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Principal investigator John M. Marshall, PhD Assistant Professor in Residence Division of Biostatistics & Epidemiology School of Public Health Innovative Genomics Institute Center for Computational Biology University of California, Berkeley Mailing address: School of Public Health, 2121 Berkeley Way #5302, UC Berkeley, Berkeley, CA 94720-7360, USA Phone: +1-510-664-4724 Office: 2121 Berkeley Way #5328 Email: john.marshall@berkeley.edu Website: http://www.MarshallLab.com Google Scholar: https://scholar.google.com/citations?user=aG77NyAAAAAJ&hl=en Current CV: JohnMarshallCV.pdf |
John received his PhD in biomathematics from UCLA in 2008 writing his dissertation on the use of GM mosquitoes to control malaria transmission. Prior to joining UC Berkeley, he worked on several aspects of this project as a PostDoc - social, cultural and regulatory issues at the UCLA Center for Society & Genetics, ecological field work at the Malaria Research and Training Center in Mali, molecular biology and population genetics at Caltech, and infectious disease modeling and epidemiological field work at Imperial College London. Here at UC Berkeley, he teaches two courses on mathematical modeling of infectious diseases and consults on this field generally. His own research focuses on the use of mathematical models to inform novel genetics-based strategies for mosquito control, and to support efforts to control and eliminate mosquito-borne diseases such as malaria, dengue and Zika virus broadly.
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PostDocs
Héctor M. Sánchez C., PhD
Héctor received his BSc in 2009 in Mechatronics Engineering and his PhD in 2017 in Computer Science at Tecnológico de Monterrey, México. In the past he collaborated in animal vocalizations research with Charles Taylor (UCLA), and the Malaria Elimination Initiative (UCSF). He was awarded one of the 2016 Google Research Awards in Latin America to work on predicting Zika epidemics through the use of social networks; and worked as a consultant for Dr. David L. Smith (UW) in the development of a framework for epidemiological simulations. His work focuses on the creation and use of computational individual-based models to contain and eliminate mosquito-borne diseases. He joined the Marshall Lab in July, 2017. He loves guitars, singing, Pusheen and FPV quadcopters... oh yeah... and programming! Email: sanchez.hmsc@berkeley.edu Website: https://chipdelmal.github.io/ |
Yogita Sharma, PhD
Yogita received her MSc in 2010 in Mathematics from Panjab University. She recently obtained her PhD in Mathematical Biology from the Department of Mathematics at the Indian Institute of Technology, Ropar. She is mainly interested in mathematical modeling of gene drive systems in insect populations. Her research focuses on understanding regime shifts in bistable biological systems, which includes occurrence of sudden, catastrophic and often irreversible shifts from one state to another. The majority of her work is based on the analysis of regime shifts using early warning signals considering mathematical models of different types of stochastic bistable biological systems. Examples include models of gene expression and ecological models of insect outbreaks in the presence of diverse stochastic environments. She will be joining the Marshall Lab in January, 2018. Email: yogita.sharma@berkeley.edu |
Tomás León, PhD
Tomás graduated from Georgia Tech with a BS in Environmental Engineering (2012) and from UC Berkeley with an MS in Global Health & Environment (2014) and a PhD in Environmental Health Sciences (2018). His dissertation research focused on environmental transmission of liver fluke (Opisthorchis viverrini) parasites in Thailand and its prevention and control, with insights from hydrology. Other experience includes laboratory work differentiating environmental and commensal E. coli, brownfields assessment and exposure modeling at CDC, and field work in China designing and testing protocols to capture Schistosoma japonicum cercariae in the environment. His postdoctoral work in the Marshall Lab will focus on measuring and modeling the role of the environment in mosquito movement and ecology, particularly as they relate to gene drive strategies. In his leisure time, he enjoys reading, hiking, and volunteering in the East Bay. Email: tomas.leon@berkeley.edu Website: https://tomasleon.com/ |
Victor Ferman, PhD
Victor graduated from Tecnológico de Monterrey, México with a BSc (2009) and a PhD (2016) in Computer Science. His dissertation research focused on the intersection of Formal Methods and Computer Security and took form as a model checker for web applications and security protocols. Before joining the Marshall Lab in October 2018 he was working on an anomaly detection platform that included Machine Learning and Data Visualization in near real time. His postdoctoral work in the Marshall Lab will focus on the use of Machine Learning, and Data Analysis and Visualization in order to assist with computational models used to contain and eliminate mosquito-borne diseases. He loves learning and discovering new stuff. Email: vferman@berkeley.edu |
