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Enter your email address below and we will send you your username Email or Customer ID Close If the address matches an existing account you will receive an email with instructions to retrieve your username COVID-19 Notice: How we support scientific communication and options for remote access to subscribed content JOURNALS The EMBO Journal EMBO Reports EMBO Molecular Medicine Life Science Alliance This Journal Anywhere Search journal Search Search EMBO Press Search Advanced search Citation search Login Close Drawer Menu Open DrawerJOURNALSClose Drawer Menu Open DrawerCurrent Issue About Aims & Scope Editors & Board EMBO Press Policies Open Access Licenses & Charges Journal Indicators Contact Editorial Office Information For Authors For Reviewers For Media For Advertisers Archive Alerts Submit CURRENT ISSUE Bypass suppression of essential genes By Jolanda van Leeuwen, Carles Pons, Brenda J. Andrews, Charles Boone and colleagues The protein expression profile of ACE2, suggested as host receptor for SARS‐CoV‐2, is assessed in various human organs. Notably, limited ACE2 expression is observed in the respiratory system both on the protein and mRNA level. The protein expression profile of ACE2 in human tissues Feria Hikmet Loren Méar Åsa Edvinsson Patrick Micke Mathias Uhlén Cecilia Lindskog The protein expression profile of ACE2, suggested as host receptor for SARS‐CoV‐2, is assessed in various human organs. Notably, limited ACE2 expression is observed in the respiratory system both on the protein and mRNA level. Close Figure Viewer Browse All Figures Return to Figure Change zoom level Zoom in Zoom out Previous Figure Next Figure Caption Latest Online Most Read Review 25 September 2020 OPEN ACCESS Enhancing scientific discoveries in molecular biology with deep generative models Romain Lopez Adam Gayoso Nir Yosef This Review provides an introduction into deep generative models and their implementation with deep learning techniques. Several applications in genomics and single‐cell biology are presented, and the interpretability of such neural network models is discussed. Article 25 September 2020 OPEN ACCESS Integrated regulatory models for inference of subtype‐specific susceptibilities in glioblastoma Yunpeng Liu Ning Shi Aviv Regev Shan He Michael T Hemann A novel computational pipeline, inTRINSiC, integrates genomic, epigenomic and transcriptomic profiles with protein signaling networks to dissect subtype‐specific regulatory networks in glioblastoma multiforme and predict subtype‐specific gene essentiality. Correspondence 23 September 2020 OPEN ACCESS Implications of initial physiological conditions for bacterial adaptation to changing environments Matthias Heinemann Markus Basan Uwe Sauer This piece discusses how the different observations of two independent studies (Kotte et al , 2014; Basan et al , 2020), regarding population‐level heterogeneity and lag times during diauxic shift, can be largely explained by different experimental protocols. Article 22 September 2020 OPEN ACCESS Proteomic patterns associated with response to breast cancer neoadjuvant treatment Anjana Shenoy Nishanth Belugali Nataraj Gili Perry Fabricio Loayza Puch Remco Nagel Irina Marin Nora Balint Noa Bossel Anya Pavlovsky Iris Barshack Bella Kaufman Reuven Agami Yosef Yarden Maya Dadiani Tamar Geiger Proteomic profiling of matched tumor and normal samples, associates distinct proteomic patterns with patient prognosis in breast cancer. Functional studies in vivo support the effectiveness of PYCR1 suppression in combination with chemotherapeutics in clinical settings. Article 17 September 2020 OPEN ACCESS Systematic analysis of bypass suppression of essential genes Jolanda van Leeuwen Carles Pons Guihong Tan Jason Zi Wang Jing Hou Jochen Weile Marinella Gebbia Wendy Liang Ermira Shuteriqi Zhijian Li Maykel Lopes Matej Ušaj Andreia Dos Santos Lopes Natascha van Lieshout Chad L Myers Frederick P Roth Patrick Aloy Brenda J Andrews Charles Boone A systematic analysis of 728 different essential yeast genes identifies 124 (17%) dispensable essential genes. Whole‐genome sequencing is used to identify the genome alterations underlying the bypass suppression. Review 26 August 2020 OPEN ACCESS SBML Level 3: an extensible format for the exchange and reuse of biological models Sarah M Keating Dagmar Waltemath Matthias König Fengkai Zhang Andreas Dräger Claudine Chaouiya Frank T Bergmann Andrew Finney Colin S Gillespie Tomáš Helikar Stefan Hoops Rahuman S Malik‐Sheriff Stuart L Moodie Ion I Moraru Chris J Myers Aurélien Naldi Brett G Olivier Sven Sahle James C Schaff Lucian P Smith Maciej J Swat Denis Thieffry Leandro Watanabe Darren J Wilkinson Michael L Blinov Kimberly Begley James R Faeder Harold F Gómez Thomas M Hamm Yuichiro Inagaki Wolfram Liebermeister Allyson L Lister Daniel Lucio Eric Mjolsness Carole J Proctor Karthik Raman Nicolas Rodriguez Clifford A Shaffer Bruce E Shapiro Joerg Stelling Neil Swainston Naoki Tanimura John Wagner Martin Meier‐Schellersheim Herbert M Sauro Bernhard Palsson Hamid Bolouri Hiroaki Kitano Akira Funahashi Henning Hermjakob John C Doyle Michael Hucka SBML Level 3 Community members Over the past two decades, scientists from different fields have been developing SBML, a standard format for encoding computational models in biology and medicine. This article summarizes recent progress and gives perspectives on emerging challenges. Commentary 26 August 2020 OPEN ACCESS Community standards to facilitate development and address challenges in metabolic modeling Maureen A Carey Andreas Dräger Moritz E Beber Jason A Papin James T Yurkovich Opportunities and challenges in implementing standards for modeling in computational biology are discussed using metabolic network modeling as case study. Article 20 August 2020 OPEN ACCESS Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite Jessica M Bryant Sebastian Baumgarten Florent Dingli Damarys Loew Ameya Sinha Aurélie Claës Peter R Preiser Peter C Dedon Artur Scherf CRISPR/dCas9‐based proteomics is used to purify specific DNA regulatory elements in their natural chromatin context and to identify novel chromatin factors associated with virulence genes in the human malaria parasite, Plasmodium falciparum . view table of contents page Review 19 June 2019 OPEN ACCESS Current best practices in single‐cell RNA‐seq analysis: a tutorial Malte D Luecken Fabian J Theis This Tutorial details the steps of a typical single‐cell RNA‐seq analysis. Best‐practice recommendations are provided and illustrated with a workflow provided in the form of an open source code repository. Article 26 July 2020 OPEN ACCESS The protein expression profile of ACE2 in human tissues Feria Hikmet Loren Méar Åsa Edvinsson Patrick Micke Mathias Uhlén Cecilia Lindskog The protein expression profile of ACE2, suggested as host receptor for SARS‐CoV‐2, is assessed in various human organs. Notably, limited ACE2 expression is observed in the respiratory system both on the protein and mRNA level. Article 18 February 2019 OPEN ACCESS A deep proteome and transcriptome abundance atlas of 29 healthy human tissues Dongxue Wang Basak Eraslan Thomas Wieland Björn Hallström Thomas Hopf Daniel Paul Zolg...