Welcome to the Colubri Laboratory (CoLabo) in the Genomics and Computational Biology Department at the University of Massachusetts Chan Medical School. Our team brings together computational scientists, software engineers, and visual designers to develop new methods and tools for infectious disease research. With our partners at the Broad Institute of MIT and Harvard and The Inspire Project, we have created Operation Outbreak, the world's first live, app-based outbreak simulator to generate ground-truth datasets, validate predictive models, and improve the response to future pandemics. We seek collaborations at the intersection of epidemiology, genomics, machine learning, data visualization, and mobile technologies with the goal of advancing an interdisciplinary vision of outbreak science.
Our Team
Current Members
  • Askar Temirbek

    Askar is a graduate student in the lab. He did undergraduate studies at UMass Amherst in Biochemistry and Molecular Biology as well as graduate studies at WPI in Bioscience Management and at Harvard in Nanotechnology. He was a Drug Product Design and Development scientist at Pfizer working on cutting-edge nanomedicines such as ACCURINS and COVID-19 vaccine. Askar is interested in creating next-generation bioinformatics visualization tools and using machine learning for a diverse range of applications.

  • Mansi Khandpekar

    Mansi recently joined CoLabo as a UX and Data Visualization Designer, having earned her master’s in Information Design and Data Viz at Northeastern University. She previously interned at CoLabo, working on a new UI for the Operation Outbreak Project. With an architecture background from India, she’s now eager to integrate design and technology for seamless user experiences in Science and Medicine. Outside of work, she enjoys evening strolls in Boston Public Gardens, doodling, and exploring new art techniques.

  • Isha Nagireddy

    Isha Nagireddy is a junior in high school at Massachusetts Academy of Math and Science at WPI. Her interests are in machine learning and bioinformatics, with her main goal being to impact the healthcare industry through computer science. In particular, Isha has done research in medical app development and disease detection models. She is currently working on the project ClinicApp at CoLabo. In her free time, she enjoys playing volleyball!

  • Andrés Colubri

    Principal Instigator at CoLabo. Andrés originally studied mathematics at the Universidad Nacional del Sur in his native Argentina, and then carried out an MFA in Design Media Arts at the University of California, Los Angles. He did work in protein folding, infectious diseases, shader programming, data visualization, and creative coding, and now brings this ecletic experience to UMass.

  • Faith Shim

    Faith is an undergraduate at Brown University concentrating in Computer Science on the Pre-Med track. Her interests range from ML and data to medicine and the intersections between both fields. She is currently working with Andres and the CoLabo members on developing ClinicApp. During her free time, she enjoys listening and playing music and taking film pictures!

  • Justin Guerra

    Justin graduated from The University of Texas at San Antonio with a B.S in Mathematics and a minor in Statistics. My current research interests are using ML and statistical methods to analyze public health data to provide insights on disease from different populations. I am currently working on analyzing data for the PERM project to predict the chance of malnutrition within Indian children from public data. Outside of work, I love playing and teaching chess around the East Coast!

  • Andonaq Grozdani

    Andi is the Mobile App Software Developer in the lab. He has a B.S. in Computer Science at the University of Massachusetts Dartmouth. He has previously developed an app called Mvral which stores memories in specific locations around the world. On his free time he likes to read, workout, and work on car mechanics.

  • Winnie Mkandawire

    Winnie is a GSBS graduate student on rotation in the lab. She holds a MSc in Bioinformatics and Computational Biology from Worcester Polytechnic Institute, MSc in Applied Epidemiology/Biostatistics, PGDip in Bioinformatics from University of Malawi – College of Medicine and BSc in Biomedical Sciences from Mzuzu University. Her rotation project is focused on using collaborative machine learning techniques to develop a COVID-19 personalized risk prediction model. Outside the lab, she enjoys music/singing, cooking and nature visitation.

  • Salihu Musa

    Dr. Musa received his PhD in Mathematical Epidemiology from the Hong Kong Polytechnic University, Hong Kong, M.Sc. from Near East University, Turkish Republic of Northern Cyprus, and B.Sc. from Kano University of Science and Technology, Nigeria. He works in the lab as a Bioinformatician (Mathematical Epidemiologist). Before joining the University of Massachusetts, Dr. Musa was a Postdoctoral Fellow at the Hong Kong Polytechnic University, Hong Kong. His research focuses on developing mathematical and statistical modeling frameworks to investigate the transmission dynamics of emerging and re-emerging infectious diseases to shed light on how pathogens spread and provides suggestions to public health decision-makers on control and prevention measures, considering minimal socioeconomic disruption. He enjoys playing soccer and spending time with his children in his spare time.

  • Trusting Inekwe

    Trusting is a graduate student pursuing a PhD in Computer Science at Worcester Polytechnic Institute (WPI) and currently doing internship with the Colubri Lab. He holds a master’s degree in Computer Science from WPI and a B.S. in Computer Engineering from Eastern Mediterranean University, North Cyprus. His research interests involve the creation of interactive systems that intersect science, art, and programming with the goal of improving the livelihood of target groups. His PhD research involves the creation of such interactive systems to help advance STEM education. During his free time, he enjoys singing and playing musical instruments.

