John Quackenbush

Biography

John Quackenbush is Professor of Computational Biology and Bioinformatics, Emeritus. John's PhD was in Theoretical Physics, but in 1992 he received a fellowship to work on the Human Genome Project. This led him through the Salk Institute, Stanford, The Institute for Genomic Research (TIGR), and to Harvard in 2005. John uses massive data to probe how many small effects combine to influence human health and disease. He has more than 300 scientific papers and over 73,000 citations. Among his honors is recognition in 2013 as a White House Open Science Champion of Change.

Awards and Honors

• Member, 2022
  National Academy of Medicine
• Recipient, 2013
  White House Open Science Champion of Change

Publications

• FERRET: Framework to Evaluate Robustness in Regulatory Networks Using Heterogeneous Cell Types.

  Eicher T, Quackenbush J. bioRxiv 2026 Jul 25

  PMID: 42539007

• Genomic, Transcriptomic, and Regulomic Analyses Do Not Support Profound Autism as a Distinct Biological Category.

  Eicher T, Ne'eman A, Quackenbush J. bioRxiv 2026 Jul 21

  PMID: 42282515

• Large-scale, interpretable gene regulatory network inference through biologically informed matrix factorization.

  Micheletti S, Fanfani V, Vogt J, Quackenbush J, Fischer J, Marx A, Mandros P. bioRxiv 2026 Jul 16

  PMID: 42523370

• PARROT: Phase-Altering Regulatory Rewiring Over Time.

  Chen C, Padi M, Quackenbush J. bioRxiv 2026 Jun 28

  PMID: 42395364

• LOESS and DE-SWAN can induce artifactual "waves" of molecular aging.

  Carbonneau M, Shutta KH, Miller JW, Snyder MP, Shen X, Quackenbush J. bioRxiv 2026 Jun 28

  PMID: 42395484