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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08.16.2024 Publications Communications Chemistry
Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex

Qi Hao, Manoj K. Rathinaswamy, Kelly L. Klinge, Matthew Bratkowski, Amirhossein Mafi, Christina K. Baumgartner, Keith M. Hamel, Gesine K. Veits, Rinku Jain, Claudio Catalano, Mark Fitzgerald, Alexander W. Hird, Eunice Park, Harit U. Vora, James A. Henderson, Kenton Longenecker, Charles W. Hutchins, Wei Qiu, Giovanna Scapin, Qi Sun, Vincent S. Stoll, Chaohong Sun, Ping Li, Dan Eaton, David Stokoe, Stewart L. Fisher, Christopher G. Nasveschuk, Marcia Paddock, and Michael E. Kort

02.28.2024 Publications Nature Communications
Structure of the p53 degradation complex from HPV16

John C. K. Wang, Hannah T. Baddock, Amirhossein Mafi, Ian T. Foe, Matthew Bratkowski, Ting-Yu Lin, Zena D. Jensvold, Magdalena Preciado López, David Stokoe, Dan Eaton, Qi Hao and Aaron H. Nile

10.04.2023 Publications Nature
The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity

Christina K. Baumgartner, Hakimeh Ebrahimi-Nik, Arvin Iracheta-Vellve, Keith M. Hamel, Kira E. Olander, Thomas G. R. Davis, Kathleen A. McGuire, Geoff T. Halvorsen, Omar I. Avila, Chirag H. Patel, Sarah Y. Kim, Ashwin V. Kammula, Audrey J. Muscato, Kyle Halliwill, Prasanthi Geda, Kelly L. Klinge, Zhaoming Xiong, Ryan Duggan, Liang Mu, Mitchell D. Yeary, James C. Patti, Tyler M. Balon, Rebecca Mathew, Carey Backus, Domenick E. Kennedy, Angeline Chen, Kenton Longenecker, Joseph T. Klahn, Cara L. Hrusch, Navasona Krishnan, Charles W. Hutchins, Jax P. Dunning, Marinka Bulic, Payal Tiwari, Kayla J. Colvin, Cun Lan Chuong, Ian C. Kohnle, Matthew G. Rees, Andrew Boghossian, Melissa Ronan, Jennifer A. Roth, Meng-Ju Wu, Juliette S. M. T. Suermondt, Nelson H. Knudsen, Collins K. Cheruiyot, Debattama R. Sen, Gabriel K. Griffin, Todd R. Golub, Nabeel El-Bardeesy, Joshua H. Decker, Yi Yang, Magali Guffroy, Stacey Fossey, Patricia Trusk, Im-Meng Sun, Yue Liu, Wei Qiu, Qi Sun, Marcia N. Paddock, Elliot P. Farney, Mark A. Matulenko, Clay Beauregard, Jennifer M. Frost, Kathleen B. Yates, Philip R. Kym, Robert T. Manguso

10.04.2023 Publications Nature
Plasma proteomic associations with genetics and health in the UK Biobank

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. Ferber, Christopher E. Gillies, Åsa K. Hedman, Sile Hu, inchi Lin, Rajesh Mikkilineni, Rion K. Pendergrass, Corran Pickering, Bram Prins, Denis Baird, Chia-Yen Chen, Lucas D. Ward, Aimee M. Deaton, Samantha Welsh, Carissa M. Willis, Nick Lehner, Matthias Arnold, Maria A. Wörheide, Karsten Suhre, Gabi Kastenmüller, Anurag Sethi, Madeleine Cule, Anil Raj, Alnylam Human Genetics, AstraZeneca Genomics Initiative, Biogen Biobank Team, Bristol Myers Squibb, Genentech Human Genetics, GlaxoSmithKline Genomic Sciences, Pfizer Integrative Biology, Population Analytics of Janssen Data Sciences, Regeneron Genetics Center, Lucy Burkitt-Gray, Eugene Melamud, Mary Helen Black, Eric B. Fauman, Joanna M. M. Howson, Hyun Min Kang, Mark I. McCarthy, Paul Nioi, Slavé Petrovski, Robert A. Scott, Erin N. Smith, Sándor Szalma, Dawn M. Waterworth, Lyndon J. Mitnaul, Joseph D. Szustakowski, Bradford W. Gibson, Melissa R. Miller and Christopher D. Whelan

08.21.2023 Publications Scientific Report
3D mouse pose from single-view video and a new dataset

Bo Hu, Bryan Seybold, Shan Yang, Avneesh Sud, Yi Liu, Karla Barron, Paulyn Cha, Marcelo Cosino, Ellie Karlsson, Janessa Kite, Ganesh Kolumam, Joseph Preciado, José Zavala-Solorio, Chunlian Zhang, Xiaomeng Zhang, Martin Voorbach, Ann E. Tovcimak, J. Graham Ruby & David A. Ross