  • Arnav Gupta

    Arnav is a current senior high-school student interning for the lab. He attends the Massachusetts Academy of Math and Science and takes dual-enrollment classes at Worcester Polytechnic Institute (WPI) focusing on computer science. His interests lie in computer science and using ML to perform data analysis in the medical field. He is working with Andres and other CoLabo members on the PREM App. During his free time, he likes to listen to music, play soccer, and play video games.

  • Hung Hong

    Hung is the Software Engineer in the lab. He holds an M.S. in Computer Science in WPI and a B.S. in Computer Science and Interactive Media & Game Design from WPI. He is currently in charge of full-stack management of the Operation Outbreak project. During his free time, he enjoys drawing, listening to music, and developing games for fun.

  • Yinan Dong

    Yinan, a UX and Data Visualization designer, holds an MFA in Information Design and Data Visualization from Northeastern University. She has been with the lab since 2021, as the UX/UI designer focusing on projects such as Muttomics, Travel Healthy, and Operation Outbreak. Outside of work, she finds pleasure in spending time with her chubby cats, creating drawings, and cooking in her daily life.

Our Team
  • Alicia Genisca

    Dr Genisca is an Assistant Professor of Emergency Medicine, Assistant Professor of Pediatrics, and Clinician Educator at Brown University. They work together with Dr Michelow in the development of predictive models for Ebola pediatric patients.

  • Dmitry Korkin

    He is a professor in the Computer Science department at Worcester Polytechnic Institute. His research is interdisciplinary and spans the fields of bioinformatics of complex diseases, computational genomics, systems biology, and biomedical data analytics. His lab brings expertise in machine learning, data mining, and massive data analytics to study molecular mechanisms underlying genetic disorders, such as cancer, diabetes, and autism, and deadly infections, such as pandemic flu.

  • Todd Brown

    Todd Brown is a Doctor of Higher Education, receipent of mulitple awards as a teacher, founder of the Inspire Project, and co-creator of the Operation Outbreak project, together with Pardis and Andres.

  • Fathom Information Design

    Fathom Information Design is a Boston-based studio that creates visualization solutions that help clients learning from their data. Fathom was founded by Ben Fry in 2010, and Andres worked with them in the initial years developing tools to explore complex biomedical datasets. Currently, Fathom and CoLabo are partnering on the Operation Outbreak project.

  • Jean-Gabriel Young

    Assistant Professor of Mathematics and Statistics at The University of Vermont, VT, USA. He also is a faculty of the Translational Global Infectious Diseases Research Center and the Vermont Complex Systems Center. His research is at the intersection of statistical inference, epidemiology, and complex systems.

  • Tim Kowalik

    Tim is a professor at the Department of Microbiology and Physiological Systems at UMass Chan Medical School. The research in his lab centers around the regulation of cellular proliferation control especially from the perspective of an infecting virus.

  • Abba B. Gumel

    Abba is a Professor of Mathematics (and The Michael and Eugenia Brin Endowed E-Nnovate Chair in Mathematics) at the Department of Mathematics, University of Maryland, College Park. His research work focuses on using mathematical approaches (modeling, rigorous analysis, and data analytics) to gain insight and provide understanding on the transmission dynamics of emerging and re-emerging infectious diseases of public health significance.

  • Irrua Specialist Teaching Hospital

    ISTH serves as a referral hospital in Edo State, Nigeria. In 2001, ISTH was designated as a Centre of Excellence in the management of Lassa fever, which is endemic in the region. Andres has been collaborating with several clinicians and scientists at ISTH, including Drs Peter Okokhere and Christopher Iruolagbe, for many years on the development of better patient data collection systems, and the study of the determinants of outcome in Lassa fever.

  • Pardis Sabeti

    Pardis Sabeti is a world-renowned geneticist and infectious disease researcher. Pardis was Andres’ mentor for many years and they continue to collaborate on the development of novel systems for infectious disease data collection, modelling, and education.

  • Tzu-Chun

    Tzu-Chun is a PhD candidate in Epidemiology and Biostatistics, concurrently pursuing a Master’s in Statistics at University of Georgia (UGA). Her research intersects cardiovascular health, infectious diseases, and machine learning. The aim of her dissertation is to enhance machine learning models for a deeper understanding and improvement of cardiovascular disease outcomes and the progression of multimorbidity in COVID-19 patients. Away from data and models, she finds joy in hiking, traveling, and spending quality time with her friends, husband, and their Lab Retriever mix

  • Laurent Hébert-Dufresne

    LHD obtained his PhD in physics in from Université Laval in Québec. He then branched out in different avenues of complex systems modeling; first in microbial and forest ecology as a James S. McDonnell Foundation Fellow at the Santa Fe Institute, and later as a researcher at the Institute for Disease Modeling. Now at the Vermont Complex Systems Center, he co-leads the modeling arm of the Joint Lab whose research focuses on the interaction and coevolution of structure and dynamics.

