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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



Integrating Clinical and Molecular in the Era of Precision Medicine



Carry the One Radio: Teaching Old Drugs New Tricks



UCSF Department of Medicine Grand Rounds: The Science Behind Real-World Data - Answering Today’s Questions Today



MELODEM Working Group: Leveraging Molecular and Clinical Data to Better Understand Alzheimer's Disease



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 (Cell Press Sneak Peak 2021) and elucidating genetic (Sci Rep 2018), transcriptomic (Front Immunol 2018), microbiome (Front Microbio 2020), environmental (Environ Health 2018), and clinical determinants of preterm birth. Moreover, through the March of Dimes (MOD) Database for Preterm Birth Research, we are leading efforts to organize scientific data and research across all MOD-funded Prematurity Research Centers with the goal of enhancing research collaboration and coordination to accelerate the overall pace of discovery in this field (Sci Data 2018). This work is funded by the National Library of Medicine at NIH, March of Dimes and The Burroughs Wellcome Fund.

Computational Approaches to Inform Therapeutics of Alzheimer's Disease

Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder caused by interactions among multiple genetic and environmental factors. Apolipoprotein (APO) E4 has been identified as the major genetic risk factor for AD. It increases the risk and lowers the age of onset of AD in a gene dose–dependent manner. The genetic complexity and multifactorial nature of AD pose unique challenges for developing effective therapies and suggest the need of a precision medicine approach that takes into account individual variability. The goal of this project is to use a multi-omics integrative approach leveraging publicly available human genomics and transcriptomics to elucidate sex-specific (bioRxiv 2020) and apoE genotype-specific (Research Square 2021) molecular pathways involved in AD with a focus towards neuroinflammation. We are further interested in seeing how these differences impact diagnostics and therapeutics (Trends Pharmacol Sci 2019).

Integrative Genomics for Autoimmune Disease

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). We have on-going projects in Systemic Lupus Erythematosus (SLE) (Nat Comms 2019, Comms Bio 2021), Rheumatoid Arthritis (RA) (bioRxiv 2020), and Dermatomyositis (ACR Open Rheum 2019). 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 (Nat Comms 2015) as well as evaluating cell lines as cancer models (Nat Comms 2019).

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. This methodology has been applied successfully to Crohn's disease and IBD (STM 2011, STM 2011), dermatomyositis (JID 2016), liver cancer (Nat Comms 2017), preterm birth (JCI Insight 2020), and most recently COVID-19 (bioRxiv 2020). 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.

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.

Tomiko Oskotsky, MD

Research Scientist

Tomiko earned a BS in Biochemistry from UCLA and an MD from the Medical College of Wisconsin. Her research interests encompass the analysis of electronic health records and investigation of drug repositioning candidates. She enjoys going for long walks and traveling with her husband.

Zachary Cutts, BS

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, BS

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, BS

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.

Sarah Woldemariam, PhD

Postdoctoral Scholar

Sarah earned a BS in Chemistry from Case Western Reserve University and a PhD in Chemistry and Chemical Biology from UCSF. She is interested in leveraging computational tools and approaches to study Alzheimer's Disease and other heterogeneous diseases of the brain.

Monica Yang, MD

Clinical Fellow

Monica is a Clinical Fellow of Rheumatology at UCSF. She earned her MD & completed her Internal Medicine Residency at Northwestern University. She is interested in utilizing transcriptomic approaches to better define disease heterogeneity & phenotypic diversity in autoimmune disease, particularly in Systemic Sclerosis.

Jacquelyn Roger, BS

Bioinformatics Graduate Student

Jackie earned her BS in bioinformatics with a minor in statistics from UCSC. She is interested in developing statistical methods to explore how clinical, biological, & social factors drive differences in pregnancy care and outcomes. In her free time, she enjoys hiking, playing tennis, going to the beach, & coffee.

Jean Costello, PhD

Postdoctoral Scholar

Jean received her PhD from UCSF for her research on the effects of maternal environmental exposures on pregnancy outcomes. She is currently interested in using electronic health records to examine bias in clinical care and preterm birth. In her free time, she enjoys weaving, going for bike rides, baking, and learning geography.

