Cathy Wu

About

Cathy Wu is a Class of 1954 Career Development Professor at the Massachusetts Institute of Technology, affiliated with the Department of Civil and Environmental Engineering and the Institute for Data, Systems, and Society. Her research intersects machine learning, optimization, and large-scale societal systems, with a recent focus on mixed autonomy systems in mobility. This involves studying the complex integration of automation, such as self-driving cars, into urban transportation systems. She aims to develop principled computational tools to enable reliable and complex decision-making for critical societal systems. Cathy Wu has collaborated broadly across fields including transportation, computer science, electrical engineering, mechanical engineering, urban planning, and public policy. Her industry collaborations include Microsoft Research, OpenAI, Google X Self-Driving Car Team, AT&T, Caltrans, Facebook, and Dropbox. She is also the founder and Chair of the Interdisciplinary Research Initiative within the ACM Future of Computing Academy, actively working to build international programs that promote interdisciplinary research in computing.

Research topics

• Computer Science
• Information Retrieval
• Bioinformatics
• World Wide Web
• Biology
• Computational biology
• Data science
• Genetics
• Software engineering
• Internet privacy

Selected publications

• UniProt: the universal protein knowledgebase in 2021

  Nucleic Acids Research · 2020 · 6992 citations

  The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completenes…

  DOI

• UniProt: the Universal Protein Knowledgebase in 2023

  Nucleic Acids Research · 2022 · 6774 citations

  The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing pipeline and to our website to adapt to an ever-increasing information content. The number of sequences in UniProtKB has risen to over 227 million and we are working towards including a reference proteome for each taxonomic group. We continue to ext…

  DOI

• The Gene Ontology resource: enriching a GOld mine

  Nucleic Acids Research · 2020 · 3820 citations

  The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to re…

  DOI

• UniProt: the Universal Protein Knowledgebase in 2025

  Nucleic Acids Research · 2024-11-18 · 1780 citations

  articleOpen access

  The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we describe ongoing changes to our production pipeline to limit the sequences available in UniProtKB to high-quality, non-redundant reference proteomes. We continue to manually curate the scientific literature to add the latest functional data and use machine lea…

  PublisherDOI

• The UniProt website API: facilitating programmatic access to protein knowledge

  Nucleic Acids Research · 2025-05-07 · 117 citations

  articleOpen access

  The UniProt REST API is a freely available, open-access resource that powers the UniProt.org website and gives users flexible programmatic interaction with protein knowledge data. It provides access to UniProtKB, UniRef, UniParc, Proteomes, GeneCentric, ARBA, UniRule, and the ID Mapping tool, along with supporting data and controlled vocabularies. Users can access the API with their favorite programming language and generate example code snippets to access the UniProt databases using the API doc…

  PublisherOA PDFDOI

Recent grants

• UniProt: A Protein Sequence and Function Resource for Biomedical Science

  NIH · $3.8M · 2014–2026

• NIH Grant R29LM005524

  NIH · $461k · 1999

• Delaware INBRE CSR Core

  NIH · $100.8M · 2001–2030

Frequent coauthors

• Darren A. Natale

  Georgetown University Medical Center

  404 shared

• Hongzhan Huang

  National Taiwan University Hospital

  376 shared

• Cecilia Arighi

  University of Delaware

  313 shared

• Alex Bateman

  289 shared

• ROBERT FINN

  European Bioinformatics Institute

  281 shared

• Rolf Apweiler

  European Bioinformatics Institute

  239 shared

• Christian Sigrist

  223 shared

• Alex Mitchell

  Pennsylvania State University

  217 shared

Education

• Ph.D.

  Purdue University

  1984

• M.S.

  Purdue University

  1982

Awards & honors

• Ole Madsen Mentoring Award (2025)
• NSF Faculty Early Career Development (CAREER) Award (2023)
• CUTC Milton Pikarsky Memorial Dissertation Award (2018)
• Outstanding Graduate Student Instructor Award, UC Berkeley (…
• ACM Future of Computing Academy, Interdisciplinary Research…

Similar researchers at Massachusetts Institute of Technology

• Xuanhe Zhaoh-104
• Franz-Josef Ulmh-77
• Herbert Einsteinh-51