Michelle Min Rui Li

MICHELLE MIN RUI LI

Email: [email protected] Website: scholar.harvard.edu/michelleli Github: michellemli Twitter: michellemli

EDUCATION Harvard University 2019 - Present Ph.D. Candidate in Biomedical Informatics Advisor: Prof. Marinka Zitnik Stanford University 2015 - 2019 B.S. Mathematical and Computational Science with Departmental Honors

RESEARCH EXPERIENCE Harvard Medical School, Department of Biomedical Informatics 2020 - Present Graduate Student Researcher Advisors: Prof. Marinka Zitnik, Dr. Isaac Kohane Harvard Medical School, Department of Biomedical Informatics 2019 Graduate Student Researcher Advisor: Prof. Michael Baym Genentech, Pharmaceutical Technical Operations 2019 Protein Analytical Chemistry Intern Stanford School of Medicine, Department of Genetics 2017 - 2019 Research Assistant Advisor: Dr. Ami Bhatt Stanford School of Medicine, Department of Emergency Medicine 2016 - 2019 Research Assistant Advisor: Dr. Samuel Yang Stanford University, Department of Biology 2016 Research Assistant Advisor: Prof. Tadashi Fukami Stanford University, Department of Biology 2016 Research Assistant Advisor: Prof. Erin Mordecai Stanford School of Medicine, Department of Infectious Diseases 2015 - 2016 Research Assistant Advisor: Dr. Julie Parsonnet Hunter College & Weill Cornell Medicine, Department of Biological Sciences 2014 - 2015 Research Assistant Advisor: Prof. Konstantinos Krampis

PUBLICATIONS Preprints & In Review · Li, M., Huang, K., Zitnik, M. Representation Learning for Networks in Biology and Medicine: Advancements, Challenges, and Opportunities. arXiv:2104.04883 (2021). · Cogill, S., Hashemi, M., Yang, X., Andini, N., Li, M., et al. Predicting high-resolution melt curves from sequence data using generative adversarial networks. In Review.

1 · Severyn, C., Siranosian, B., Kong, S., Moreno, A., Li, M., et al. Impact of gut decontamination on the intestinal microbiome composition and the risk of bloodstream infection (BSI) in pediatric allogeneic hematopoietic stem cell transplant (allo-HSCT) patients. In Review.

Peer-Reviewed Articles · ‡Trella, A., Argaw, P.∗, Li, M.∗, Hay, J. Discrepancies in Epidemiological Modeling of Aggregated Heterogeneous Data. International Joint Conference on Artiﬁcial Intelligence (IJCAI) Workshop on AI for Social Good (2021). · †Li, M., Zitnik, M. Deep Contextual Learners for Protein Networks. International Conference on Machine Learning (ICML) Workshop on Computational Biology (2021). · Alsentzer, E.∗, Finlayson, S.∗, Li, M., Zitnik, M. Subgraph Neural Networks. NeurIPS (2020). · Yang, X., Hashemi, M., Andini, N., Li, M., et al. RNA markers for ultra-rapid molecular antimicrobial suscep- tibility testing in ﬂuoroquinolone-treated Klebsiella pneumoniae. Journal of Antimicrobial Chemotherapy (2020). · Severyn, C., London, W., Kao, P., Silverstein, S., Li, M., et al. Longitudinal Changes in the Intestinal Micro- biome Composition Following Gut Decontamination in Pediatric Allogeneic Hematopoietic Stem Cell Transplant Patients: A Pilot Study. Blood (2019). · Durrant, M., Li, M., et al. A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation. Cell Host & Microbe (2019).