Silvia Miramontes, BA, MIDS

Bioinformatics Graduate Student

Silvia earned her BA in Applied Math and Master's of Information & Data Science from UC Berkeley. She previously worked in computer vision for applications in cancer and Alzheimer's Disease (AD). She is interested in developing a prediction model to explore how non-clinical features affect patients' risk of AD.

Lay Kodama, PhD

Postdoctoral Fellow

Lay is an MD/PhD student at UCSF currently applying to psychiatry residency programs. She received her PhD in Neuroscience working with Dr. Li Gan on neuroimmunological sex-differences in Alzheimer's disease. Lay is interested in leveraging EHR and bioinformatic tools to better understand neuropsychiatric symptoms of dementia.

Laura Almonte, BS

Bioinformatics Graduate Student

Laura graduated from the National Autonomous University of Mexico with a BS in Genomic Sciences. They are interested in developing tools for data integration with an emphasis on autoimmune disease. Outside of lab, Laura is a bird enthusiast and an avid patron of museums and local drag queen shows.

Umair Khan, BS

Bioinformatics Graduate Student

Umair graduated from Portland State University with a BS in Computer Science and Mathematics. He is interested in developing novel computational approaches to better understand disease, broadly construed. (Co-advised with Michael Keiser.).

Ernest Lee, MD

Clinical Fellow

Ernest is a dermatologist and physician-scientist with a BS in Physics from Caltech and MD/PhD in Bioengineering from UCLA. His primary research interests lie in combining structural and data-driven approaches to engineer novel therapies for autoimmune and inflammatory skin diseases, with a focus on precision medicine in dermatology.

Ophelia Yin, MD

Clinical Fellow

Ophelia is a clinical fellow in Maternal-Fetal Medicine at UCSF. She completed her MD at Johns Hopkins and her residency in Ob/Gyn at UCLA. She is interested in utilizing transcriptomic approaches to understand the immunologic contributions to placentation disorders in pregnancy, including placenta accreta and preeclampsia.

You!

We are hiring!

Check out our open positions here.





Alumni

  • Garret Bland, PhD, Postdoctoral Scholar (Data Scientist, Amunix)
  • Wendy Su, UCLA Undergraduate Student (Graduate Student, University of Pennsylvania)
  • Vienna Huang, UC Berkeley Undergraduate Student
  • Adi Siddharth, Bioinformatics Programmer / Research Associate (Graduate Student, Johns Hopkins University)
  • Alennie Roldan, Bioinformatics Programmer / Research Associate (Medical Student, Burrell College of Osteopathic Medicine)
  • Brian Le, PhD, Postdoctoral Scholar (Computational Biologist, Inflammatix)
  • Isha Karim, High School Student, Saint Francis High School
  • Grace Yang, High School Student, Dougherty Valley High School
  • Silvia Pineda, PhD, Postdoctoral Scholar (Assistant Professor in Statistical and Data Science, Universidad Complutense de Madrid)
  • Dmitry Rychkov, PhD, Postdoctoral Scholar (Scientist II, Engine Biosciences)
  • Stella Belonwu, PhD, PSPG Graduate Student (Science Communications Intern, Genentech)
  • Katharine Yu, PhD, BMS Graduate Student (Bioinformatics Scientist, Atreca)
  • Daniel Pique, PhD, Postdoctoral Scholar / Pediatrics Resident (Medical Genetics Resident, University of Colorado)
  • Gaia Andreoletti, PhD, Postdoctoral Scholar (Bioinformatics Scientist, Audentes Therapeutics)
  • 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

  • Antonio Leo Parraga, PhD: Aug 2022 - Dec 2022 (Spain)
  • Camilla Wibrand, PhD: Aug 2022 - Apr 2023 (Denmark)
  • Karolin Froelich, PhD: Apr 2019 - Sept 2019 (Germany)
  • Isam Ben Soltane: Apr 2019 - Aug 2019 (France)
  • Ramy Karam Aziz: Aug 2018 (Egypt)

Rotation Students

  • Cindy Barrios, BMI
  • Umair Khan, BMI
  • Grace Ramey, BMI
  • Ana Laura Almonte, BMI
  • Jay Liu, BMI
  • Sebastián Cruz González, BMI
  • Silvia Miramontes, BMI
  • Susanna Morin, BMI
  • 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)
  • Jennifer Yokoyama, PhD, Caroline Warly Solsberg (Memory and Aging Center, UCSF)

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.

