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Massive Reverse Genomics to Decipher Gene Regulatory Grammar

Deliverables

Website

Project website for visibility, raising awareness and dissemination purposes. The website will be maintained throughout the execution and will stay alive at least 2 years after the project end.

Publications

The interaction landscape between transcription factors and the nucleosome

Author(s): Fangjie Zhu, Lucas Farnung, Eevi Kaasinen, Biswajyoti Sahu, Yimeng Yin, Bei Wei, Svetlana Dodonova, Patrick Cramer, Jussi Taipale
Published in: Nature, 2017, ISSN 2520-1158
Publisher: Nature
DOI: 10.1101/240598

Gene expression variability across cells and species shapes innate immunity

Author(s): Tzachi Hagai, Xi Chen, Ricardo J. Miragaia, Tomas Gomes, Raghd Rostom, Natalia Kunowska, Valentina Proserpio, Giacomo Donati, Lara Bossini-Castillo, Guy Naamati, Guy Emerton, Gosia Trynka, Ivanela Kondova, Mike Denis, Sarah A Teichmann
Published in: Nature, 2017, ISSN 2520-1158
Publisher: Nature
DOI: 10.1101/137992

Genome-wide CRISPR screens in T helper cells reveal pervasive cross-talk between activation and differentiation

Author(s): Johan Henriksson, Xi Chen, Tomás Gomes, Ubaid Ullah, Kerstin B Meyer, Ricardo Miragaia, Graham Duddy, Jhuma Pramanik, Kosuke Yusa, Riita Lahesmaa, Sarah A. Teichmann
Published in: Cell, 2017, ISSN 2073-4409
Publisher: Cell
DOI: 10.1101/196022

A rapid and robust method for single cell chromatin accessibility profiling

Author(s): Xi Chen, Kedar Nath Natarajan, Sarah A Teichmann
Published in: Nature Communiction, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/309831

Developmental enhancers and chromosome topology

Author(s): Eileen E. M. Furlong, Michael Levine
Published in: Science, 2018, ISSN 1095-9203
Publisher: Science Magazine
DOI: 10.1126/science.aau0320

A Synthetic Oligo Library and Sequencing Approach Reveals an Insulation Mechanism Encoded within Bacterial σ 54 Promoters

Author(s): Lior Levy, Leon Anavy, Oz Solomon, Roni Cohen, Michal Brunwasser-Meirom, Shilo Ohayon, Orna Atar, Sarah Goldberg, Zohar Yakhini, Roee Amit
Published in: Cell Reports, 21/3, 2017, Page(s) 845-858, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2017.09.063

Genome-wide analysis of fitness data and its application to improve metabolic models

Author(s): Edward Vitkin, Oz Solomon, Sharon Sultan, Zohar Yakhini
Published in: BMC Bioinformatics, 19/1, 2018, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-018-2341-9

Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression

Author(s): Michal Brunwasser-Meirom, Yaroslav Pollak, Sarah Goldberg, Lior Levy, Orna Atar, Roee Amit
Published in: Nature Communications, 7, 2016, Page(s) 10407, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms10407

A Looping-Based Model for Quenching Repression

Author(s): Yaroslav Pollak, Sarah Goldberg, Roee Amit
Published in: PLOS, 2017
Publisher: plos.org
DOI: 10.1371/journal.pcbi.1005337

Datasets

Additional file 2: of Genome-wide analysis of fitness data and its application to improve metabolic models

Author(s): Vitkin, Edward; Solomon, Oz; Sultan, Sharon; Yakhini, Zohar
Published in: figshare

Additional file 3: of Genome-wide analysis of fitness data and its application to improve metabolic models

Author(s): Vitkin, Edward; Solomon, Oz; Sultan, Sharon; Yakhini, Zohar
Published in: figshare