PeopleofSuperintelligence

Researcher

Carl Kingsford

Also known as Carleton Kingsford

Carl Kingsford is a Carnegie Mellon computer scientist who applies machine learning to genomics. He studied computer science and mathematics at Duke, completed a computer science PhD at Princeton in 2005, and joined Carnegie Mellon in 2012. With collaborators, he developed Sailfish in 2014 and Salmon in 2017 to estimate gene activity from RNA sequencing data. He became an ISCB fellow in 2024 and coauthored a 2026 system that used Bayesian optimization and contrastive learning to choose parameters for RNA analysis software. As of October 2026, he directs the Center for Machine Learning in Health and is CEO of Ellumigen, the company he co-founded as Ocean Genomics.

Now at
Carnegie Mellon University and Ellumigen
Works
186
Citations
23,702
h-index
38
Badges

Publication numbers from OpenAlex, as of 27 October 2026.

Timeline

  1. 2000–2005

    Computer science at Duke and Princeton

    He completes undergraduate studies in computer science and mathematics at Duke University in 2000. At Princeton University, he completes an MA in computer science in 2002 and a PhD in computer science in 2005.

  2. 2012

    Joining Carnegie Mellon's biology faculty

    After appointments as a postdoctoral fellow and assistant professor at the University of Maryland, College Park, he joins Carnegie Mellon's Computational Biology Department in 2012. His research applies machine learning and algorithm design to genomics.

  3. 2012

    A Sloan Research Fellowship

    In 2012, he receives a Sloan Research Fellowship in evolutionary and computational molecular biology while on the University of Maryland faculty.

  4. 2014

    Sailfish measures gene activity

    Working with Rob Patro at CMU's Lane Center for Computational Biology and Stephen M. Mount at the University of Maryland, he develops Sailfish in 2014. The software estimates gene expression from RNA sequencing data and eliminates the step of mapping each read to its original position in an RNA molecule.

  5. 2017

    Salmon corrects sequencing biases

    In 2017, he and Rob Patro lead the research on Salmon, a method for estimating gene expression that corrects technical biases in RNA sequencing data. Published in Nature Methods in March 2017, the work models these biases for individual samples while retaining fast analysis.

  6. 2023

    Ocean Genomics receives investment

    In 2023, Ocean Genomics receives a strategic investment from Accenture Ventures. As its co-founder and CEO, he leads a bioinformatics company that uses machine learning and AI to help biopharmaceutical companies improve diagnosis and personalized medicine.

  7. 2024

    An ISCB fellowship

    The International Society for Computational Biology elects him as a fellow in 2024. His contributions include methods for quantifying gene expression and algorithms for searching unassembled sequence data.

  8. 2026

    AI tunes transcript assemblers

    In 2026, he coauthors "Data-driven AI system for learning how to run transcript assemblers" with Yihang Shen and Zhiwen Yan. The system uses Bayesian optimization and contrastive learning to recommend parameter settings for individual RNA sequencing samples, transferring knowledge from existing samples to new ones.

  9. May 2026

    An Introduction to String Algorithms

    In May 2026, Princeton University Press publishes his book An Introduction to String Algorithms. It covers string processing, data structures and proof techniques for computational research.

  10. As of October 2026

    Professor and health center director

    As of October 2026, he holds the Herbert A. Simon Professorship in Carnegie Mellon's Ray and Stephanie Lane Computational Biology Department. He directs the Center for Machine Learning in Health and the Center for Innovation in Health, co-directs the joint CMU–University of Pittsburgh PhD Program in Computational Biology, and is CEO of Ellumigen, formerly Ocean Genomics. His group develops machine learning methods for biological data and works on automated algorithm design.

Career

  1. NowCarnegie Mellon UniversityDirector, Center for Machine Learning in Health, Herbert A. Simon Professor
  2. NowEllumigenCEO
  3. 2006–2012University of MarylandPostdoctoral Fellow, Assistant Professor
  4. Ocean GenomicsCo-founder and CEO

Education

  1. 2005Princeton UniversityPhD in computer science
  2. 2002Princeton UniversityMA in computer science
  3. 2000Duke UniversityUndergraduate studies in computer science and mathematics

From the biography and OpenAlex affiliations (the years of papers that list the organization), so some years are approximate.

Checked career sources: kingsfordlab.cbd.cmu.edu.

Colleagues

People named in this biography, and people with dated positions at the same organization in the same years.

Sources and credits

Photo: We have no published photo of Carl Kingsford yet. Send us a free-licensed photo.

  1. Carl Kingsford - Quantum Computing and Information Technologies qcit.cmu.edu. Checked 27 October 2026.
  2. SCS Celebrates Simon, Alumni Research Professorships ri.cmu.edu. Checked 27 October 2026.
  3. Dr. Kingsford Receives Sloan Research Fellowship cs.umd.edu. Checked 27 October 2026.
  4. Press Release: Computational Method Dramatically Speeds Up Estimates of Gene Expression, CMU, UMD Researchers Report cmu.edu. Checked 27 October 2026.
  5. Computational Method Makes Gene Expression Analyses More Accurate cmu.edu. Checked 27 October 2026.
  6. Accenture Invests in Ocean Genomics cmu.edu. Checked 27 October 2026.
  7. March 8, 2024: ISCB Congratulates and Introduces the 2024 Class of Fellows! iscb.org. Checked 27 October 2026.
  8. Data-driven AI system for learning how to run transcript assemblers kingsfordlab.cbd.cmu.edu. Checked 27 October 2026.
  9. An Introduction to String Algorithms by Carl Kingsford releases May 19, 2026 cmu.edu. Checked 27 October 2026.
  10. Carl Kingsford kingsfordlab.cbd.cmu.edu. Checked 27 October 2026.