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

Kouznetsov RC, Belonwu S, Li Y, Andreolett G, Oskotsky TT, Kodama L, Sirota M. Identifying Age-Specific Transcriptomic and Metabolomic Changes Induced by apoE Genotype in Mice. SSRN. 2023. DOI Name: 10.2139/ssrn.4465497
Yu K, Basu A, Yau C, Wolf DM, Goodarzi H, Bandyopadhyay S, Korkola JE, Hirst GL, Asare S, I-SPY 2 TRIAL investigators, Demichele A, Hylton N, Yee D, Esserman L, Veer L van ’t, Sirota M. Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes. bioRxiv. 2023. DOI Name: 10.1101/2023.03.30.534178
Roger J, Xie F, Costello J, Tang A, Liu J, Oskotsky T, Woldemariam S, Kosti I, Le B, Snyder M, Giudice L, Torgerson D, Shaw G, Stevenson D, Rajkovic A, Aghaeepour N, Glymour M, Cakmak H, Lathi R, Sirota M. Leveraging electronic health records to identify risk factors for recurrent pregnancy loss across two medical centers: a case-control study. Research Square. 2023. DOI Name: 10.21203/rs.3.rs-2631220/v1
Tang AS, Rankin KP, Cerono G, Miramontes S, Mills H, Roger J, Zeng B, Nelson C, Soman K, Woldemariam S, Li Y, Lee A, Bove Ri, Glymour M, Oskotsky T, Miller Z, Allen I, Sanders SJ, Baranzini S, Sirota M. Leveraging Electronic Medical Records and Knowledge Networks to Predict Disease Onset and Gain Biological Insight Into Alzheimer's Disease. medRxiv. 2023. medRxiv. 2023. DOI Name: 10.1101/2023.03.14.23287224
Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M. VMAP: Vaginal Microbiome Atlas During Pregnancy. medRxiv. 2023 DOI Name: 10.1101/2023.03.21.23286947
Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, Angelis MD, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee Li YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. medRxiv. 2023. DOI Name: 10.1101/2023.03.07.23286920
Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu H, Spillinger A, Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MV, Vanderboon EN, Hazard FK, Cho S, Avedian RS, Mohler DG, Zimel M, Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA. Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities. bioRxiv. 2023. DOI Name: 10.1101/2023.01.19.524562
Oskotsky TT, Bhoja A, Bunis D, Le BL, Kosti I, Li C, Houshdaran S, Sen S, Vallvé-Juanico J, Wang W, Arthurs E, Mahoney L, Lang L, Gaudilliere B, Stevenson DK, Irwin JC, Giudice LC, McAllister S, Sirota M. Applying a computational transcriptomics-based drug repositioning pipeline to identify therapeutic candidates for endometriosis. medRxiv. 2022. DOI Name: 10.1101/2022.12.20.22283736
Mortlock S, Houshdaran S, Kosti I, Rahmioglu N, Nezhat C, Vitonis AF, Andrews SV, Grosjean P, Paranjpe M, Horne AW, Jacoby A, Opoku-Anane J, Vo KC, Manvelyan E, Sen S, Ghukasyan Z, Collins F, Santamaria X, Saunders P, Kober K, McRae AF, Terry KL, Vallvé-Juanico J, Becker C, Rogers PAW, Irwin JC, Zondervan K, Montgomery GW, Missmer S, Sirota M, Giudice L. Global Endometrial DNA Multi-omics Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk. bioRxiv. 2022. DOI Name: 10.1101/2022.11.27.518106v1
Minot SM, Garb B, Roldan A, Tang A, Oskotsky T, Rosenthal C, Hoffman NG, Sirota M, Golob JL. Robust Harmonization of Microbiome Studies by Phylogenetic Scaffolding with MaLiAmPi. bioRxiv. 2022. DOI Name: 10.1101/2022.07.26.501561
Trowbridge J, Abrahamsson D, Jiang T, Wang M, Park JS, Morello-Frosch R, Sirota M, Goin DE, Zlatnick M, Woodruff TJ. Extending non-targeted exposure discovery of environmental chemical exposures during pregnancy and their association with pregnancy complications—a cross-sectional study. medRxiv. 2022. DOI Name: 10.1101/2022.03.07.22272040v1
Cuyler L, Yu K, Okimoto RA, Sirota M. Transcriptional fidelity enhances cancer cell line selection in pediatric cancers. bioRxiv. 2021. DOI Name: 10.1101/2021.10.01.462682v1
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
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