PRESENTATIONS Invited Talks & Seminars · Trella, A., Argaw, P.∗, Li, M.∗, Hay, J. Discrepancies in Epidemiological Modeling of Aggregated Heterogeneous Data. Talk presented at: 3rd Workshop on Artiﬁcial Intelligence for Social Good at IJCAI; 2021 August; Virtual. · Li, M., Zitnik, M. Deep Contextual Learners for Protein Networks. Spotlight talk and poster§ presented at: ICML Workshop on Computational Biology; 2021 July; Virtual. · Li, M. Deep Contextual Learners for Protein Networks. Seminar talk presented at: Summer Institute in Biomed- ical Informatics at Harvard Medical School; 2021 July; Virtual. · Li, M. Primer: Deep Learning for Biomedical Networks: Methods, Challenges, and Frontiers. Seminar talk presented at: Models, Inference & Algorithms Seminar at the Broad Institute; 2021 May; Virtual. · Li, M.∗, Yang, A.∗ Metagenomics: The Variance of Microbial Communities Based on Environmental Conditions. Paper, poster, and talk presented at: New York City STEM Colloquium at the American Museum of Natural History; 2015 June 20; New York, NY.

Selected Poster Presentations · Li, M., Zitnik, M. From Single-Cells to Patients: Formulating Learning Tasks for Biomedical Graphs. Poster session presented at: 11th Annual Graph Exploitation Symposium; 2021 May; Virtual. · Li, M., Zitnik, M. Deep Learning for Interconnected Biomedical Data. Poster session presented at: NHGRI Annual Meeting; 2021 April; Virtual. · Li, M.∗, Dong, G.∗, Ryu, J.∗, Tang, A.∗, Bˇrinda,K., Baym, M. Benchmark of assembly tools for Nanopore sequencing of phage genomes. Poster session presented at: NHGRI Annual Meeting; 2020 March; Virtual. · Li, M., Li, D., Tam, J., Moore, B., Yang, F. Standardized Disulﬁde Mapping Workﬂow for IND and BLA Reports. Poster session presented at: 2019 Annual Intern Poster Day; 2019 August 5; South San Francisco, CA. · Severyn, C., Li, M., Bhatt, AS., Whangbo, J. Impact of gut decontamination on intestinal microbiome composition in pediatric allogeneic hematopoietic stem cell transplant patients. Poster session presented at: 2019 Cold Spring Harbor meeting: Microbiome; 2019 July 18-21; Cold Spring Harbor, NY.

‡Selected for full-length oral presentation ∗Equal contribution †Selected for spotlight presentation §Best Poster Award

2 · Severyn, C., Li, M., Bhatt, AS. Understanding how the microbiome inﬂuences outcomes with pediatric hematology & oncology patients. Poster session presented at: Inaugural 2018 Maternal and Child Health Research Institute Symposium; 2018 November 16; Stanford, CA. · Li, M., Durrant, M., Bhatt, AS. Mustache: A new tool to identify strain-level insertion sequence variants from bacterial isolates and metagenomic whole-genome sequencing data. Poster session presented at: Symposia of Undergraduate Research and Public Service; 2018 April 28; Stanford, CA. · Li, M.∗, Vervillow, A.∗, Ke, PJ., Fukami, T. Plant-Soil Relationships in Bodega Dunes. Poster session presented at: Symposia of Undergraduate Research and Public Service; 2016 August 26; Stanford, CA.

TEACHING EXPERIENCE Harvard Medical School · Tutor, Department of Biomedical Informatics, Fall 2021. · Teaching Fellow, BMIF 201, Concepts in Genome Analysis, Summer 2020, Fall 2020.

Alexander Twilight Academy · Lead Teacher, Game Development Incubator, Fall 2020 - Spring 2021, Summer 2021. · Lead Teacher, Foundations of Coding Through Graphics, Fall 2020 - Spring 2021. · Lead Teacher, Coding Through Creative Expression, Summer 2020. · Lead Teacher, Introduction to Probability, Fall 2019 - Spring 2020.

Stanford University · Section Leader, CS 106A, Code in Place, Spring 2020, Spring 2021. · Grader, Math 51, Linear Algebra and Diﬀerential Calculus of Several Variables, Fall 2017. · Instructor, Music 4SI, Interactive Introduction to North American Taiko, Winter 2015, Winter 2018.

