Welcome New Faculty, Fellows, Students, and Staff to Yale BIDS (Fall 2024)

Haoyu Cheng, PhD joins Yale’s Department of Biomedical Informatics and Data Science (BIDS) as a tenure-track Assistant Professor. His groundbreaking research focuses on developing computational methodologies for genomic applications, including genome assembly, read alignment, variant calling, and string indexing. Dr. Cheng played a pivotal role in creating the de novo genome assembly algorithm hifiasm, which has been widely adopted in major sequencing projects such as the Human Pangenome Reference Consortium and the Vertebrate Genomes Project. His work significantly advances genomic research while opening new possibilities in precision medicine and evolutionary biology.

Prior to joining Yale, Dr. Cheng was a Postdoctoral Scholar at Dana-Farber Cancer Institute and Harvard Medical School. He earned his Ph.D. in Computer Science from the University of Science and Technology of China. At Yale, he is eager to leverage the department's resources and collaborative environment to push the boundaries of genomics and bioinformatics on a global scale.

When asked what excites him most about joining BIDS, Dr. Cheng shared, "The incredibly welcoming and supportive environment. In just a short time, I’ve found the community to be both enthusiastic and collegial, with everyone eager to help me settle in and succeed. The resources at BIDS provide an exceptional foundation for growth and innovation." In his free time, Dr. Cheng enjoys exploring New Haven’s hiking and biking trails, as well as its beautiful beaches.

Anran Li, PhD is a Postdoctoral Associate in the Department of Biomedical Informatics and Data Science (BIDS) at Yale School of Medicine. She holds a Ph.D. from the University of Science and Technology of China and was previously a Research Fellow at Nanyang Technological University, Singapore. Dr. Li’s research focuses on trustworthy AI, medical large language models, federated learning, and graph learning. Currently, she works on privacy issues in medical LLMs, including memorization and federated medical LLMs. In her free time, she enjoys playing badminton and traveling.

Andrew Loza, MD, PhD is a Postdoctoral Research Fellow in Biomedical Informatics and Data Science (BIDS) at Yale and the VA Connecticut Healthcare System. He holds a PhD in biophysics from Washington University in St. Louis, where he studied collective cell migration using computer vision and statistical models, as well as an MD from Yale School of Medicine. After completing his residency in Internal Medicine-Pediatrics and a Clinical Informatics Fellowship at Yale/VA, his research now focuses on optimizing care delivery for chronic conditions and predicting critical events in hospitalized patients using transformer-based generative models.

Dr. Loza is excited to join Yale BIDS for its collaborative and creative environment, where he aims to tackle some of healthcare’s toughest challenges. Outside of work, he enjoys running, cycling, and spending time with his three kids and Australian shepherd.

Julia Wolleb, PhD is a Postdoctoral Researcher in the Department of Biomedical Informatics and Data Science (BIDS) at Yale. She holds a Master's degree in Mathematics from the University of Basel, where she specialized in numerics and algebra. She pursued her Ph.D. in Biomedical Engineering, focusing on automatic detection of pathological regions in medical images. Dr. Wolleb’s research interests include developing deep learning methods for medical image analysis, with a current focus on AI solutions for healthcare in low-resource settings. Outside of work, she enjoys swing dancing and horseback riding.

Weipeng Zhou, PhD is a Postdoctoral Researcher in the Department of Biomedical Informatics and Data Science (BIDS) at Yale. He completed his Ph.D. in clinical natural language processing (NLP) at the University of Washington, under the guidance of Dr. Meliha Yetisgen, and holds a bachelor's degree in computer science and statistics from the University of Wisconsin. Dr. Zhou’s research focuses on the intersection of NLP and healthcare, with projects exploring out-of-hospital cardiac arrest, Long COVID, and clinical note section identification models. At Yale, he is currently working on patient representation using multi-modal data, including clinical notes, vital signs, and CT images. Outside of research, Dr. Zhou enjoys hiking and discovering new local restaurants.

João Cardoso is a Software Engineer at Yale’s Department of Biomedical Informatics and Data Science (BIDS). He holds dual master’s degrees—an MSc in Software Engineering from the Polytechnic of Porto in Portugal and an MEng in Artificial Intelligence from Duke University. With over six years of experience in backend development, including five years at Farfetch where he contributed to their ecommerce platform, João brings a strong blend of industry expertise to Yale BIDS. Currently, he is working on the BIKE (Biomedical Information Knowledge Explorer) project.

João is excited to bridge the gap between industry and academia by applying his skills in AI and software development to healthcare. Outside of work, João enjoys traveling, listening to metal and hardcore music, attending concerts, and playing sports like basketball, soccer, and tennis.

Catherine Barabas is a Research Assistant I MS at Yale’s Department of Biomedical Informatics and Data Science (BIDS) at Yale. With over 20 years of experience at Yale, including roles in the Physics Department and the School of Public Health's Contact Tracing Team, she brings a wealth of administrative expertise. Catherine holds a Bachelor of Science in Information Systems and is excited to contribute to the dynamic environment at Yale BIDS. In her free time, she enjoys crocheting and playing tabletop role-playing games like Dungeons & Dragons.