2023

Baglaenko Y, Wagner C, Bhoj VG, Brodin P, Gershwin ME, Graham D, Invernizzi P, Kidd KK, Korunsky I, Levy M, Mammen AL, Nizet V, Ramirez-Valle F, Stites EC, Williams MS, Wilson M, Rose NR, Ladd V, Sirota M. Making inroads to precision medicine for the treatment of autoimmune diseases: harnessing genomic studies to better diagnose and treat complex disorders. Cambridge Prisms: Precision Medicine. 2023. DOI name: 10.1017/pcm.2023.14
Vora B, Wen A, Yee SW, Trinh K, Azimi M, Green EAE, Sirota M, Greenberg AS, Newman JW, Giacomini KM. The Effect of Trimethoprim on Thiamine Absorption: A Transporter-Mediated Drug-Nutrient Interaction. Clin Pharmacol Ther. 2023. PMID: 37151050
Sperry MM*, Oskotsky TT*, Marić I, Kaushal S, Takeda T, Horvath V, Powers RK, Rodas M, Furlong B, Soong M, Prabhala P, Goyal G, Carlson KE, Wong RJ, Kosti I, Le BL, Logue J, Hammond H, Frieman M, Stevenson DK, Ingber DE, Sirota M**, Novak R**. Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients. PLoS Comput Biol. 2023. PMID: 37146076
Laurent SA, Strauli NB, Eggers EL, Wu H, Michel B, Demuth S, Palanichamy A, Wilson MR, Sirota M, Hernandez RD, Cree BAC, Herman AE, von Büdingen HC. Effect of Ocrelizumab on B- and T-Cell Receptor Repertoire Diversity in Patients With Relapsing Multiple Sclerosis From the Randomized Phase III OPERA Trial. Neurol Neuroimmunol Neuroinflamm. 2023 PMID: 37094998
Woldemariam SR, Tang AS, Oskotsky TT, Yaffe K, Sirota M. Similarities and differences in Alzheimer's dementia comorbidities in racialized populations identified from electronic medical records. Commun Med. 2023 PMID: 37031271
Rahmioglu N, Mortlock S, Ghiasi M, Møller PL, Stefansdottir L, Galarneau G, Turman C, Danning R, Law MH, Sapkota Y, Christofidou P, Skarp S, Giri A, Banasik K, Krassowski M, Lepamets M, Marciniak B, Nõukas M, Perro D, Sliz E, Sobalska-Kwapis M, Thorleifsson G, Topbas-Selcuki NF, Vitonis A, Westergaard D, Arnadottir R, Burgdorf KS, Campbell A, Cheuk CSK, Clementi C, Cook J, De Vivo I, DiVasta A, Dorien O, Donoghue JF, Edwards T, Fontanillas P, Fung JN, Geirsson RT, Girling JE, Harkki P, Harris HR, Healey M, Heikinheimo O, Holdsworth-Carson S, Hostettler IC, Houlden H, Houshdaran S, Irwin JC, Jarvelin