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Received — 24 December 2024 ⏭ Favourites

How to build the virtual cell with artificial intelligence: Priorities and opportunities

✇Cell
By: Charlotte Bunne · Yusuf Roohani · Yanay Rosen · Ankit Gupta · Xikun Zhang · Marcel Roed · Theo Alexandrov · Mohammed AlQuraishi · Patricia Brennan · Daniel B. Burkhardt · Andrea Califano · Jonah Cool · Abby F. Dernburg · Kirsty Ewing · Emily B. Fox · Matthias Haury · Amy E. Herr · Eric Horvitz · Patrick D. Hsu · Viren Jain · Gregory R. Johnson · Thomas Kalil · David R. Kelley · Shana O. Kelley · Anna Kreshuk · Tim Mitchison · Stephani Otte · Jay Shendure · Nicholas J. Sofroniew · Fabian Theis · Christina V. Theodoris · Srigokul Upadhyayula · Marc Valer · Bo Wang · Eric Xing · Serena Yeung-Levy · Marinka Zitnik · Theofanis Karaletsos · Aviv Regev · Emma Lundberg · Jure Leskovec · Stephen R. Quake
12 December 2024 at 08:00
Advances in AI and omics enable the creation of AI virtual cells (AIVCs)—multi-scale, multimodal neural network models that simulate molecules, cells, and tissues across diverse states. This vision outlines their design and collaborative development, promising to transform biological research through high-fidelity simulations, accelerating discoveries, and fostering interdisciplinary open science collaborations.

Bridge RNAs direct programmable recombination of target and donor DNA

✇Nature - Issue - nature.com science feeds
By: Matthew G. Durrant · Nicholas T. Perry · James J. Pai · Aditya R. Jangid · Januka S. Athukoralage · Masahiro Hiraizumi · John P. McSpedon · April Pawluk · Hiroshi Nishimasu · Silvana Konermann · Patrick D. Hsu
26 June 2024 at 08:00

Nature, Published online: 26 June 2024; doi:10.1038/s41586-024-07552-4

A bispecific non-coding RNA expressed by the IS110 family of mobile genetic elements forms the basis of a programmable genome-editing system that enables the insertion, excision or inversion of specific target DNA sequences.

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability

✇Cell
By: Mariko Takahashi， Harrison B. Chong， Siwen Zhang， Tzu-Yi Yang， Matthew J. Lazarov， Stefan Harry， Michelle Maynard， Brendan Hilbert， Ryan D. White， Heather E. Murrey， Chih-Chiang Tsou， Kira Vordermark， Jonathan Assaad， Magdy Gohar， Benedikt R. Dürr， Marianne Richter， Himani Patel， Gregory Kryukov， Natasja Brooijmans， Aliyu Sidi Omar Alghali， Karla Rubio， Antonio Villanueva， Junbing Zhang， Maolin Ge， Farah Makram， Hanna Griesshaber， Drew Harrison， Ann-Sophie Koglin， Samuel Ojeda， Barbara Karakyriakou， Alexander Healy， George Popoola， Inbal Rachmin， Neha Khandelwal， Jason R. Neil， Pei-Chieh Tien， Nicholas Chen， Tobias Hosp， Sanne van den Ouweland， Toshiro Hara， Lillian Bussema， Rui Dong， Lei Shi， Martin Q. Rasmussen， Ana Carolina Domingues， Aleigha Lawless， Jacy Fang， Satoshi Yoda， Linh Phuong Nguyen， Sarah Marie Reeves， Farrah Nicole Wakefield， Adam Acker， Sarah Elizabeth Clark， Taronish Dubash， John Ka
22 April 2024 at 08:00
DrugMap serves as a roadmap to develop covalent ligands for oncogenic drivers.