Gordana Rašić, PhD
Gordana received her MSc in biology in 2005 from the University of Belgrade (Serbia) working on Drosophila population genetics, and her PhD in biology in 2011 from the University of Western Ontario (Canada) where she built an empirical model system in Landscape Genetics using pitcher plant insects. Since 2012, her work has been focused on the development of molecular and bioinformatics tools and analytical frameworks for the implementation of innovative vector control strategies, such as Wolbachia-based suppression of arboviral diseases transmitted by Aedes mosquitoes. Gordana has established mosquito population genomics/bioinformatics platforms within two Australian research institutions (University of Melbourne and QIMR Berghofer) and she leads this research component on several international collaborative projects within the Mosquito Control Laboratory at QIMR Berghofer, as well as advises projects in France, Singapore and Spain. With Dr. Marshall, Gordana is devising robust approaches for inferring mosquito dispersal patterns and their impact on innovative vector control strategies in different landscapes. Email: Gordana.Rasic@qimrberghofer.edu.au |
Samson S. Kiware, PhD
Samson is a visiting PostDoc on a Wellcome Trust fellowship with special interests in developing informatics systems and mathematical models based on infectious diseases, especially malaria. His current research projects involve developing and supporting informatics system for collecting and standardizing entomological and environmental datasets. He is also working with a team to create effective user-friendly interfaces that enable multiple researchers to more effectively collaborate, share and synthesize data using standardized formats across multiple studies and sites. His main focus is to develop a vector control optimization model that can be used to evaluate impacts and cost-effectiveness of combined vector control tools. Other research plans include developing a one-stop-shop for all malaria-related data and vector-human transmission models to evaluate vector control interventions and antimalarial drugs. Other research interests include advanced technologies to sample and analyze mosquitoes, the role of human movement in malaria transmission, and development of user-friendly interfaces for malaria data and models to increase uptake by NMCPs. Email: skiware@ihi.or.tz Website: http://ihi.or.tz/staff/dr-samson-kiware/ |
Graduate students
Sean L. Wu, MPH
Sean graduated from UC Irvine in 2013 where he studied International Relations & Statistics. In 2016 he obtained his MPH from UC Berkeley in Epidemiology & Biostatistics. He is currently pursuing his PhD in Epidemiology with a concentration in Computational Biology under Dr. John Marshall at UC Berkeley. He is interested in applying ideas from dynamical systems and stochastic process theory to questions of vector-borne disease control. He simultaneously likes and hates programming, and purely likes cooking, archery, hiking, and drawing. Email: slwu89@berkeley.edu Website: https://slwu89.github.io |
Jared Bennett, BSc
Jared completed honors bachelors of science in Biochemistry, Molecular Genetics, and Physics with honors minors in Math and Music Performance from The Ohio State University in 2014. After graduation, he worked under Dr. Richard Fishel studying DNA Mismatch Repair using single-molecule microscopy techniques. In the fall of 2016, Jared began a PhD program at UC Berkeley in Biophysics with a designated emphasis in Computational Biology. He is currently studying the evolutionary characteristics of CRISPR/Cas mediated gene drives. Email: jared_bennett@berkeley.edu |
Valeri Vasquez, MS
Valeri Vasquez is a PhD student with the Energy and Resources Group, a Moore/Sloan Fellow at the Berkeley Institute for Data Science, and a former research scholar in the Renewable and Appropriate Energy Laboratory. Valeri’s research interests include the use of computational models to examine the environmental drivers and economic impacts of infectious diseases. She is currently studying questions relevant to the use of gene drive systems for malarial control. Prior to graduate school, Valeri focused on international and domestic climate change issues at the U.S. Department of State, the Center for American Progress, and the White House Council on Environmental Quality. In addition, she served as primary advisor to the co-chair of the United Nations negotiations that culminated in the Paris Agreement on climate change in 2015. Valeri received her MS from the University of California, Berkeley and her BA from the College of William and Mary. Email: vnvasquez@berkeley.edu |