MR, Kamatani Y, Kennedy SH, Kepka E, Kettunen J, Kubo M, Kulig B, Kurra V, Laivuori H, Laufer MR, Lindgren CM, MacGregor S, Mangino M, Martin NG, Matalliotaki C, Matalliotakis M, Murray AD, Ndungu A, Nezhat C, Olsen CM, Opoku-Anane J, Padmanabhan S, Paranjpe M, Peters M, Polak G, Porteous DJ, Rabban J, Rexrode KM, Romanowicz H, Saare M, Saavalainen L, Schork AJ, Sen S, Shafrir AL, Siewierska-Górska A, Słomka M, Smith BH, Smolarz B, Szaflik T, Szyłło K, Takahashi A, Terry KL, Tomassetti C, Treloar SA, Vanhie A, Vincent K, Vo KC, Werring DJ, Zeggini E, Zervou MI; DBDS Genomic Consortium; FinnGen Study; FinnGen Endometriosis Taskforce; Celmatix Research Team; 23andMe Research Team; Adachi S, Buring JE, Ridker PM, D'Hooghe T, Goulielmos GN, Hapangama DK, Hayward C, Horne AW, Low SK, Martikainen H, Chasman DI, Rogers PAW, Saunders PT, Sirota M, Spector T, Strapagiel D, Tung JY, Whiteman DC, Giudice LC, Velez-Edwards DR, Uimari O, Kraft P, Salumets A, Nyholt DR, Mägi R, Stefansson K, Becker CM, Yurttas-Beim P, Steinthorsdottir V, Nyegaard M, Missmer SA, Montgomery GW, Morris AP, Zondervan KT. The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions. Nat Genet. 2023. PMID: 36914876
De Francesco D, Reiss JD, Roger J, Tang AS, Chang AL, Becker M, Phongpreecha T, Espinosa C, Morin S, Berson E, Thuraiappah M, Le BL, Ravindra NG, Payrovnaziri SN, Mataraso S, Kim Y, Xue L, Rosenstein MG, Oskotsky T, Marić I, Gaudilliere B, Carvalho B, Bateman BT, Angst MS, Prince LS, Blumenfeld YJ, Benitz WE, Fuerch JH, Shaw GM, Sylvester KG, Stevenson DK, Sirota M, Aghaeepour N. Data-driven longitudinal characterization of neonatal health and morbidity. Sci Transl Med. 2023. PMID: 36791208
Benítez R, Yu K, Sirota M, Malats N, Pineda S. Characterization of the tumor-infiltrating immune repertoire in muscle invasive bladder cancer. Front Immunol. 2023. DOI name: 10.3389/fimmu.2023.986598
Maïer B, Tsai AS, Einhaus JF, Desilles JP, Ho-Tin-Noé B, Gory B, Sirota M, Leigh R, Lemmens R, Albers G, Olivot JM, Mazighi M, Gaudillière B. Neuroimaging is the new "spatial omic": multi-omic approaches to neuro-inflammation and immuno-thrombosis in acute ischemic stroke. Semin Immunopathol. 2023. PMID: 36786929

