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Received — 24 December 2024 ⏭ Favourites

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.

A meta-analysis on global change drivers and the risk of infectious disease

✇Nature - Issue - nature.com science feeds
By: Michael B. Mahon · Alexandra Sack · O. Alejandro Aleuy · Carly Barbera · Ethan Brown · Heather Buelow · David J. Civitello · Jeremy M. Cohen · Luz A. de Wit · Meghan Forstchen · Fletcher W. Halliday · Patrick Heffernan · Sarah A. Knutie · Alexis Korotasz · Joanna G. Larson · Samantha L. Rumschlag · Emily Selland · Alexander Shepack · Nitin Vincent · Jason R. Rohr
8 May 2024 at 08:00

Nature, Published online: 08 May 2024; doi:10.1038/s41586-024-07380-6

Reducing greenhouse gas emissions, managing ecosystem health, and preventing biological invasions and biodiversity loss could help to reduce the burden of plant, animal and human diseases, especially when coupled with improvements to social and economic determinants of health.

3D genomic mapping reveals multifocality of human pancreatic precancers

✇Nature - Issue - nature.com science feeds
By: Alicia M. Braxton · Ashley L. Kiemen · Mia P. Grahn · André Forjaz · Jeeun Parksong · Jaanvi Mahesh Babu · Jiaying Lai · Lily Zheng · Noushin Niknafs · Liping Jiang · Haixia Cheng · Qianqian Song · Rebecca Reichel · Sarah Graham · Alexander I. Damanakis · Catherine G. Fischer · Stephanie Mou · Cameron Metz · Julie Granger · Xiao-Ding Liu · Niklas Bachmann · Yutong Zhu · YunZhou Liu · Cristina Almagro-Pérez · Ann Chenyu Jiang · Jeonghyun Yoo · Bridgette Kim · Scott Du · Eli Foster · Jocelyn Y. Hsu · Paula Andreu Rivera · Linda C. Chu · Fengze Liu · Elliot K. Fishman · Alan Yuille · Nicholas J. Roberts · Elizabeth D. Thompson · Robert B. Scharpf · Toby C. Cornish · Yuchen Jiao · Rachel Karchin · Ralph H. Hruban · Pei-Hsun Wu · Denis Wirtz · Laura D. Wood
1 May 2024 at 08:00

Nature, Published online: 01 May 2024; doi:10.1038/s41586-024-07359-3

Quantitative multimodal 3D reconstruction of human pancreatic tissue at single-cell resolution reveals a high burden of multifocal, genetically heterogeneous pancreatic intraepithelial neoplasias in the normal adult pancreas.

Epigenetic scores of blood-based proteins as biomarkers of general cognitive function and brain health

✇Most Recent Articles: Clinical Epigenetics
By: Hannah M. Smith， Joanna E. Moodie， Karla Monterrubio-Gómez， Danni A. Gadd， Robert F. Hillary， Aleksandra D. Chybowska， Daniel L. McCartney， Archie Campbell， Paul Redmond， Danielle Page， Adele Taylor， Janie Corley， Sarah E. Harris， Maria Valdés Hernández， Susana Muñoz Maniega， Mark E. Bastin＆hellip；
25 March 2024 at 08:00
Epigenetic Scores (EpiScores) for blood protein levels have been associated with disease outcomes and measures of brain health, highlighting their potential usefulness as clinical biomarkers. They are typicall...

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: 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

The extracellular matrix dictates regional competence for tumour initiation

✇Nature - Issue - nature.com science feeds
By: Nordin Bansaccal · Pauline Vieugue · Rahul Sarate · Yura Song · Esmeralda Minguijon · Yekaterina A. Miroshnikova · Dagmar Zeuschner · Amandine Collin · Justine Allard · Dan Engelman · Anne-Lise Delaunois · Mélanie Liagre · Leona de Groote · Evy Timmerman · Delphi Van
15 November 2023 at 08:00

Nature, Published online: 15 November 2023; doi:10.1038/s41586-023-06740-y

Experiments in mice show that expression of the oncogene SmoM2 induces basal cell carcinoma in the ear epidermis but not in the back skin, and that this difference in susceptibility is regulated by the extracellular matrix.

