Publications

Calico scientists and collaborators regularly publish in high quality publications to inform the scientific community of discoveries from Calico labs and our collaborators.

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09.15.2026 Publications Cancer Research
PTPN1/2 Inhibition Remodels the Pulmonary Myeloid Landscape to Induce Alveolar Macrophage-Mediated Control of Lung Metastasis

Yue Liu, Im-Meng Sun, Marc Creixell, Jordan Brown, Samir Kharbanda, James J Lee, Varahram Shahryari, Kayley Hake, Jacqueline O’Hara, Kenneth J Finn, Nianxin Yang, Lolita Penland, Jiaxi Wang, Ka Man Li, John Balibalos, Aaron W Stebbins, Patrick M Godfrey, Po-Han Tai, Evangelia Malahias, Wenjun Kong, Nicole Fong, David Hendrickson, Shagun Gupta, Leanne Jg Chan, Fiona E McAllister, Chirag H Patel, Marcia N Paddock, Tuan Andrew Nguyen, Fiona A Harding, Jonathan D Powell

08.07.2026 Publications Sceince Advances
The microenvironment dictates glyco-immune surveillance via HSF1-mediated metabolism

Kevin M Tharp, Sangwoo Park, Greg A Timblin, Alicia L Richards, Jordan A Berg, Nicholas M Twells, Nicholas M Riley, Kyle Alvarez, Allen Lee, Egan L Peltan, D Judy Shon, Erica Stevenson, Kimberly Tsui, Francesco Palomba, Austin E Y T Lefebvre, Ross W Soens, Jaya L Thangaraj, Nadia M E Ayad, Joseph A Rhodenhiser, Johanna Ten Hoeve, Kevin Healy, Michelle Digman, Andrew Dillin, Nevan J Krogan, Carolyn R Bertozzi, Dan S Kaufman, Sanju Sinha, Danielle L Swaney, Lara K Mahal, Jason R Cantor, Matthew J Paszek, Valerie M Weaver

07.15.2026 Publications Nature
An encyclopedia of human enhancer-gene regulatory interactions

Andreas R Gschwind, Kristy S Mualim, Alireza Karbalayghareh, Maya U Sheth, Kushal K Dey, Evelyn Jagoda, Ramil N Nurtdinov, Wang Xi, Anthony S Tan, James Galante, Hank Jones, X Rosa Ma, David Yao, Dulguun Amgalan, Judhajeet Ray, Chad J Munger, Joseph Nasser, Žiga Avsec, Benjamin T James, Muhammad S Shamim, Neva C Durand, Suhas S P Rao, Ragini Mahajan, Benjamin R Doughty, Kalina Andreeva, Jacob C Ulirsch, Kaili Fan, Elizabeth M Perez, Tri C Nguyen, David R Kelley, Hilary K Finucane, Jill E Moore, Zhiping Weng, Manolis Kellis, Michael C Bassik, Berk Ustun, Alkes L Price, Michael A Beer, Roderic Guigó, John A Stamatoyannopoulos, Erez Lieberman Aiden, William J Greenleaf, Christina S Leslie, Lars M Steinmetz, Anshul Kundaje, Jesse M Engreitz

06.08.2026 Publications Nature
GPR15-guided CD8+ T regulatory cells control intestinal inflammation

Cui J, Chen Z, Cheng YH, Nie J, Zhu MH, Xiang C, Chauvin S, Lassoued W, Liu C, Padhan K, Song J, Pai JA, Ocón B, Yang Y, Yao Y, Park AY, Gabrielski JQ, Zheng L, Jiang PD, Zhang Y, Jing H, Xu L, Chen V, Calabresi BA, Pittaluga S, Kleiner DE, Dalgard CL, Sari S, Can S, Karakoc-Aydiner E, Baris S, Erman B, Field M, Silvester JA, Saccocia G, Buhamrah EK, Husain K, Chavoshzadeh Z, Rezaei N, İşlek A, Baş H, Devrez FD, Mackeh R, Fuss IJ, Reich DS, Bailey S, Sater HA, Gulley JL, Kabat J, Smelkinson M, Ganesan S, Chen Z, Grayson PC, Redekar N, Lack J, Lu Z, Lo B, Abolhassani H, Ozen A, Bousvaros A, Snapper SB, Butcher EC, Ravell J, Bosselut R, Su HC, Wu C, Lenardo MJ.