Thien-An Ha, BS
Thien-An received her BS in Biology from the University of Maryland, Baltimore County with minors in Chemistry and English. During her undergraduate studies, her research focused mainly on genetic diseases such as Cystic Fibrosis. Her focus shifted towards infectious diseases when she traveled abroad and noticed the impact of poor health infrastructure on low-income Asian communities. She is currently in her first year of the Epidemiology & Biostatistics MPH program at UC Berkeley and is excited to learn more about math modeling and its capabilities of tackling global health issues. Email: thienanha@berkeley.edu |
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Francois Rerolle, MS
Francois graduated from Ecole Polytechnique in Paris in 2014 where he studied Engineering, Mathematics and Physics. In 2015 he obtained his MS from Stanford University in Environmental Engineering. He is currently pursuing his PhD in Epidemiology at UCSF under the supervision of Dr. Adam Bennett and Dr. Hugh Sturrock at the Malaria Elimination Initiative (MEI). He is interested in geo-spatial modeling, sampling designs and mathematical models to target high risk populations and inform national programs working towards malaria eradication. With Dr. John Marshall, Francois is trying to evaluate vector control intervention parameters to be included in predictive risk mapping. He is an outdoor guy, enjoying surfing, sailing, hiking and climbing and sneaks out of the lab whenever he gets a chance. Email: Francois.Rerolle@ucsf.edu |
Undergraduate students
Biyonka Liang
Biyonka Liang is a rising junior studying Statistics with a Mathematics concentration. She works most closely with Sean Wu, especially on the MASH project. When she’s not coding away in R, she enjoys rock climbing, learning new piano pieces and playing video games. Email: biyonkaliang@berkeley.edu |
Sarafina Smith
Sarafina is a second year studying Computer Science. She and Sabrina Wong code under the mentorship of Dr. Héctor Sanchez, mainly for the MGDrive project. Apart from coding Sarafina enjoys dancing, hiking, cooking and traveling. Email: sarafinasmith@berkeley.edu |
Sejal Mohata
Sejal is a visiting scholar from India in her junior year studying Computer Science. She is an AI researcher mainly interested in Computer Vision. She will be working under the mentorship of Tomás León for the MGDrive project. When she is not coding, she drinks coffee and writes poems. Email: sejalmohata@berkeley.edu Website: https://smohata.github.io/ |
Maya Shen
Maya is a junior studying Computer Science. She is working on target product profiles for gene drive systems intended for malaria control under the mentorship of Dr. Héctor Sánchez. In her free time, Maya enjoys reading, doodling, hiking, and dreaming about exploring Scotland and Spain. Email: mayashen@berkeley.edu |
Gillian Chu
Gillian is a junior studying Computer Science and Bioengineering. This semester, she's working on clustering and landscape analysis under the mentorship of Dr. Hector Sanchez. In her free time, Gillian likes to read, run, cook and build things she thinks should exist. Email: gillichu@berkeley.edu |
Yi Li
Yi Li is a senior studying towards an honors degree in theoretical mathematics and data analytics at the Ohio State University. He is currently working on close-kin mark-recapture methods and their potential applications to the MGDrive project. Apart from coding and reading papers, he enjoys hiking, traveling around the world and playing badminton. Email: li.5520@osu.edu |
Lab alumni
- Benjamín Valdés Aguirre (Tecnológico de Monterrey, Mexico, Computer Science): Former visiting teaching faculty, 2018
- Graham Northrup (UC Berkeley, PhD Computational Biology): Former graduate researcher, 2018
- Qinlong Jing (Sun Yat-sen University, China, PhD Epidemiology & Medical Statistics): Former visiting graduate researcher, 2017-2018
- Partow Imani (UC Berkeley, PhD Biostatistics): Former graduate researcher, 2017-2018
- Suzanne Dufault (UC Berkeley, PhD Biostatistics): Former graduate researcher, 2017-2018
- Sabrina Wong (UC Berkeley, Applied Mathematics major): Former undergraduate researcher, 2017-2018
- Shaina Desai (UC Berkeley, Public Health major): Former undergraduate researcher, 2017-2018
- Aiden Baek (UC Berkeley, Public Health major): Former undergraduate researcher, 2017-2018
- Chloe Tarrasch (UC Berkeley, Statistics major): Former undergraduate researcher, 2016-2017
- Lina Montoya (UC Berkeley, MA Biostatistics): Former graduate researcher, 2016
- Jaclyn Guerrero (UC Berkeley, MPH Epidemiology & Biostatistics): Former MPH thesis student, 2015-2016
- Hannah Sumiko Daly (UC Berkeley, Public Health major): Former undergraduate researcher, 2015
- Raíra Marotta (Escola Nacional de Ciências Estatísticas, Brazil, Statistics major): Former visiting undergraduate researcher, 2015
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