Non-Proﬁt Organizations · Instructor, Workshop in Computational Biology with Girls Teaching Girls to Code, Winter 2017. · Instructor, Workshop in Artiﬁcial Intelligence with Girls Teaching Girls to Code, Winter 2015. · Peer Tutor, After-school Mandarin with the TEAK Fellowship, Fall 2014 - Summer 2015.

RESEARCH GRANTS

Misra, A., Dawkins, J., Arizti, J., Kang, JB., Li, M. Characterizing changes of the skin microbiome of patients with chronic pain (small fiber neuropathy) in response to intravenous immunoglobulin treatment. CMIT-HST Clinical Study Award, November 2019, $50,000 funded. Li, M., Durrant, M, Moss, E, Bhatt, AS. Pipeline for Predicting Functional Effects of Insertion Sequences in Anti-PD-1 Immunotherapy Patients’ Gut Microbiomes. Stanford Undergraduate Advising and Research Major Grant, April 2018, $7,000 funded. Li, M., Bhatt, AS. Pipeline for Predicting Functional Effects of Insertion Sequences in Anti-PD-1 Immunotherapy Patients’ Gut Microbiomes. RBC College Success Fund of The TEAK Fellowship, April 2018, $1,700 funded. Li, M., Durrant, M, Bhatt, AS. Survey of Insertion Sequences in the Skin Microbiome. Stanford Undergraduate Advising and Research Major Grant, March 2017, $7,000 funded.

HONORS & AWARDS Harvard University · Sigma Xi, The Scientiﬁc Research Honor Society, Associate Membership Nomination, 2021. · National Science Foundation (NSF) Graduate Research Fellowship, 2021. · NHGRI T32 Training Grant in the Bioinformatics and Integrative Genomics Program, 2019 - 2021. · Graduate Prize Fellowship, 2019.

3 Stanford University · Barry M. Goldwater Scholarship Honorable Mention, 2018. · The Jane McConnell and T. J. Heyman Undergraduate Scholarship Fund, Fall 2018 - Spring 2019. · The Richard Beleson Scholarship Fund in Honor of Professor Allan Campbell and Doctor Alice del Campillo Campbell, Fall 2018 - Spring 2019. · Gabriel, William & Antoinette Scholarship, Fall 2017 - Spring 2018. · Stanford Exposure to Research and Graduate Education Program, Fall 2017. · The Marcia Cass and Richard I. Stewart Scholarship Fund, Fall 2016 - Spring 2017. · Stanford VPUE Department of Biology Program, Summer 2016, $7,000 research stipend awarded.

VOLUNTEERING EXPERIENCE Conferences & Panels · Lead Organizer, Transforming Simple Musings into Well-Deﬁned Research Questions, 08/2021. · Panelist, My Journey into Geometric ML at London Geometry and Machine Learning Summer School, 07/2021. · Panelist, AI Research Panel at Rewriting the Code: Tech Tuesday, 03/2021. · Publicity & Public Relations Co-Chair, NSF Nat. Symp. on Drug Repurp. for Future Pandemics, 11/2020. · Panelist, Graduate School Panel at the TEAK Fellowship, 08/2020. · Student Volunteer, 2020 Programming Language Design and Implementation Conference, 06/2020.

Journal Review & Editorial Boards · Reviewer: SIGKDD (2021), ISMB/ECCB (2021), NeurIPS (2021). · Member, National Human Genome Research Institute (NHGRI) Editorial Board, 04/2020 - Present. · Copy Editor, Reviewer, Journal of Emerging Investigators, 09/2019 - Present.

Mentorship & Outreach · Board Member, SRMPmachine, American Museum of Natural History, 07/2021 - Present. · Mentor, MITxHarvard Women in Artiﬁcial Intelligence, 09/2020 - Present. · Founding Co-Chair, Mentor, Young Women in STEM: Mentoring Program in India, 07/2020 - Present. · Executive Board Member, Harvard Graduate Women in Science and Engineering, 07/2020 - Present. · Mentor, Women in STEM Mentoring Program at Harvard College, 09/2019 - Present.