Large language models encode clinical knowledge

✇Nature - Issue - nature.com science feeds
By: Karan Singhal · Shekoofeh Azizi · Tao Tu · S. Sara Mahdavi · Jason Wei · Hyung Won Chung · Nathan Scales · Ajay Tanwani · Heather Cole-Lewis · Stephen Pfohl · Perry Payne · Martin Seneviratne · Paul Gamble · Chris Kelly · Abubakr Babiker · Nathanael Schärli · Aakanksha
12 July 2023 at 08:00

Nature, Published online: 12 July 2023; doi:10.1038/s41586-023-06291-2

Med-PaLM, a state-of-the-art large language model for medicine, is introduced and evaluated across several medical question answering tasks, demonstrating the promise of these models in this domain.

Single-cell spatial landscapes of the lung tumour immune microenvironment

✇Nature - Issue - nature.com science feeds
By: Mark Sorin · Morteza Rezanejad · Elham Karimi · Benoit Fiset · Lysanne Desharnais · Lucas J. M. Perus · Simon Milette · Miranda W. Yu · Sarah M. Maritan · Samuel Doré · Émilie Pichette · William Enlow · Andréanne Gagné · Yuhong Wei · Michele Orain · Venkata S. K. M
1 February 2023 at 08:00

Nature, Published online: 01 February 2023; doi:10.1038/s41586-022-05672-3

Using imaging mass cytometry, the tumour and immunological spatial landscapes of 416 lung adenocarcinomas are characterized, which, when combined with deep learning, can predict clinical outcomes with high accuracy.

Spatial genomics maps the structure, nature and evolution of cancer clones

✇Nature - Issue - nature.com science feeds
By: Artem Lomakin · Jessica Svedlund · Carina Strell · Milana Gataric · Artem Shmatko · Gleb Rukhovich · Jun Sung Park · Young Seok Ju · Stefan Dentro · Vitalii Kleshchevnikov · Vasyl Vaskivskyi · Tong Li · Omer Ali Bayraktar · Sarah Pinder · Andrea L. Richardson · Sandro
9 November 2022 at 08:00

Nature, Published online: 09 November 2022; doi:10.1038/s41586-022-05425-2

A workflow centred around base-specific in situ sequencing generates detailed maps of, and can phenotypically characterize, the unique set of subclones of cancers.

Collagenolysis-dependent DDR1 signalling dictates pancreatic cancer outcome

✇Nature - Issue - nature.com science feeds
By: Hua Su · Fei Yang · Rao Fu · Brittney Trinh · Nina Sun · Junlai Liu · Avi Kumar · Jacopo Baglieri · Jeremy Siruno · Michelle Le · Yuhan Li · Stephen Dozier · Ajay Nair · Aveline Filliol · Nachanok Sinchai · Sara Brin Rosenthal · Jennifer Santini · Christian M. Metallo · A
5 October 2022 at 08:00

Nature, Published online: 05 October 2022; doi:10.1038/s41586-022-05169-z

Cleaved and intact type I collagen have different effects on pancreatic ductal adenocarcinoma (PDAC), and remodelling of type I collagen—mediated through DDR1 signalling—is a prognostic indicator for the survival of patients with PDAC.

Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer

✇Nature - Issue - nature.com science feeds
By: Cameron Herberts · Matti Annala · Joonatan Sipola · Sarah W. S. Ng · Xinyi E. Chen · Anssi Nurminen · Olga V. Korhonen · Aslı D. Munzur · Kevin Beja · Elena Schönlau · Cecily Q. Bernales · Elie Ritch · Jack V. W. Bacon · Nathan A. Lack · Matti Nykter · Rahul Aggarwal
20 July 2022 at 08:00

Nature, Published online: 20 July 2022; doi:10.1038/s41586-022-04975-9

Deep whole-genome sequencing of serial blood samples and matched metastatic tissue reveals that circulating tumour DNA profiling enables detailed study of treatment-driven subclone dynamics, epigenomics and genome-wide somatic evolution in metastatic human cancers.

Targeted genetic and epigenetic profiling of esophageal adenocarcinomas and non-dysplastic Barrett’s esophagus

✇Most Recent Articles: Clinical Epigenetics
By: Rita Pinto， Tobias Hauge， Marine Jeanmougin， Heidi D. Pharo， Stine H. Kresse， Hilde Honne， Sara B. Winge， May-Britt Five， Theresa Kumar， Tom Mala， Truls Hauge， Egil Johnson and Guro E. Lind
14 June 2022 at 08:00
Despite the efforts to describe the molecular landscape of esophageal adenocarcinoma (EAC) and its precursor lesion Barrett’s esophagus (BE), discrepant findings are reported. Here, we investigated the prevale...
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