Kipoi - Seminar
The monthly virtual seminar series is designed as a platform for interested Kipoi users and developers and will host talks on the applications of deep learning on biological data. The seminar is held on every first Wednesday of the month at 5:30 p.m. - 6:30 p.m. CET. We are also happy to share the recordings of the seminar on YouTube.
How to take part
The Virtual Seminar Series takes place via Zoom. To take part in the seminar, you can register for the online Zoom conference. Your personal join link will be valid for all upcoming lectures of the series.
How to apply as a speaker
The seminar is a great opportunity to present your recent work to a large international audience. If you want to apply as a speaker, please use the contact in the registration confirmation email.
Next seminar
Title: PARM: The regulatory grammar of human promoters uncovered by MPRA-trained deep learning
2 April 2025 5:30 p.m. - 6:30 p.m. Central European TimeSpeaker: Lucía Barbadilla, De Ridder Group, UMC Utrecht
Abstract:One of the major challenges in genomics is to build computational models that accurately predict genome-wide gene expression from the sequences of regulatory elements. At the heart of gene regulation are promoters, yet their regulatory logic is still incompletely understood. Here, we report PARM, a cell-type specific deep learning model trained on specially designed massively parallel reporter assays that query human promoter sequences. PARM reliably predicts autonomous promoter activity throughout the genome from DNA sequence alone, in multiple cell types. PARM can even design purely synthetic strong promoters. We leveraged PARM to systematically identify binding sites of transcription factors (TFs) that are likely to contribute to the activity of each natural human promoter. We uncovered and experimentally confirmed striking positional preferences of TFs that differ between activating and repressive regulatory functions, as well as a complex grammar of motif-motif interactions. For example, many, but not all, TFs act as repressors when their binding motif is located near or just downstream of the transcription start site. Our approach lays the foundation towards a deep understanding of the regulation of human promoters by TFs.
Upcoming speakers
- 7 May 2025 - Laura Martens, Gagneur lab, Technical University Munich
- 4 June 2025 - Katherine Pollard, Gladstone Institute of Data Science & Biotechnology
Previous speakers
- 5 March 2025 - Alexander Sasse, Heidelberg University
- 5 February 2025 - Pedro Tomaz da Silva, Gagneur lab, Technical University Munich
- 4 December 2024 - Dmitry Penzar, autosome.org team
- 6 November 2024 - Abdul Muntakim Rafi (Rafi) - Carl de Boer lab, The University of British Columbia
- 2 October 2024 - Avantika Lal, Genentech
- 4 September 2024 - Max Horlbeck and Ruochi Zhang (Buenrostro lab), Harvard University and Broad Institute
- 3 July 2024 - Sagar Gosai - Sabeti (Broad), Reilly (Yale) & Tewhey lab (Jackson laboratories), Broad Institute of Harvard and MIT
- 5 June 2024 - Sara Mostafavi, University of Washington
- 8 May 2024 - Thomas Pierrot, InstaDeep
- 3 April 2024 - Kseniia Dudnyk, Jian Zhou lab, UT Southwestern Medical Center
- 6 March 2024 - Maria Brbić, EPFL, Lausanne
- 7 February 2024 - Eric Nguyen, Christopher Ré lab, Stanford University
- 10 January 2024 - Peter Koo, Cold Spring Harbor Laboratory
- 6 December 2023 - Irene Kaplow, Duke University
- 8 November 2023 - David Kelley, Calico
- 5 July 2023 - Stein Aerts, KU Leuven
- 3 May 2023 - Alexander Karollus, Julien Gagneur lab, Technical University Munich
- 5 April 2023 - Bernardo P. de Almeida, Alex Stark lab, Research Institute of Molecular Pathology, Vienna
- 3 March 2023 - Ewa Szczurek, University of Warsaw
- 1 February 2023 - Mingyao Li, University of Pennsylvania
- 7 December 2022 - Jian Zhou, UT Southwestern
- 2 November 2022 - Marc Horlacher, Helmholtz Zentrum Munich
- 5 October 2022 - William Stafford Noble, University of Washington
- 7 September 2022 - Burkhard Rost, Technical University Munich
- 6 July 2022 - Anna Schaar and David Fischer, Helmholtz Zentrum Munich
- 1 June 2022 - Yoshua Bengio, Université de Montréal, Mila – Quebec Artificial Intelligence Institute
- 4 May 2022 - Francesco Paolo Casale, Helmholtz Pioneer Campus, Helmholtz Zentrum Munich
- 6 April 2022 - Kyle Farh, Head of Artificial Intelligence Lab, Illumina, San Francisco Bay Area
- 2 March 2022 - Jonathan Frazer & Mafalda Dias, Debora Marks Lab, Harvard Medical School, Boston
- 2 February 2022 - Benjamin Schubert, Helmholtz Zentrum, Munich
- 1 December 2021 - Annalisa Marsico, Helmholtz Zentrum, Munich
- 3 November 2021 - Žiga Avsec, DeepMind, London
- 6 October 2021 - Mohammad Lotfollahi, Helmholtz Zentrum, Munich
- 1 September 2021 - Ansh Kapil, AstraZeneca, Munich
- 4 August 2021 - Christina Leslie, Sloan Kettering Institute, New York
- 7 July 2021 - Qiangfeng Cliff Zhang, Tsinghua University, Beijing
- 2 June 2021 - Johannes Linder, University of Washington, Seattle
- 5 May 2021 - Anshul Kundaje, Stanford University, Stanford
- 7 April 2021 - Yingxin Cao, UC Irvine, Irvine
- 3 March 2021 - Avanti Shrikumar, Stanford University, Stanford
- 3 February 2021 - Uwe Ohler, Max-Delbrück-Center for Molecular Medicine, Berlin
- 2 December 2021 - Ron Schwessinger, Radcliffe Department of Medicine, Oxford
- 4 November 2020 - David Kelley, Calico, San Francisco
- 7 October 2020 - Vikram Agarwal, Calico, San Francisco
The scientific committee
- Julien Gagneur, Technical University Munich, Munich
- Annalisa Marsico, Helmholtz Zentrum Munich, Munich
- Johannes Linder, Stanford University, Stanford
- Laura Martens, Technical University Munich & Helmholtz Zentrum Munich, Munich
- Maria Ryabtseva, Technical University Munich, Munich