Publications
Preprints
Papers in review or in revision
Shared and distinct molecular effects of regulatory genetic variants provide insight into mechanisms of distal enhancer-promoter communication
Helen Ray-Jones, Zeji Song, Alexander Haglund, Pavel Artemov, Monica Della Rosa, Frances Burden, Roman Kreuzhuber, Anna Litovskikh, Vanessa Xue Hui Tan, Lai Ting Chan, Mattia Frontini, Chris Wallace, Valeriya Malysheva*, Leonardo Bottolo*, Elena Vigorito*, Mikhail Spivakov*
High-resolution promoter interaction analysis in Type 3 Innate Lymphoid Cells implicates Batten Disease gene CLN3 in Crohn’s Disease aetiology
Valeriya Malysheva, Helen Ray-Jones, Tareian A. Cazares, Owen Clay, David Ohayon, Pavel Artemov, Joseph A. Wayman, Monica Della Rosa, Carmen Petitjean, Clarissa Booth, Joseph I.J. Ellaway, William R. Orchard, Xiaoting Chen, Sreeja Parameswaran, Takashi Nagano, Peter Fraser, Stefan Schoenfelder, Matthew T. Weirauch, Leah C. Kottyan, David F. Smith, Nick Powell, Jill Weimer, Chris Wallace, Emily R. Miraldi, Stephen Waggoner, Mikhail Spivakov
Gene regulatory network reconstruction incorporating 3D chromosomal architecture reveals key transcription factors and DNA elements driving neural lineage commitment
Valeriya Malysheva, Marco Antonio Mendoza-Parra, Matthias Blum, Mikhail Spivakov and Hinrich Gronemeyer
Patents
Published
Novel method for studying chromatin organization from rare cell types
Valeriya Malysheva, Stefan Schoenfelder, Mikhail Spivakov, Takashi Nagano and Peter Fraser
Reference number WO2021064430A1
Papers
Published or in press
Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools
Paula Freire-Pritchett, Helen Ray-Jones, Monica Della Rosa, Chris Q. Eijsbouts, William R. Orchard, Steven W. Wingett, Chris Wallace, Jonathan Cairns, Mikhail Spivakov* and Valeriya Malysheva* (* joint corresponding authors)
Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data
Jonathan Cairns*, William R. Orchard*, Valeriya Malysheva*, Mikhail Spivakov (* joint first authors)
Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models
Jessica Sook Yuin Ho, Bobo Wing-Yee Mok, Laura Campisi, Tristan Jordan, Soner Yildiz, Sreeja Parameswaran, Joseph A Wayman, Natasha N Gaudreault, David A Meekins, Sabarish V. Indran, Igor Morozov, Jessie D Trujillo, Yesai S Fstkchyan, Raveen Rathnasinghe, Zeyu Zhu, Simin Zheng, Nan Zhao, Kris White, Helen Ray-Jones, Valeriya Malysheva, Michiel J Thiecke, Siu-Ying Lau, Honglian Liu, Anna Junxia Zhang, Andrew Chak-Yiu Lee, Wen-Chun Liu, Teresa Aydillo, Betsaida Salom Melo, Ernesto Guccione, Robert Sebra, Elaine Shum, Jan Bakker, David A. Kaufman, Andre L. Moreira, Mariano Carossino, Udeni B R Balasuriya, Minji Byun, Emily R Miraldi, Randy A Albrecht, Michael Schotsaert, Adolfo Garcia-Sastre, Sumit K Chanda, Anand D Jeyasekharan, Benjamin R TenOever, Mikhail Spivakov, Matthew T Weirauch, Sven Heinz, Honglin Chen, Christopher Benner, Juergen A Richt, Ivan Marazzi
Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancer
Michiel J. Thiecke, Gordana Wutz, Matthias Muhar, Wen Tang, Stephen Bevan, Valeriya Malysheva, Roman Stocsits, Tobias Neumann, Johannes Zuber, Peter Fraser, Stefan Schoenfelder, Jan-Michael Peters, Mikhail Spivakov
A comprehensive resource for retrieving, visualizing, and integrating functional genomics data
Matthias Blum, Pierre-Etienne Cholley, Valeriya Malysheva, Samuel Nicaise, Julien Moehlin, Hinrich Gronemeyer, Marco Antonio Mendoza-Parra
Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis
Valeriya Malysheva, Marco-Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem and Hinrich Gronemeyer
Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells
Marco-Antonio Mendoza-Parra, Valeriya Malysheva, Mohamed-Ashick M. Saleem and Hinrich Gronemeyer
LOGIQA: A database dedicated to Long-range Genome Interactions Quality Assessment
Marco Antonio Mendoza-Parra, Matthias Blum, Valeriya Malysheva, Pierre-Etienne Cholley, Hinrich Gronemeyer