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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.

Author Correction: π-HuB: the proteomic navigator of the human body

✇Nature - Issue - nature.com science feeds
By: Fuchu He · Ruedi Aebersold · Mark S. Baker · Xiuwu Bian · Xiaochen Bo · Daniel W. Chan · Cheng Chang · Luonan Chen · Xiangmei Chen · Yu-Ju Chen · Heping Cheng · Ben C. Collins · Fernando Corrales · Jürgen Cox · Weinan E · Jennifer E. Van Eyk · Jia Fan · Pouya Faridi · Daniel Figeys · George Fu Gao · Wen Gao · Zu-Hua Gao · Keisuke Goda · Wilson Wen Bin Goh · Dongfeng Gu · Changjiang Guo · Tiannan Guo · Yuezhong He · Albert J. R. Heck · Henning Hermjakob · Tony Hunter · Narayanan Gopalakrishna Iyer · Ying Jiang · Connie R. Jimenez · Lokesh Joshi · Neil L. Kelleher · Ming Li · Yang Li · Qingsong Lin · Cui Hua Liu · Fan Liu · Guang-Hui Liu · Yansheng Liu · Zhihua Liu · Teck Yew Low · Ben Lu · Matthias Mann · Anming Meng · Robert L. Moritz · Edouard Nice · Guang Ning · Gilbert S. Omenn · Christopher M. Overall · Giuseppe Palmisano · Yaojin Peng · Charles Pineau · Terence Chuen Wai Poon · Anthony W. Purcell · Jie Qiao · Roger R. Reddel · Phillip J. Robinson · Paola Roncada · Chris Sander · Jiahao Sha · Erwei Song · Sanjeeva Srivastava · Aihua Sun · Siu Kwan Sze · Chao Tang · Liuju
23 December 2024 at 08:00

Nature, Published online: 23 December 2024; doi:10.1038/s41586-024-08555-x

Author Correction: π-HuB: the proteomic navigator of the human body

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.

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.

Genome-wide characterization of circulating metabolic biomarkers

✇Nature - Issue - nature.com science feeds
By: Minna K. Karjalainen · Savita Karthikeyan · Clare Oliver-Williams · Eeva Sliz · Elias Allara · Wing Tung Fung · Praveen Surendran · Weihua Zhang · Pekka Jousilahti · Kati Kristiansson · Veikko Salomaa · Matt Goodwin · David A. Hughes · Michael Boehnke · Lilian Fernandes Silva · Xianyong Yin · Anubha Mahajan · Matt J. Neville · Natalie R. van Zuydam · Renée de Mutsert · Ruifang Li-Gao · Dennis O. Mook-Kanamori · Ayse Demirkan · Jun Liu · Raymond Noordam · Stella Trompet · Zhengming Chen · Christiana Kartsonaki · Liming Li · Kuang Lin · Fiona A. Hagenbeek · Jouke Jan Hottenga · René Pool · M. Arfan Ikram · Joyce van Meurs · Toomas Haller · Yuri Milaneschi · Mika Kähönen · Pashupati P. Mishra · Peter K. Joshi · Erin Macdonald-Dunlop · Massimo Mangino · Jonas Zierer · Ilhan E. Acar · Carel B. Hoyng · Yara T. E. Lechanteur · Lude Franke · Alexander Kurilshikov · Alexandra Zhernakova · Marian Beekman · Erik B. van den Akker · Ivana Kolcic · Ozren Polasek · Igor Rudan · Christian Gieger · Melanie Waldenberger · Folkert W. Asselbergs · Caroline Hayward · Jingyuan Fu · A
6 March 2024 at 08:00

Nature, Published online: 06 March 2024; doi:10.1038/s41586-024-07148-y

A meta-analysis of genome-wide association studies for 233 circulating metabolites from 33 cohorts reveals more than 400 loci and suggests probable causal genes, providing insights into metabolic pathways and disease aetiology.

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.

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

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

Mitochondrial dysfunction abrogates dietary lipid processing in enterocytes

✇Nature - Issue - nature.com science feeds
By: Chrysanthi Moschandrea · Vangelis Kondylis · Ioannis Evangelakos · Marija Herholz · Farina Schneider · Christina Schmidt · Ming Yang · Sandra Ehret · Markus Heine · Michelle Y. Jaeckstein · Karolina Szczepanowska · Robin Schwarzer · Linda Baumann · Theresa Bock · Efte
20 December 2023 at 08:00

Nature, Published online: 20 December 2023; doi:10.1038/s41586-023-06857-0

Mitochondria have a pivotal role in the transport of dietary lipids in enterocytes, a finding that might have relevance to understanding the aberrant gastrointestinal function in patients with mitochondrial disorders.

Garbage in, garbage out: mitigating risks and maximizing benefits of AI in research

✇Nature - Issue - nature.com science feeds
By: Brooks Hanson · Shelley Stall · Joel Cutcher-Gershenfeld · Kristina Vrouwenvelder · Christopher Wirz · Yuhan (Douglas) Rao · Ge Peng
31 October 2023 at 08:00

Nature, Published online: 31 October 2023; doi:10.1038/d41586-023-03316-8

Artificial-intelligence tools are transforming data-driven science — better ethical standards and more robust data curation are needed to fuel the boom and prevent a bust.

Scalable genetic screening for regulatory circuits using compressed Perturb-seq

✇Nature Biotechnology - Issue - nature.com science feeds
By: Douglas Yao · Loic Binan · Jon Bezney · Brooke Simonton · Jahanara Freedman · Chris J. Frangieh · Kushal Dey · Kathryn Geiger-Schuller · Basak Eraslan · Alexander Gusev · Aviv Regev · Brian Cleary
23 October 2023 at 08:00

Nature Biotechnology, Published online: 23 October 2023; doi:10.1038/s41587-023-01964-9

Compressed Perturb-seq incorporates compressed sensing to genetic screening for scalable discovery of genetic interactions.

Plasma proteomic associations with genetics and health in the UK Biobank

✇Nature - Issue - nature.com science feeds
By: Benjamin B. Sun · Joshua Chiou · Matthew Traylor · Christian Benner · Yi-Hsiang Hsu · Tom G. Richardson · Praveen Surendran · Anubha Mahajan · Chloe Robins · Steven G. Vasquez-Grinnell · Liping Hou · Erika M. Kvikstad · Oliver S. Burren · Jonathan Davitte · Kyle L. Fe
4 October 2023 at 08:00

Nature, Published online: 04 October 2023; doi:10.1038/s41586-023-06592-6

The Pharma Proteomics Project generates the largest open-access plasma proteomics dataset to date, offering insights into trans protein quantitative trait loci across multiple biological domains, and highlighting genetic influences on ligand–receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks.
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