06.13.2023 Publications Life Science Alliance
An immune-based tool platform for in vivo cell clearance

Jieqiong Zhang, Tatsuya Tsukui, Xiumin Wu, Alyssa Brito, John Maxwell Trumble, Juan C Caraballo, Greg M Allen, José Zavala-Solorio, Chunlian Zhang, Jonathan Paw, Wendell A Lim, Jiefei Geng, Yuliya Kutskova, Adam Freund, Ganesh Kolumam, Dean Sheppard and Robert L Cohen

05.26.2023 Publications Science Advances
Global analysis of the yeast knockout phenome

Gina Turco, Christie Chang, Rebecca Y Wang, Griffin Kim, Emily H Stoops, Brianna Richardson, Vanessa Sochat, Jennifer Rust, Rose Oughtred, Nathaniel Thayer, Fan Kang, Michael S Livstone, Sven Heinicke, Mark Schroeder, Kara J Dolinski, David Botstein and Anastasia Baryshnikova

03.09.2023 Publications Science
Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase

Kevin G. Hicks, Ahmad A. Cluntun, Heidi L. Schubert, Sean R. Hackett, Jordan A. Berg, Paul G. Leonard, Mariana A. Ajalla Aleixo, Youjia Zhou, Alex J. Bott, Sonia R. Salvatore, Fei Chang, Aubrie Blevins, Paige Barta, Samantha Tilley, Aaron Leifer, Andrea Guzman, Ajak Arok, Sarah Fogarty, Jacob M. Winter, Hee-Chul Ahn, Karen N. Allen, Samual Block, Iara A. Cardoso, Jianping Ding, Ingrid Dreveny, William C. Gasper, Quinn Ho, Atsushi Matsuura, Michael J. Palladino, Sabin Prajapati, Pengkai Sun, Kai Tittmann, Dean R. Tolan, Judith Unterlass, Andrew P. Vandemark, Matthew G. Vander Heiden, Bradley A. Webb, Cai-Hong Yun, Pengkai Zhao, Bei Wang, Francisco J. Schopfer, Christopher P. Hill, Maria Cristina Nonato, Florian L. Muller, James E. Cox, Jared Rutter

03.06.2023 Publications Journal of Medicinal Chemistry
Discovery of a Potent Chloroacetamide GPX4 Inhibitor with Bioavailability to Enable Target Engagement in Mice, a Potential Tool Compound for Inducing Ferroptosis In Vivo

John T. Randolph, Matthew J. O’Connor, Fei Han, Charles W. Hutchins, Y. Amy Siu, Min Cho, Yunan Zheng, Jonathan A. Hickson, Jana L. Markley, Vlasios Manaves, Mikkel Algire, Kenton A. Baker, Alex M. Chapman, Sujatha M. Gopalakrishnan, Sanjay C. Panchal, Kelly Foster-Duke, DeAnne F. Stolarik, Anita Kempf-Grote, Darby Dammeier, Stacey Fossey, Qi Sun, Chaohong Sun, Yu Shen, Michael J. Dart, Warren M. Kati, Albert Lai, Ari J. Firestone and Michael E. Kort

02.06.2023 Publications Cancer Discovery
Senescence Rewires Microenvironment Sensing to Facilitate Antitumor Immunity

Hsuan-An Chen, Yu-Jui Ho, Riccardo Mezzadra, Jose M Adrover, Ryan Smolkin, Changyu Zhu, Katharina Woess, Nicholas Bernstein, Georgia Schmitt, Linda Fong, Wei Luan, Alexandra Wuest, Sha Tian, Xiang Li, Caroline Broderick, Ronald C Hendrickson, Mikala Egeblad, Zhenghao Chen, Direna Alonso-Curbelo and Scott W Lowe

01.27.2023 Publications The Journals of Gerontology: Series A
An automated, home-cage, video monitoring-based mouse frailty index detects age-associated morbidity in C57BL and Diversity Outbred mice

J Graham Ruby, PhD, Andrea Di Francesco, PhD, Paulo Ylagan, BS, Angela Luo, BA, Robert Keyser, BS, Owen Williams, BA, Sarah Spock, BS, Wenzhou Li, PhD, Nalien Vongtharangsy, BS, Sandip Chatterjee, PhD, Cricket A Sloan, MS, MS, Charles Ledogar, MEng, Veronica Kuiper, BS, Janessa Kite, MSc, Marcelo Cosino, Paulyn Cha, BS, Eleanor M Karlsson, DVM

11.23.2022 Publications Cell
Architecture of the outbred brown fat proteome defines regulators of metabolic physiology

Haopeng Xiao, Luiz H M Bozi, Yizhi Sun, Christopher L Riley, Vivek M Philip, Mandy Chen, Jiaming Li, Tian Zhang, Evanna L Mills, Margo P Emont, Wenfei Sun, Anita Reddy, Ryan Garrity, Jiani Long, Tobias Becher, Laura Potano Vitas, Dina Laznik-Bogoslavski, Martha Ordonez, Xinyue Liu, Xiong Chen, Yun Wang, Weihai Liu, Nhien Tran, Yitong Liu, Yang Zhang, Aaron M Cypess, Andrew P White, Yuchen He, Rebecca Deng, Heiko Schöder, Joao A Paulo, Mark P Jedrychowski, Alexander S Banks, Yu-Hua Tseng, Paul Cohen, Linus T Tsai, Evan D Rosen, Samuel Klein, Maria Chondronikola, Fiona E McAllister, Nick Van Bruggen, Edward L Huttlin, Bruce M Spiegelman, Gary A Churchill, Steven P Gygi and Edward T Chouchani