2022

Tang A, Woldemariam S, Roger J, Sirota M. Translational Bioinformatics to Enable Precision Medicine for All: Elevating Equity across Molecular, Clinical, and Digital Realms. Yearb Med Inform. 2022. PMID: 36463867
Sigdel TK, Fields PA, Liberto J, Damm I, Kerwin M, Hood J, Towfighi P, Sirota M, Robins HS, Sarwal MM. Perturbations of the T-cell immune repertoire in kidney transplant rejection. Front Immunol. 2022 PMID: 36466928
Abraham A, Le B, Kosti I, Straub P, Velez-Edwards DR, Davis LK, Newton JM, Muglia LJ, Rokas A, Bejan CA, Sirota M, Capra JA. Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth. BMC Med. 2022. PMID: 36167547
Goin DE, Abrahamsson D, Wang M, Jiang T, Park JS, Sirota M, Morello-Frosch R, DeMicco E, Zlatnik MG, Woodruff TJ. Disparities in chemical exposures among pregnant women and neonates by socioeconomic and demographic characteristics: A nontargeted approach. Environ Res. 2022. PMID: 36049512
Patterson SL, Sun S, Rychkov D, Katz P, Tsitsiklis A, Nakamura MC, Serpa PH, Langelier CR, Sirota M. Physical Activity Associates with Lower Systemic Inflammatory Gene Expression in Rheumatoid Arthritis. J Rheumatol. 2022 PMID: 35777820
Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye J, Sirota M. Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity. Front. Immunol. 2022. PMID: 35799782
Andrews S, Yang IJ, Froehlich K, Oskotsky T, and Sirota M. Large-scale placenta DNA methylation mega-analysis reveals fetal sex-specific differentially methylated CpG sites and regions. Scientific Reports. 2022. PMID: 35672357
Abrahamsson D, Siddharth A, Young TM, Sirota M, Park JS, Martin JW, Woodruff TJ. In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecular Structures. J Am Soc Mass Spectrom. 2022. PMID: 35649165
Lanata CM, Nititham J, Taylor KE, Solomon O, Chung SA, Blazer A, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Barcellos LF, Criswell LA. The dynamics of methylation of CpG sites associated with SLE subtypes in a longitudinal cohort. Arthritis Rheumatol. 2022. PMID: 35635730
Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, Sirota M. Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer's Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions. Frontiers in Aging Neuroscience. 2022. PMID: 35572130
Goin DE, Abrahamsson D, Wang M, Park JS, Sirota M, Morello-Frosch R, DeMicco E, Trowbridge J, August L, O’Connell S, Ladella S, Zlatnik MG, Woodruff TJ. Investigating geographic differences in environmental chemical exposures in maternal and cord sera using non-targeted screening and silicone wristbands in California. Journal of Exposure Science & Environmental Epidemiology. 2022. PMID: 35449448
Zinter MS, Versluys AB, Lindemans CA, Mayday MY, Reyes G, Sunshine S, Chan M, Fiorino EK, Cancio M, Prevaes S, Sirota M, Matthay MA, Kharbanda S, Dvorak CC, Boelens JJ, DeRisi JL. Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates. Sci Transl Med. 2022. PMID: 35263147
Ishiyama K, Arakawa-Hoyt J, Aguilar OA, Damm I, Towfighi P, Sigdel T, Tamaki S, Babdor J, Spitzer MH, Reed EF, Sarwal MM, Lanier LL; CMV Systems Immunobiology Group. Mass cytometry reveals single-cell kinetics of cytotoxic lymphocyte evolution in CMV-infected renal transplant patients. Proc Natl Acad Sci USA. 2022. PMID: 35181606
Tang AS, Oskotsky T, Havaldar S, Mantyh W, Bicak M, Warly-Solsberg C, Woldemariam S, Zeng B, Hu Z, Oskotsky B, Dubal D, Allen IE, Glicksberg B, and Sirota M. Deep phenotyping of Alzheimer's Disease Leveraging Electronic Medical Records Data Identifies Sex-Specific Clinical Associations. Nat Commun. 2022. PMID: 35115528
Oskotsky T*, Bajaj R*, Burchard J*, Cavazos T*, Chen I*, Connell W*, Eaneff S*, Grant T*, Kanungo I*, Lindquist K*, Myers-Turnbull D*, Naing ZZC*, Tang A*, Vora B*, Wang J*, Karim I*, Swadling C*, Yang J*, Lindstaedt B and Sirota M. Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students. PLOS Computational Biology. 2022. PMID: 35100256
Bunis D, Wang W, Vallve-Juanico J, Houshdaran S, Sen S, Soltane IB, Kosti I, Vo KC, Irwin J, Giudice LC, and Sirota M. Whole-tissue deconvolution and scRNAseq analysis identify altered endometrial cellular compositions and functionality associated with endometriosis. Front. Immunol. 2022. PMID: 35069565
Yu K, Ravoor A, Malats N, Pineda S, and Sirota M. A pan-cancer analysis of tumor-infiltrating B cell repertoires. Front. Immunol. 2022. PMID: 35069569

