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: Sequence basis of transcription Initiation in human genome
3 April 2024 5:30 p.m. - 6:30 p.m. Central European TimeSpeaker: Kseniia Dudnyk, Jian Zhou lab, UT Southwestern Medical Center
Abstract:Transcription initiation is an essential process for ensuring proper function of any gene, however, we still lack a unified understanding of sequence patterns and rules that explains most transcription initiation sites in human genome. By explaining transcription initiation at basepair resolution from sequence with a deep learning-inspired explainable modeling approach, we show that simple rules can explain the vast majority of human promoters. We identified key sequence patterns that contribute to human promoter function, each activating transcription with a distinct position-specific effect curve that likely reflects its mechanism of promoting transcription initiation. Most of these position-specific effects have not been previously characterized, and we verified them using experimental perturbations of transcription factors and sequences. We revealed the sequence basis of bidirectional transcription at promoters and links between promoter selectivity and gene expression variation across cell types. Additionally, by analyzing 241 mammalian genomes and mouse transcription initiation site data, we showed that the sequence determinants are conserved across mammalian species. Taken together, we provide a unified model of the sequence basis of transcription initiation at the basepair level that is broadly applicable across mammalian species, and shed new light on basic questions related to promoter sequence and function.
Upcoming speakers
- 8 May 2024 - TBD,
- 5 June 2024 - TBD,
- 3 July 2024 - Sagar Gosai, Ryan Tewhey lab, The Jackson laboratory
Previous speakers
- 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