Tumor-selective activity of RAS-GTP inhibition in pancreatic cancer

✇Nature - Issue - nature.com science feeds
By: Urszula N. Wasko · Jingjing Jiang · Tanner C. Dalton · Alvaro Curiel-Garcia · A. Cole Edwards · Yingyun Wang · Bianca Lee · Margo Orlen · Sha Tian · Clint A. Stalnecker · Kristina Drizyte-Miller · Marie Menard · Julien Dilly · Stephen A. Sastra · Carmine F. Palermo · Marie C. Hasselluhn · Amanda R. Decker-Farrell · Stephanie Chang · Lingyan Jiang · Xing Wei · Yu C. Yang · Ciara Helland · Haley Courtney · Yevgeniy Gindin · Karl Muonio · Ruiping Zhao · Samantha B. Kemp · Cynthia Clendenin · Rina Sor · William P. Vostrejs · Priya S. Hibshman · Amber M. Amparo · Connor Hennessey · Matthew G. Rees · Melissa M. Ronan · Jennifer A. Roth · Jens Brodbeck · Lorenzo Tomassoni · Basil Bakir · Nicholas D. Socci · Laura E. Herring · Natalie K. Barker · Junning Wang · James M. Cleary · Brian M. Wolpin · John A. Chabot · Michael D. Kluger · Gulam A. Manji · Kenneth Y. Tsai · Miroslav Sekulic · Stephen M. Lagana · Andrea Califano · Elsa Quintana · Zhengping Wang · Jacqueline A. M. Smith · Matthew Holderfield · David Wildes · Scott W. Lowe · Michael A. Badgley · Andrew J. Aguirre · Ro
8 April 2024 at 08:00

Nature, Published online: 08 April 2024; doi:10.1038/s41586-024-07379-z

Tumor-selective activity of RAS-GTP inhibition in pancreatic cancer

Potential role of lipophagy impairment for anticancer effects of glycolysis-suppressed pancreatic ductal adenocarcinoma cells

✇Cell Death Discovery nature.com science feeds
By: Zhiheng Zhang · Haruna Aoki · Keitaro Umezawa · Joshua Kranrod · Natsumi Miyazaki · Taichi Oshima · Takuya Hirao · Yuri Miura · John Seubert · Kousei Ito · Shigeki Aoki
5 April 2024 at 08:00

Cell Death Discovery, Published online: 05 April 2024; doi:10.1038/s41420-024-01933-4

Potential role of lipophagy impairment for anticancer effects of glycolysis-suppressed pancreatic ductal adenocarcinoma cells

Embracing cancer complexity: Hallmarks of systemic disease

✇Cell
By: Charles Swanton， Elsa Bernard， Chris Abbosh， Fabrice André， Johan Auwerx， Allan Balmain， Dafna Bar-Sagi， René Bernards， Susan Bullman， James DeGregori， Catherine Elliott， Ayelet Erez， Gerard Evan， Mark A. Febbraio， Andrés Hidalgo， Mariam Jamal-Hanjani， Johanna A. Joyce， Matthew Kaiser， Katja Lamia， Jason W. Locasale， Sherene Loi， Ilaria Malanchi， Miriam Merad， Kathryn Musgrave， Ketan J. Patel， Sergio Quezada， Jennifer A. Wargo， Ashani Weeraratna， Eileen White， Frank Winkler， John N. Wood， Karen H. Vousden， Douglas Hanahan
28 March 2024 at 08:00
Cancer is a systemic disease in more than one dimension, in terms of its evolutionary course, direct crosstalk with the microenvironment, and intricate communication with the macro-environment. This broad perspective encompasses our understanding of cancer’s systemic features, mapping out the path for tackling its complexity to bridge what we can learn and who we need to help.

Single-cell multiplex chromatin and RNA interactions in ageing human brain

✇Nature - Issue - nature.com science feeds
By: Xingzhao Wen · Zhifei Luo · Wenxin Zhao · Riccardo Calandrelli · Tri C. Nguyen · Xueyi Wan · John Lalith Charles Richard · Sheng Zhong
27 March 2024 at 08:00

Nature, Published online: 27 March 2024; doi:10.1038/s41586-024-07239-w

We introduce multinucleic acid interaction mapping in single cells (MUSIC), for concurrent profiling of multiplex chromatin interactions, gene expression and RNA–chromatin associations within individual nuclei, as a tool for exploring chromatin architecture and transcription.