2021

Ahn R, Schaenman J, Qian Z, Pickering H, Groysberg V, Rossetti M, Llamas M, Hoffmann A, Gjertson D, Deng M, Bunnapradist S, Reed EF; CMV Systems Immunobiology Group. Acute and Chronic Changes in Gene Expression After CMV DNAemia in Kidney Transplant Recipients. Front Immunol. 2021 PMID: 34867983
Oskotsky T*, Marić I*, Tang A, Oskotsky B, Wong RJ, Aghaeepour N, Sirota M**, Stevenson DK**. Mortality Risk Among Patients With COVID-19 Prescribed Selective Serotonin Reuptake Inhibitor Antidepressants. JAMA Network Open. 2021. PMID: 34779847
Belonwu S, Li Y, Bunis D, Rao AA, Warly-Solsberg C, Tang A, Fragiadakis G, Dubal D, Oskotsky T, and Sirota M. Sex-stratified single-cell RNA-Seq analysis identifies sex-specific and cell type-specific transcriptional responses in Alzheimer's disease across two brain regions. Mol Neurobiol. 2021. PMID: 34669146
Le BL, Sper R, Nielsen SCA, Pineda S, Nguyen, QH, Lee JY, Boyd SD, Mackenzie, TC and Sirota M. Maternal and Infant Immune Repertoire Sequencing Analysis Identifies Distinct Ig and TCR Development in Term and Preterm Infants. J Immunol. 2021. PMID: 34654689
Taubes A Nova P, Zalocusky K. A, Kosti I, Bicak M, Zilberter M. Y, Hao Y, Yoon SY, Oskotsky T, Pineda S, Chen B, Jones AEA, Choudhary K, Grone B, Balestra ME, Chaudhry F, Paranjpe I, De Freitas J, Koutsodendris N, Chen N, Wang C, Chang W, An A, Glicksberg BS, Sirota M, Huang Y. Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease. Nature Aging. 2021. PMID: 36172600
Kim GJ, Mo H, Liu H, Wu Z, Chen S, Zheng J, Zhao X, Nucum D, Shortland J, Peng L, Elepano M, Tang B, Olson S, Paras N, Li H, Renslo AR, Arkin MR, Huang B, Lu B, Sirota M, Guo S. A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons. Elife. 2021. PMID: 34550070
Pineda S, López De Maturana E, Yu K, Ravoor A, Wood I, Malats N and Sirota M. Tumor-infiltrating B and T cell repertoire in pancreatic cancer associated with host and tumor features. Front Immunol. 2021. PMID: 34630409
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. Front Aging Neurosci. 2021. PMID: 34658838
Tang A, Oskotsky T, Sirota M. Personalizing routine lab tests with machine learning. Nat Med. 2021. PMID: 34518677
Sarma A, Christenson SA, Byrne A, Mick E, Pisco AO, DeVoe C, Deiss T, Ghale R, Zha BS, Tsitsiklis A, Jauregui A, Moazed F, Detweiler AM, Spottiswoode N, Sinha P, Neff N, Tan M, Serpa PH, Willmore A, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA; COMET Consortium, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS. Nat Commun. 2021. PMID: 34446707
Davis EJ, Solsberg CW, White CC, Miñones-Moyano E, Sirota M, Chibnik L, Bennett DA, De Jager PL, Yokoyama JS, Dubal, DB. Sex-Specific Association of the X Chromosome With Cognitive Change and Tau Pathology in Aging and Alzheimer Disease. JAMA Neurol. 2021. PMID: 34424272
Gillis-Buck E, Miller H, Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC. Extrathymic Aire-expressing cells support maternal-fetal tolerance. Sci Immunol. 2021. PMID: 34272228
Abrahamsson D, Wang A, Jiang T, Wang M, Siddharth A, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ. Comprehensive Non-Targeted Analysis Study of the Prenatal Exposome. Environ Sci Technol. 2021. PMID: 34260856
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. Cell Reports Medicine. 2021. PMID: 34195686
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. Scientific Reports. 2021. PMID: 34112877
Rychkov D, Neely J, Oskotsky T, Yu S, Perlmutter N, Nititham J, Carvidi A, Krueger M, Gross A, Criswell LA, Ashouri JF, Sirota M. Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis. Frontiers in Immunology. 2021. PMID: 34177888
Vora B, Brackman DJ, Zou L, Garcia‐Cremades M, Sirota M, Savic RM, Giacomini KM. Oxypurinol pharmacokinetics and pharmacodynamics in healthy volunteers: Influence of BCRP Q141K polymorphism and patient characteristics. Clinical and Translational Science. 2021. PMID: 33931953
Andreoletti G, Lanata CM, Trupin L, Paranjpe I, Jain TS, Nititham J, Taylor KE, Combes AJ, Maliskova L, Ye CJ, Katz P, Era MD, Yazdany J, Criswell LA, Sirota M. Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures. Communications Biology. 2021. PMID: 33883687
Yee SW, Vora B, Oskotsky T, Zou L, Jakobsen S, Enogieru OJ, Koleske ML, Kosti I, Rödin M, Sirota M, Giacomini KM. Drugs in COVID19 clinical trials: Predicting transporter‐mediated drug‐drug interactions using in vitro assays and real‐world data. Clinical Pharmacology and Therapeutics. 2021. PMID: 33759449
Wang A, Abrahamsson D, Jiang T, Wang M, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ. Suspect Screening, Prioritization, and Confirmation of Environmental Chemicals in Maternal-Newborn Pairs from San Francisco. Environ Sci Technol. 2021. PMID: 33726493
Enogieru OJ, Koleske ML, Vora B, Ngo H, Yee SW, Chatad D,Sirota M, Giacomini KM. The Effects of Genetic Mutations and Drugs on the Activity of the Thiamine Transporter, SLC19A2. AAPS. 2021. DOI: 10.1208/s12248-021-00562-4
Marić 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. PMID: 33614688
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. PMID: 33406429
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. 2021. DOI name: 10.1182/blood.2020009246