05.24.2026 Publications Journal of Medicinal Chemistry
Discovery of Potent and Orally Bioavailable Novel Cluster of Differentiation 38 (CD38) Small Molecule Inhibitors

Reza Shiroodi, Timothy J Montavon, Brandon M Nelson, John T Randolph, Daniel E O’Flynn, Leo Iu, Charles W Hutchins, Tomas Baikstis, Javier Izquierdo-Ferrer, Don Smyth, Navasona Krishnan, Mohammad Mehdi Maneshi, Jordan W Brown, Gustavo A Afanador, Rinku Jain, Sarathy Karunan Partha, Lance Bigelow, Boguslaw Nocek, Lukas Talaga, Sujatha M Gopalakrishnan, Anand Balakrishnan, Mike M Sheehan, Victoria A Kurschner, Purvi C Jejurkar, Omprakash Nacham, Dongjian Hu, Anna Yarilina, Noah P Bradley, Alex M Chapman, Ashish Thakur, Sanjay C Panchal, Mihiro Sunose, Ioanna Zoi, Michael J Dart, J Brad Shotwell, Madhurima Benekareddy, Renee N Sadowski, Andrew M Swensen

05.19.2026 Journal of Medicinal Chemistry
Discovery of Fosigotifator, a Potent eIF2B Activator with Desired Properties for Human Studies

Jennifer M Frost, Yunsong Tong, Xiangdong Xu, Lei Shi, Marina Pliushchev, Kathleen J Murauski, Kathy Kohlhaas, Diana L Donnelly-Roberts, Michael M Sheehan, Stephan Riedmaier, Hardeep S Oberoi, Jun Chen, Janani Prakash, Charles W Hutchins, Clarissa G Jakob, Rinku Jain, Wei Qiu, Rodger F Henry, Rohinton Edalji, Chaohong Sun, Tracy Carr, Ana M Basso, Brian S Brown, Eric A Voight, Carmela Sidrauski, Michael J Dart

04.29.2026 Publications Nature
Spatial atlas of diabetic kidney disease reveals a B cell-rich subgroup

Bernhard Dumoulin, Jonathan Levinsohn, Konstantin A. Klötzer, Chenyu Li, Liran Mao, Eunji Ha, Samer Mohandes, Thao Nguyen, Luca Paruzzo, Daigoro Hirohama, Victoria Fang, Vijay G. Bhoj, Hamideh Parhiz, Magaiver Andrade-Silva, Amin Abedini, Andi Bergeson, Daniel Traum, Michael J. May, Klaus H. Kaestner, Marco Ruella, Fiona Elizabeth McAllister, A. Ari Hakimi, Mingyao Li, Matthew Palmer, E. John Wherry, Christopher A. Hunter, Michael Paul Cancro, TRIDENT consortium & Katalin Susztak

03.27.2026 Publications Molecular Systems Biology
Progress and new challenges in image-based profiling

Erik Serrano, John Peters, Jesko Wagner, Rebecca E Graham, Zhenghao Chen, Brian Y Feng, Gisele Miranda, Alexandr A Kalinin, Loan Vulliard, Jenna Tomkinson, Cameron Mattson, Michael J Lippincott, Ziqi Kang, Divya Sitani, Dave Bunten, Srijit Seal, Neil O Carragher, Anne E Carpenter, Shantanu Singh, Paula A Marin Zapata, Juan C Caicedo, Gregory P Way

03.11.2026 Publications Nature
Intestinal interoceptive dysfunction drives age-associated cognitive decline

Timothy O Cox, Ashwarya S Devason, Alan de Araujo, Sydney Mason, Madhav Subramanian, Andrea F M Salvador, Hélène C Descamps, Junwon Kim, Yixuan Zhu, Lev Litichevskiy, Sunhee Jung, Won-Suk Song, Adrián Cortés-Martín, Nathan T Henderson, Kuei-Pin Huang, Thao Nguyen, Wisath Sae-Lee, Iboro C Umana, Maria Sacta, Ryan J Rahman, Stephen Wisser, J Andrew D Nelson, Ilona Golynker, Alana M McSween, Eric F Hohmann, Shaan Patel, Anna L Bub, Clara Soekler, Niklas Blank, Kevt’her Hoxha, Lavinia Boccia, Andrea C Wong, Klaas Bahnsen, Jihee Kim, Natalie Biderman, Dina Abbasian, Clarissa Shoffler, Christopher Petucci, Fiona E McAllister, Amber L Alhadeff, Marc V Fuccillo, Colin Hill, Cholsoon Jang, J Nicholas Betley, Guillaume de Lartigue, Virginia Y-M Lee, Maayan Levy, Christoph A Thaiss

02.09.2026 Publications Molecular Cancer Therapeutics
Microsatellite instable cancer cells acquire on-target resistance mutations to WRN helicase inhibitors

Faith Fowler, Jessica Gajda, Amirhossein Mafi, Aileen Kelly, Cynthia L Jeffries, Phuong Le, Lei Shi, Mariam George, Nathaniel Elsen, Alla V Korepanova, Sarah M Zerbs, Orville A Pemberton, Xiangdong Xu, Nathan Gesmundo, Wei Qiu, Fei Han, Henry Tang, Sanjay C Panchal, Michael Dart, Jonathan Hickson, Chaohong Sun, Yunsong Tong, Ari J Firestone

