Philippe J. Batut, PhD

  • Assistant Professor of Genetics and Development
Profile Headshot


Philippe J. Batut, PhD, grew up in France and received his BS in Biology from the University of Toulouse. During his Master’s, a year in the Genome Sciences program at the University of Washington in Seattle sparked his interest in genetics and gene regulation. He went on to receive his PhD from the School of Biological Sciences at Cold Spring Harbor Laboratory, where he developed experimental and computational methods for transcriptome analysis in the laboratory of Thomas R. Gingeras. These approaches identified novel developmental roles for promoters and enhancers and revealed regulatory contributions from transposons – mobile genetic elements once considered “parasitic” entities, but increasingly appreciated as an important source of regulatory elements.

Philippe was appointed as an Assistant Professor in the Departments of Genetics & Development and Obstetrics & Gynecology in 2024. His lab at Columbia University explores the genomic organization of regulatory elements into complex “regulatory landscapes” and investigates the mechanisms of gene regulation with a focus on 3D genome organization, epigenetics, and non-coding RNA biology.

Academic Appointments

  • Assistant Professor of Genetics and Development


  • French

Credentials & Experience

Education & Training

  • PhD, Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
  • MS, Genetics, Cell Biology & Development, Université Paul Sabatier, Toulouse, France
  • BS, Biology, Université Paul Sabatier, Toulouse, France
  • Internship: Genome Sciences program, University of Washington, Seattle, WA
  • Fellowship: Princeton University, Princeton, NJ


Vast expanses of our genome correspond to regulatory sequences that control the activity of our genes – a far greater proportion, in fact, than is devoted to protein-coding sequences themselves. Philippe Batut’s research aims to characterize these regulatory sequences and understand the molecular mechanisms by which they modulate gene expression during the development of a new organism.

Philippe's graduate work contributed to the ENCODE Project’s efforts towards the functional annotation of the human genome, and to a growing realization that much of our genome is transcribed into long non-coding RNAs (lncRNAs). These lncRNAs are a diverse class of molecules that, despite resembling mRNAs, do not encode proteins – and while a small subset has been shown to play important roles in regulating gene expression, their functions remain largely unexplored. Philippe used evolutionary transcriptomics approaches to show that many lncRNAs in the Drosophila genome are deeply conserved, suggesting that they are biologically relevant. Their expression is extremely dynamic during embryonic development, and these temporal dynamics are also highly conserved.

In his postdoctoral research at Princeton University, he leveraged quantitative live imaging approaches to study the mechanisms of transcriptional regulation in development in the group of Michael S. Levine. This work established, through the use of emerging genome engineering technologies, that the three-dimensional organization of the genome in the space of the nucleus plays a key role in regulating the temporal dynamics of gene expression. His work further paved the way for single-cell studies of the regulatory roles non-coding RNAs in developing embryos.

Learn more about his research at the Batut Lab.

Research Interests

  • Developmental Genetics
  • Epigenetics
  • Functional Genomics
  • Gene Regulation
  • Genome Organization
  • Microscopy and Imaging
  • Non-coding RNAs (ncRNAs)
  • Regulatory Sequences

Selected Publications

  1. Batut PJ, Bing XY, Sisco Z, Raimundo J, Levo M, Levine MS (2022). Genome organization controls transcriptional dynamics during development. Science 375(6580):566-570.
  2. Bing XY, Batut PJ, Levo M, Levine M, Raimundo J (2020). SnapShot: The Regulatory Genome. Cell 182(6):1674.
  3. Batut PJ & Gingeras TR (2017). Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. eLife 2017;6:e29005.
  4. Batut P, Dobin A, Plessy C, Carninci P, and Gingeras TR (2013). High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research 23(1):169-180.
  5. Dobin A, Davis C, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15-21.
  6. Djebali, S. et al. (2012). Landscape of transcription in human cells. Nature 489(7414):101-108.