2020

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. 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. PMID: 32379974
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. PMID: 32454518
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. PMID: 32322240
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. PMID: 32123307
Le BL, Iwatani S, Wong RJ, Stevenson DK, Sirota M. Computational discovery of therapeutic candidates for preventing preterm birth. JCI Insight. 2020. 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. 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. 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. 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. 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. 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. 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. 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. PMID: 31395879.
Paranjpe MD, Taubes A, Sirota M. Insights into Computational Drug Repurposing for Neurodegenerative Disease. Trends Pharmacol Sci. 2019. 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. 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. 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. 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. 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. 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. 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. 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. PMID: 30075861.
Pineda S, Sirota M . Determining Significance in the New Era for p-Values. J Pediatr Gastroenterol Nutr. 2018. 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. 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. PMID: 29867970.
Kosti I, Sirota M. Electronic Medical Records Enable Precision Medicine Approaches for Celiac Disease. J Pediatr Gastroenterol Nutr. 2018. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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.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. 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. 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.PMID: 28353614.
Sirota M, Sarwal M. Transplantomics: Towards Precision Medicine in Transplantation Research. Transplantation, 2017. 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. 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. 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. PMID: 27860440.
Wang A, Padula A, Sirota M, Woodruff TJ. Environmental influences on reproductive health: the importance of chemical exposures. Fertil Steril, 2016. Review. 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. 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. 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. 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. 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. 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. 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. 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.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. 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.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. 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. 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. PMID: 22499789.

2012

Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol, 2012. 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. 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. 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. 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. PMID: 21849664.
Sirota M, Butte AJ. The role of bioinformatics in studying rheumatic and autoimmune disorders. Nat Rev Rheumatol, 2011. 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. 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. 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. 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. 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. 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. PMID: 18096039.

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