10.27.2025 Publications Molecular Biology of the Cell
The biophysical mechanism of mitochondrial pearling

Gabriel Sturm, Kayley Hake, Austin E Y T Lefebvre, Caleb J Rux, Daria Ivanova, Alfred Millett-Sikking, Kevin M Tharp, Beiduo Rao, Michael Closser, Adam James Waite, Magdalena Precido-Lopez, Alex T Ritter, Sophie Dumont, Wen Lu, Suliana Manley, Juan C Landoni, Wallace F Marshall

09.18.2025 Publications Cancer Research
Loss of UXS1 Selectively Depletes Pyrimidines and Induces Replication Stress in KEAP1-Mutant Lung Cancer

Melat T Gebru, Timothy E Hoffman, Aaron Boudreau, Ngoc Vu, Fei Han, Putianqi Wang, Eddie Folk, Xiumin Wu, James Newton, Kelly D Foster-Duke, Jessica Gajda, Sammy Villa, Nianxin Yang, Celeste M Sandoval, Christian Grant, Samantha E Wildeboer, Wayne R Buck, Jonathan A Hickson, Ari J Firestone, Michael Kort, Bryson D Bennett, Brad Shotwell, Noel S Wilson, David Stokoe

09.17.2025 Publications Nature
Covariation MS uncovers a protein that controls cysteine catabolism

Haopeng Xiao, Martha Ordonez, Emma C Fink, Taylor A Covington, Hilina B Woldemichael, Junyi Chen, Mika Sarkin Jain, Milan H Rohatgi, Shelley M Wei, Nils Burger, Muneeb A Sharif, Julius Jan, Yaoyu Wang, Jonathan J Petrocelli, Katherine Blackmore, Amanda L Smythers, Bingsen Zhang, Matthew Gilbert, Hakyung Cheong, Sumeet A Khetarpal, Arianne Smith, Dina Bogoslavski, Yu Lei, Laura Pontano Vaites, Fiona E McAllister, Nick Van Bruggen, Katherine A Donovan, Edward L Huttlin, Evanna L Mills, Eric S Fischer, Edward T Chouchani

06.05.2025 Publications Journal of Medicinal Chemistry
Validation, Key Pharmacophores, and X-ray Cocrystal Structures of Novel Biochemically and Cellularly Active WRN Inhibitors Derived from a DNA-Encoded Library Screen

Yunsong Tong, Kenton A Baker, Alex M Chapman, Nathaniel L Elsen, Faith Fowler, Mariam D George, Nathan J Gesmundo, Harry Hatton, Michael Hickey, Charles W Hutchins, Cynthia L Jeffries, Aileen Kelly, Alla Korepanova, Iain R Miller, Boguslaw Nocek, Sanjay C Panchal, Orville A Pemberton, Wei Qiu, Nari N Talaty, Henry Yue Hin Tang, Danli Towne, Maomao Zhang, Yiming Zhao, Sujatha M Gopalakrishnan, Chaohong Sun, Michael E Kort, Michael J Dart, Ari J Firestone

04.16.2025 Publications Cell
Rewriting regulatory DNA to dissect and reprogram gene expression

Gabriella E Martyn, Michael T Montgomery, Hank Jones, Katherine Guo, Benjamin R Doughty, Johannes Linder, Deepa Bisht, Fan Xia, Xiangmeng S Cai, Ziwei Chen, Kelly Cochran, Kathryn A Lawrence, Glen Munson, Anusri Pampari, Charles P Fulco, Nidhi Sahni, David R Kelley, Eric S Lander, Anshul Kundaje, Jesse M Engreitz

03.31.2025 Publications Nature Microbiology
Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice

Lev Litichevskiy, Maya Considine, Jasleen Gill, Vasuprada Shandar, Timothy O Cox, Hélène C Descamps, Kevin M Wright, Kevin R Amses, Lenka Dohnalová, Megan J Liou, Monika Tetlak, Mario R Galindo-Fiallos, Andrea C Wong, Patrick Lundgren, Junwon Kim, Giulia T Uhr, Ryan J Rahman, Sydney Mason, Carter Merenstein, Frederic D Bushman, Anil Raj, Fiona Harding, Zhenghao Chen, G V Prateek, Martin Mullis, Andrew G Deighan, Laura Robinson, Ceylan Tanes, Kyle Bittinger, Meenakshi Chakraborty, Ami S Bhatt, Hongzhe Li, Ian Barnett, Emily R Davenport, Karl W Broman, Maayan Levy, Robert L Cohen, David Botstein, Adam Freund, Andrea Di Francesco, Gary A Churchill, Mingyao Li, Christoph A Thaiss

02.02.2025 Publications