  • Adam Levine

    Dr Levine is an Associate Professor of Emergency Medicine and Director of the Division of Global Emergency Medicine at the Warren Alpert Medical School of Brown University. He led the humanitarian response of International Medical Corps during the West African Ebola outbreak in 2015-2017, and they have been collaborating since in the development of diagnostic and prognostic models for Ebola Virus Disease.

  • Apurv Soni

    Apurv is a professor at the Department of Medicine at UMass Chan Medical School, and director of the Program in Digital Medicine. His research goal is to integrate digital health technology in clinical workflows and community-based paradigms to improve clinical outcomes and reduce health disparities.

  • Elinor Karlsson

    Elinor Karlsson is professor at the department of Genomics and Integrative Biology at UMass Chan Medical School and director of the Vertebrate Genomics Group at the Broad Institute of MIT and Harvard. She is excited by the potential for using our own evolutionary history to understand how the human genome works, and in how that knowledge can lead to advances in healthcare.

  • Ian Michelow

    Dr Michelow is an Associate Professor of Pediatrics at Brown University. His activities include the study of malaria pathogenesis and vaccine discovery, Ebola virus disease, clinical epidemiology and biomarkers of pneumonia and viral infections in hospitalized children. Andres works in collaboration with Drs Michelow and Genisca to develop novel diagnostic and prognostic models for Ebola Virus Disease.

  • Mary-Anne Hartley

    Mary-Anne “Annie” Hartley is an Assistant Professor in Biomedical Informatics and Data Science. Her research is focused on developing and validating novel data-driven tools designed to improve healthcare in low-resource settings, with a special interest in Africa.

  • Zhiping Weng

    Zhiping is the chair of the department of Genomics and Integrative Biology at UMass Chan Medical School. She spends all her time writing grants and papers, teaching, and running Zlab. She is confident that one day she will figure out how to write a computer program to do all of the above.

  • Regina LaRocque

    Regina LaRocque is an Associate Professor of Medicine at Harvard Medical School. She is a faculty member of the Division of Infectious Diseases at Massachusetts General Hospital. Her clinical and research interests are in infectious diseases, enteric infections, and travel medicine. Dr. LaRocque received her MD from Duke University School of Medicine and MPH from the Harvard School of Public Health. She completed her residency training and fellowship at Brigham and Women’s Hospital. Dr. LaRocque is a Fellow of the Infectious Diseases Society of America and of the International Society of Travel Medicine. She currently serves as Chief Medical Editor of the CDC Yellow Book: Health Information for International Travel.

Our Team
  • Brian Wee

    Originally from Boulder, Colorado, Brian is an undergraduate student at Harvard College studying Chemical and Physical Biology and Government. He is currently working under Andrés and Pardis on a computational epidemiology project utilizing hierarchical linear models and machine learning to analyze the impact of COVID-19 on disrupting medical care for individuals with underlying medical conditions. Outside of the lab, Brian enjoys hiking, escape rooms, and month-long lifestyle changes, along with being involved in various Harvard organizations including the World Pre-Health Conference and Harvard College Undergraduate Research Association.

  • Nathan Hill

    Nathan Hill did his graduate theses at Harvard College, where he studied Molecular and Cellular Biology, under with Andrés and Pardis as advisers. His thesis explored the spread of the 2009 Swine Flu pandemic in Florida. In his free time, he enjoys distance running, reading fiction, and playing the trombone.

  • Elo

    Elo is a User Experience designer originally from Beijing, China. She is an undergraduate student pursuing a combined degree in Computer Science and Design at Northeastern University. With a group of friends, she designed and implemented a transportation system for characters to move in an online collaboration space. Besides programming, she is passionate about making sciences easier to understand with data visualization. Outside of the labs, Elo loves stand-up comedy shows, seafood restaurants, and trips to tropical islands. She has a Shiba Inu back home.

  • Michael Fileto

    Michael completed his Bachelor’s of Science in Biology at the University of California Riverside. He became interested in studying Computer Science after taking a course in Genomics and Bioinformatics at UCR. Michael aims to bring both disciplines in Biology and CS together to create applications that transform data within Biology.

  • Ben Kresge

    Ben is an undergraduate student at Worcester Polytechnic Institute, doing a Bachelor of Science in Computer Science and a Minor in Bioinformatics and Computational Biology. He’s interning at CoLabo during the summer to work on proximity detection algorithms using the Herald library.

  • Rachel Goldstein

    A Texas native, Rachel graduated with a B.S. in Biochemistry and Molecular Biology from Trinity University. During her rotation, Rachel learned about the applications of epidemiological models to current outbreaks and diseases. When she gets screen fatigue and can’t binge TV shows, she likes to explore New England’s hiking trails.

  • Kelsey Butler

    Kelsey is a graduate student in the lab, and she holds a B.A. in Psychology from the University of Vermont and a B.S. in Chemistry from Castleton University. Her current project is focused on using machine learning techniques to develop a model to predict outcome in Lassa fever patients. When she isn’t in the lab, she enjoys running, yoga, and gardening.

  • Shannen Lin

    Shannen is an undergraduate at Worcester Polytechnic Institute majoring in Computer Science and Psychology. During her time in the lab, she is working on the Operation Outbreak project to develop a prototype mobile app to test new features. In her free time, she enjoys baking and reading.