Evolutionary trajectories of small cell lung cancer under therapy

✇Nature - Issue - nature.com science feeds
By: Julie George · Lukas Maas · Nima Abedpour · Maria Cartolano · Laura Kaiser · Rieke N. Fischer · Andreas H. Scheel · Jan-Philipp Weber · Martin Hellmich · Graziella Bosco · Caroline Volz · Christian Mueller · Ilona Dahmen · Felix John · Cleidson Padua Alves · Lisa Werr · Jens Peter Panse · Martin Kirschner · Walburga Engel-Riedel · Jessica Jürgens · Erich Stoelben · Michael Brockmann · Stefan Grau · Martin Sebastian · Jan A. Stratmann · Jens Kern · Horst-Dieter Hummel · Balazs Hegedüs · Martin Schuler · Till Plönes · Clemens Aigner · Thomas Elter · Karin Toepelt · Yon-Dschun Ko · Sylke Kurz · Christian Grohé · Monika Serke · Katja Höpker · Lars Hagmeyer · Fabian Doerr · Khosro Hekmath · Judith Strapatsas · Karl-Otto Kambartel · Geothy Chakupurakal · Annette Busch · Franz-Georg Bauernfeind · Frank Griesinger · Anne Luers · Wiebke Dirks · Rainer Wiewrodt · Andrea Luecke · Ernst Rodermann · Andreas Diel · Volker Hagen · Kai Severin · Roland T. Ullrich · Hans Christian Reinhardt · Alexander Quaas · Magdalena Bogus · Cornelius Courts · Peter Nürnberg · Kerstin Becker
13 March 2024 at 08:00

Nature, Published online: 13 March 2024; doi:10.1038/s41586-024-07177-7

We uncover key processes of the genomic evolution of small cell lung cancer under therapy, identify the common ancestor as the source of clonal diversity at relapse and show central genomic patterns associated with drug response.

Pan-cancer proteogenomics characterization of tumor immunity

✇Cell
By: Francesca Petralia， Weiping Ma， Tomer M. Yaron， Francesca Pia Caruso， Nicole Tignor， Joshua M. Wang， Daniel Charytonowicz， Jared L. Johnson， Emily M. Huntsman， Giacomo B. Marino， Anna Calinawan， John Erol Evangelista， Myvizhi Esai Selvan， Shrabanti Chowdhury， Dmitry Rykunov， Azra Krek， Xiaoyu Song， Berk Turhan， Karen E. Christianson， David A. Lewis， Eden Z. Deng， Daniel J.B. Clarke， Jeffrey R. Whiteaker， Jacob J. Kennedy， Lei Zhao， Rossana Lazcano Segura， Harsh Batra， Maria Gabriela Raso， Edwin Roger Parra， Rama Soundararajan， Ximing Tang， Yize Li， Xinpei Yi， Shankha Satpathy， Ying Wang， Maciej Wiznerowicz， Tania J. González-Robles， Antonio Iavarone， Sara J.C. Gosline， Boris Reva， Ana I. Robles， Alexey I. Nesvizhskii， D.R. Mani， Michael A. Gillette， Robert J. Klein， Marcin Cieslik， Bing Zhang， Amanda G. Paulovich， Robert Sebra， Zeynep H. Gümüş， Galen Hostetter， David Fenyö， Gilbert S. Omenn， Lewis C
14 February 2024 at 08:00
Immunotherapy holds strong promise for cancer treatment but at present benefits only a small proportion of cases. A pan-cancer analysis of the immune landscape in more than 1,000 tumors across ten cancer types reveals immune surveillance and immune evasion mechanisms as well as potential molecular target that could augment future immunotherapy and precision medicine strategies.

Nuclear export of circular RNA

✇Nature - Issue - nature.com science feeds
By: Linh H. Ngo · Andrew G. Bert · B. Kate Dredge · Tobias Williams · Vincent Murphy · Wanqiu Li · William B. Hamilton · Kirstyn T. Carey · John Toubia · Katherine A. Pillman · Dawei Liu · Jessica Desogus · Jeffrey A. Chao · Andrew J. Deans · Gregory J. Goodall · Vihandha O. Wickramasinghe
14 February 2024 at 08:00

Nature, Published online: 14 February 2024; doi:10.1038/s41586-024-07060-5

Circular RNAs are exported from the nucleus by Ran-GTP, exportin-2 and IGF2BP1 in a mechanism analogous to protein export rather than mRNA export.