Gui Yang is a Research Intern and visiting undergraduate at Yale’s Department of Biomedical Informatics and Data Science (BIDS). Currently a senior at Nanjing University, Gui is majoring in Life Sciences with a deep passion for AI, particularly its intersection with life sciences. Gui’s research experience includes analyzing single-cell RNA sequencing data for pan-cancer biomarker studies and applying BERT models to predict protein expression strength from yeast promoter sequences. At Yale BIDS, Gui is involved in projects focusing on large language models for diagnosis, Named Entity Recognition (NER), and Relation Extraction (RE) tasks in PubMed papers. Outside of work, Gui enjoys anime, mobile games, e-books and board games with friends.

Mukund Aravapalli is a Software Engineer at Yale's Department of Biomedical Informatics and Data Science (BIDS). He holds a Bachelor of Business Administration from Emory University and is currently pursuing a Master of Computer Science at Johns Hopkins. His expertise includes Full Stack Development, Large Language Models, and Machine Learning. At Yale BIDS, Mukund is involved in two major projects within Dr. Hua Xu's Clinical NLP Lab, redesigning a project website and developing an AI chatbot using RAG frameworks. Outside of work, Mukund enjoys outdoor activities, playing tennis, guitar, reading and drawing.

Jennifer Arango is the Program Manager for the Department of Biomedical Informatics and Data Science (BIDS) at Yale. She holds a Master of Public Health from Southern Connecticut State University and a Bachelor's Degree in health sciences from Quinnipiac University. With extensive experience in project management, informatics, quality improvement, and clinical research, Jennifer has held pivotal roles in radiology, the Smilow Cancer Center, and business planning at Yale. Certified in LEAN Six Sigma, Change Management, and Imaging Informatics, Jennifer has also contributed to numerous publications. During her undergraduate studies, she completed an internship at the Yale morgue. Outside of work, Jennifer is a dedicated hockey mom, orchid collector, and animal lover.

Ahmed Abdelhady is a Software Engineer at Yale's Department of Biomedical Informatics and Data Science (BIDS). He holds a B.S. in Computer Science with a minor in Mathematics from the University of Connecticut. Ahmed is currently working on the ECHO Cohort Visualization project in Dr. Hua Xu’s Clinical NLP Lab. He is excited to collaborate with experts in the rapidly advancing field of biomedical informatics and looks forward to contributing to the innovative work at Yale BIDS. In his free time, Ahmed enjoys playing the trombone, a skill he honed during university, and spending time with his two pet cockatiels.

Winnie Ng is a Software Engineer at Yale's Department of Biomedical Informatics and Data Science (BIDS). She holds degrees in Financial Economics and Mathematics from SUNY Binghamton. Before transitioning into software engineering, Winnie worked in Operations and Marketing in the consumer-packaged goods industry, focusing on natural and organic products. As a software engineer for the past two years, she has contributed to ecommerce and research service companies.

Winnie is excited to join Dr. Hua Xu's Clinical NLP Lab at Yale BIDS, as its mission aligns with her passion for building technology solutions that improve health and quality of life. In her free time, she enjoys traveling, trying new cuisines, archery, reading, drawing, and hiking.

Vincent Zhang is a Software Engineer specializing in coding within the Department of Biomedical Informatics and Data Science (BIDS) at Yale. He holds a Bachelor’s degree in Computer Science from Carleton University and is currently pursuing a Master’s in Electrical and Computer Engineering at Northeastern University. Vincent’s research interests include machine learning and system programming, and he is currently working on projects such as Kiwi, a medical NLP tool, and CDEMapper, an AI mapping tool.

Excited to join Yale BIDS, Vincent looks forward to collaborating with experts and honing his skills in using big data to solve real-world problems. In his free time, he enjoys playing acoustic and electric guitar.

Atharva Sapre is a Postgraduate Associate in the Taylor Lab (Decile Lab), working under the mentorship of Dr. Andrew Taylor in the Department of Emergency Medicine and Biomedical Informatics and Data Science (BIDS) at Yale. He earned his master's in data science from Northeastern University, where, as a Research Assistant, he developed AI models to analyze brain signals and their impact on political ideologies. Atharva also brings experience as a Data Scientist, where he built predictive models and used NLP to assess health risks, drawing insights from large healthcare datasets to support insurance decision-making.

His research interests lie at the intersection of healthcare and data science, with a focus on using AI, deep learning, and NLP to tackle critical healthcare challenges. Currently, Atharva is working on projects that examine how Point-of-Care Ultrasound (POCUS) impacts emergency department admissions and patient outcomes. He is also using machine learning to predict agitation events in the emergency department, helping clinicians respond more effectively and improve patient care.

At Yale BIDS, Atharva is looking forward to working alongside talented researchers and leveraging advanced data science techniques to address real-world healthcare challenges. He views this as a valuable opportunity to further develop his skills while making meaningful contributions to healthcare research.

Outside of work, Atharva enjoys cooking, working out, and is a loyal FC Barcelona fan—despite the emotional cardio that often comes with supporting the team.