cohort. J Endocr Soc. 2019. PubMed PMID: 31993549

2019

Neely J, Rychkov D, Paranjpe M, Waterfield M, Kim S, Sirota M. Gene Expression Meta‐Analysis Reveals Concordance in Gene Activation, Pathway, and Cell‐Type Enrichment in Dermatomyositis Target Tissues ACR Open Rheumatology. PubMed PMID 31872188.
Vora B, Green EAE, Khuri N, Ballgren F, Sirota M, Giacomini KM. Drug-nutrient interactions: discovering prescription drug inhibitors of the thiamine transporter ThTR-2 (SLC19A3). Am J Clin Nutr. 2019. PubMed PMID: 31764942.
Paik H, Kan MJ, Rappoport N, Hadley D, Sirota M, Chen B, Manber U, Cho SB, Butte AJ. Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia. Sci Data. 2019. PubMed PMID: 31615985.
Tsur A, Batsry L, Toussia-Cohen S, Rosenstein MG, Barak O, Brezinov Y, Yoeli-Ullman R, Sivan E, Sirota M, Druzin ML, Stevenson DK, Blumenfeld YJ, Aran D. Development and validation of a machine learning model for prediction of shoulder dystocia. Ultrasound Obstet Gynecol. 2019. PubMed PMID: 31587401.
Lanata CM, Paranjpe I, Nititham J, Taylor KE, Gianfrancesco M, Paranjpe M, Andrews S, Chung SA, Rhead B, Barcellos LF, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Criswell LA. A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus. Nat Commun. 2019. PubMed PMID: 31467281.
Ashouri JF, Hsu LY, Yu S, Rychkov D, Chen Y, Cheng DA, Sirota M, Hansen E, Lattanza L, Zikherman J, Weiss A. Reporters of TCR signaling identify arthritogenic T cells in murine and human autoimmune arthritis. Proc Natl Acad Sci U S A. 2019. PubMed PMID: 31455730.
Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ, Goldstein T, Sirota M. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types. Nat Commun. 2019. PubMed PMID: 31395879.
Paranjpe MD, Taubes A, Sirota M. Insights into Computational Drug Repurposing for Neurodegenerative Disease. Trends Pharmacol Sci. 2019. PubMed PMID: 31326236.
Pineda S, Sigdel TK, Liberto JM, Vincenti F, Sirota M, Sarwal MM. Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing. Nat Commun. 2019. PubMed PMID: 31015506.
Chen J, Bhattacharya S, Sirota M, Laiudompitak S, Schaefer H, Thomson E, Wiser J, Sarwal MM, Butte AJ. Assessment of Postdonation Outcomes in US Living Kidney Donors Using Publicly Available Data Sets. JAMA Netw Open. 2019. PubMed PMID: 30977847.
Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M. A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm. J Reprod Immunol. 2019. PubMed PMID: 30852461.
BGhaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N. Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Bioinformatics. 2019. PubMed PMID: 30561547.

2018

Baer RJ, McLemore MR, Adler N, Oltman SP, Chambers BD, Kuppermann M, Pantell MS, Rogers EE, Ryckman KK, Sirota M, Rand L, Jelliffe-Pawlowski LL. Pre-pregnancy or first-trimester risk scoring to identify women at high risk of preterm birth. Eur J Obstet Gynecol Reprod Biol. 2018. PubMed PMID: 30439652.
Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, Muglia L, Ober C, England SK, Parry S, Macones G, Driscol D, Shaw GM, Stevenson DK, Simpson JL, Thomson E, Butte AJ; March of Dimes Prematurity Research Centers. Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Sci Data. 2018. PubMed PMID: 30398470.
Padula AM, Huang H, Baer RJ, August LM, Jankowska MM, Jellife-Pawlowski LL, Sirota M, Woodruff TJ. Environmental pollution and social factors as contributors to preterm birth in Fresno County. Environ Health. 2018. PubMed PMID: 30157858 .
Huang H, Woodruff TJ, Baer RJ, Bangia K, August LM, Jellife-Palowski LL, Padula AM, Sirota M. Investigation of association between environmental and socioeconomic factors and preterm birth in California. Environ Int. 2018. PubMed PMID: 30075861.
Pineda S, Sirota M . Determining Significance in the New Era for p-Values. J Pediatr Gastroenterol Nutr. 2018. PubMed PMID: 30052572.
Wang A, Gerona RR, Schwartz JM, Lin T, Sirota M , Morello-Frosch R, Woodruff TJ. A Suspect Screening Method for Characterizing Multiple Chemical Exposures among a Demographically Diverse Population of Pregnant Women in San Francisco. Environ Health Perspect. 2018. PubMed PMID: 30044231.
Vora B, Wang A, Kosti I, Huang H, Paranjpe I, Woodruff TJ, MacKenzie T, Sirota M. Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth. Front Immunol. 2018. PubMed PMID: 29867970.
Kosti I, Sirota M. Electronic Medical Records Enable Precision Medicine Approaches for Celiac Disease. J Pediatr Gastroenterol Nutr. 2018. PubMed PMID: 29746345.
Huang H, Wang A, Morello-Frosch R, Lam J, Sirota M, Padula A, Woodruff TJ. Cumulative Risk and Impact Modeling on Environmental Chemical and Social Stressors. Curr Environ Health Rep. 2018. PubMed PMID: 29441463.
Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A, Chen R, Sirota M, Kodama K, Hadley D, Butte AJ. Are minor alleles more likely to be risk alleles? BMC Med Genomics. PubMed PMID: 29351777.
Rappoport N*, Toung J*, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Darmstadt GL, Wang X, Bustamante CD, Snyder MP, Ziv E, Patsopoulos NA, Muglia LJ, Burchard E, Shaw GM, O'Brodovich HM, Stevenson DK, Butte AJ*, Sirota M*. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Sci Rep. 2018. PubMed PMID:29317701.

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. Frontiers in Immunology, 2017. PubMed PMID: 29259604.
Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N, Sirota M, Tishkoff SA, Sondheimer N. Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth. J Pediatr. 2017. PubMed PMID: 29249523.
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. PubMed 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.