Author Correction: Genotyping, sequencing and analysis of 140,000 adults from Mexico City

✇Nature - Issue - nature.com science feeds
By: Andrey Ziyatdinov · Jason Torres · Jesús Alegre-Díaz · Joshua Backman · Joelle Mbatchou · Michael Turner · Sheila M. Gaynor · Tyler Joseph · Yuxin Zou · Daren Liu · Rachel Wade · Jeffrey Staples · Razvan Panea · Alex Popov · Xiaodong Bai · Suganthi Balasubramanian · Lukas Habegger · Rouel Lanche · Alex Lopez · Evan Maxwell · Marcus Jones · Humberto García-Ortiz · Raul Ramirez-Reyes · Rogelio Santacruz-Benítez · Abhishek Nag · Katherine R. Smith · Amy Damask · Nan Lin · Charles Paulding · Mark Reppell · Sebastian Zöllner · Eric Jorgenson · William Salerno · Slavé Petrovski · John Overton · Jeffrey Reid · Timothy A. Thornton · Gonçalo Abecasis · Jaime Berumen · Lorena Orozco-Orozco · Rory Collins · Adolfo Ferrando · Michael Cantor · Giovanni Coppola · Andrew Deubler · Aris Economides · Katia Karalis · Luca A. Lotta · Lyndon J. Mitnaul · John D. Overton · Jeffrey G. Reid · Alan Shuldiner · Katherine Siminovitch · Christina Beechert · Erin D. Brian · Laura M. Cremona · Hang Du · Caitlin Forsythe · Zhenhua Gu · Kristy Guevara · Michael Lattari · Alexander Lopez · Kia
8 February 2024 at 08:00

Nature, Published online: 08 February 2024; doi:10.1038/s41586-024-07051-6

Author Correction: Genotyping, sequencing and analysis of 140,000 adults from Mexico City

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

✇Nature Biotechnology - Issue - nature.com science feeds
By: Delphine Larivière · Linelle Abueg · Nadolina Brajuka · Cristóbal Gallardo-Alba · Bjorn Grüning · Byung June Ko · Alex Ostrovsky · Marc Palmada-Flores · Brandon D. Pickett · Keon Rabbani · Agostinho Antunes · Jennifer R. Balacco · Mark J. P. Chaisson · Haoyu Cheng · Joanna Collins · Melanie Couture · Alexandra Denisova · Olivier Fedrigo · Guido Roberto Gallo · Alice Maria Giani · Grenville MacDonald Gooder · Kathleen Horan · Nivesh Jain · Cassidy Johnson · Heebal Kim · Chul Lee · Tomas Marques-Bonet · Brian O’Toole · Arang Rhie · Simona Secomandi · Marcella Sozzoni · Tatiana Tilley · Marcela Uliano-Silva · Marius van den Beek · Robert W. Williams · Robert M. Waterhouse · Adam M. Phillippy · Erich D. Jarvis · Michael C. Schatz · Anton Nekrutenko · Giulio Formenti
26 January 2024 at 08:00

Nature Biotechnology, Published online: 26 January 2024; doi:10.1038/s41587-023-02100-3

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution

✇Nature Biotechnology - Issue - nature.com science feeds
By: Jason Z. Zhang · William H. Nguyen · Nathan Greenwood · John C. Rose · Shao-En Ong · Dustin J. Maly · David Baker
25 January 2024 at 08:00

Nature Biotechnology, Published online: 25 January 2024; doi:10.1038/s41587-023-02107-w

Computationally designed sensors map the activity and signaling environment of Ras.

Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation

✇Most Recent Articles: Clinical Epigenetics
By: Laura K. Godfrey， Jan Forster， Sven-Thorsten Liffers， Christopher Schröder， Johannes Köster， Leonie Henschel， Kerstin U. Ludwig， David Lähnemann， Marija Trajkovic-Arsic， Diana Behrens， Aldo Scarpa， Rita T. Lawlor， Kathrin E. Witzke， Barbara Sitek， Steven A. Johnsen， Sven Rahmann＆hellip；
16 January 2024 at 08:00
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor prognosis. It is marked by extraordinary resistance to conventional therapies including chemotherapy and radiation, as well as to essen...

Author Correction: A genomic mutational constraint map using variation in 76,156 human genomes

✇Nature - Issue - nature.com science feeds
By: Siwei Chen · Laurent C. Francioli · Julia K. Goodrich · Ryan L. Collins · Masahiro Kanai · Qingbo Wang · Jessica Alföldi · Nicholas A. Watts · Christopher Vittal · Laura D. Gauthier · Timothy Poterba · Michael W. Wilson · Yekaterina Tarasova · William Phu · Riley Grant · Mary T. Yohannes · Zan Koenig · Yossi Farjoun · Eric Banks · Stacey Donnelly · Stacey Gabriel · Namrata Gupta · Steven Ferriera · Charlotte Tolonen · Sam Novod · Louis Bergelson · David Roazen · Valentin Ruano-Rubio · Miguel Covarrubias · Christopher Llanwarne · Nikelle Petrillo · Gordon Wade · Thibault Jeandet · Ruchi Munshi · Kathleen Tibbetts · Maria Abreu · Carlos A. Aguilar Salinas · Tariq Ahmad · Christine M. Albert · Diego Ardissino · Irina M. Armean · Elizabeth G. Atkinson · Gil Atzmon · John Barnard · Samantha M. Baxter · Laurent Beaugerie · Emelia J. Benjamin · David Benjamin · Michael Boehnke · Lori L. Bonnycastle · Erwin P. Bottinger · Donald W. Bowden · Matthew J. Bown · Harrison Brand · Steven Brant · Ted Brookings · Sam Bryant · Sarah E. Calvo · Hannia Campos · John C. Chambers · Juli
15 January 2024 at 08:00

Nature, Published online: 15 January 2024; doi:10.1038/s41586-024-07050-7

Author Correction: A genomic mutational constraint map using variation in 76,156 human genomes

Proteomics: A new dimension to decode small cell lung cancer

✇Cell
By: Haobin Chen， Benjamin J. Drapkin， John D. Minna
4 January 2024 at 08:00
Small cell lung cancer (SCLC) is a recalcitrant malignancy. Conquering it will require deep insight into its biology. In this issue of Cell, Liu and colleagues describe proteomic and phosphoproteomic landscapes of resected SCLC tumors and illustrate the potential of this knowledge to identify new SCLC vulnerabilities.

Organ aging signatures in the plasma proteome track health and disease

✇Nature - Issue - nature.com science feeds
By: Hamilton Se-Hwee Oh · Jarod Rutledge · Daniel Nachun · Róbert Pálovics · Olamide Abiose · Patricia Moran-Losada · Divya Channappa · Deniz Yagmur Urey · Kate Kim · Yun Ju Sung · Lihua Wang · Jigyasha Timsina · Dan Western · Menghan Liu · Pat Kohlfeld · John Budde · Edw
6 December 2023 at 08:00

Nature, Published online: 06 December 2023; doi:10.1038/s41586-023-06802-1

Blood plasma protein data was combined with machine learning models for a simple method to determine differences in organ-specific aging; the study provides a basis for the prediction of diseases and aging effects using plasma proteomics.

Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

✇Cell
By: Yifat Geffen， Shankara Anand， Yo Akiyama， Tomer M. Yaron， Yizhe Song， Jared L. Johnson， Akshay Govindan， Özgün Babur， Yize Li， Emily Huntsman， Liang-Bo Wang， Chet Birger， David I. Heiman， Qing Zhang， Mendy Miller， Yosef E.
14 August 2023 at 08:00
An analytical resource of post-translational modifications from over 1,000 patients across 11 cancer types reveals pan-cancer changes involved in hallmark cancer processes and reveals potential new therapeutic avenues.
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