09.23.2022 Publications Nature
A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation

Ranit Kedmi, Tariq A. Najar, Kailin R. Mesa, Allyssa Grayson, Lina Kroehling, Yuhan Hao, Stephanie Hao, Maria Pokrovskii, Mo Xu, Jhimmy Talbot, Jiaxi Wang, Joe Germino, Caleb A. Lareau, Ansuman T. Satpathy, Mark S. Anderson, Terri M. Laufer, Iannis Aifantis, Juliet M. Bartleson, Paul M. Allen, Helena Paidassi, James M. Gardner, Marlon Stoeckius and Dan R. Littman

03.07.2022 Publications Nature Cancer
An anti-PD-1-GITR-L bispecific agonist induces GITR clustering-mediated T cell activation for cancer immunotherapy

Sarah Chan, Nicole Belmar, Sun Ho, Bryan Rogers, Marcia Stickler, Michelle Graham, Eileen Lee, Ninian Tran, Dong Zhang, Priyanka Gupta, Mien Sho, Tracy MacDonough, Andrew Woolley, Han Kim, Hong Zhang, Wei Liu, Pingping Zheng, Zoltan Dezso, Kyle Halliwill, Michele Ceccarelli, Susan Rhodes, Archana Thakur, Charles M. Forsyth, Mengli Xiong, Siu Sze Tan, Ramesh Iyer, Marc Lake, Enrico Digiammarino, Li Zhou, Lance Bigelow, Kenton Longenecker, Russell A. Judge, Cassie Liu, Max Trumble, Jonathan P. Remis, Melvin Fox, Belinda Cairns, Yoshiko Akamatsu, Diane Hollenbaugh, Fiona Harding and Hamsell M. Alvarez

02.04.2022 Publications eLife
Novel insights from a multiomics dissection of the Hayflick limit

Michelle Chan, Han Yuan, Ilya Soifer, Tobias M Maile, Rebecca Y Wang, Andrea Ireland, Jonathon J O’Brien, Jérôme Goudeau, Leanne JG Chan, Twaritha Vijay, Adam Freund, Cynthia Kenyon, Bryson D Bennett, Fiona E McAllister, David R Kelley, Margaret Roy, Robert L Cohen, Arthur D Levinson, David Botstein, David G Hendrickson

01.20.2022 Publications Nature Immunology
The immunoregulatory landscape of human tuberculosis granulomas

Erin F. McCaffrey, Michele Donato, Leeat Keren, Zhenghao Chen, Alea Delmastro, Megan B. Fitzpatrick, Sanjana Gupta, Noah F. Greenwald, Alex Baranski, William Graf, Rashmi Kumar, Marc Bosse, Christine Camacho Fullaway, Pratista K. Ramdial, Erna Forgó, Vladimir Jojic, David Van Valen, Smriti Mehra, Shabaana A. Khader, Sean C. Bendall, Matt van de Rijn, Daniel Kalman, Deepak Kaushal, Robert L. Hunter, Niaz Banaei, Adrie J. C. Steyn, Purvesh Khatri, Michael Angelo

12.08.2021 Publications Nature
Exercise plasma boosts memory and dampens brain inflammation via clusterin

Zurine De Miguel, Nathalie Khoury, Michael J. Betley, Benoit Lehallier, Drew Willoughby, Niclas Olsson, Andrew C. Yang, Oliver Hahn, Nannan Lu, Ryan T. Vest, Liana N. Bonanno, Lakshmi Yerra, Lichao Zhang, Nay Lui Saw, J. Kaci Fairchild, Davis Lee, Hui Zhang, Patrick L. McAlpine, Kévin Contrepois, Mehrdad Shamloo, Joshua E. Elias, Thomas A. Rando and Tony Wyss-Coray

09.03.2021 Commentaries & Reviews Biological Reviews Cambridge Philosophical Society
The naked truth: a comprehensive clarification and classification of current ‘myths’ in naked mole-rat biology

Rochelle Buffenstein, Vincent Amoroso, Blazej Andziak, Stanislav Avdieiev, Jorge Azpurua, Alison J. Barker, Nigel C. Bennett, Miguel A. Brieño-Enríquez, Gary N. Bronner, Clive Coen, Martha A. Delaney, Christine M. Dengler-Crish, Yael H. Edrey, Chris G. Faulkes, Daniel Frankel, Gerard Friedlander, Patrick A. Gibney, Vera Gorbunova, Christopher Hine, Melissa M. Holmes, Jennifer U. M. Jarvis, Yoshimi Kawamura, Nobuyuki Kutsukake, Cynthia Kenyon, Walid T. Khaled, Takefumi Kikusui, Joseph Kissil, Samantha Lagestee, John Larson, Amanda Lauer, Leonid A. Lavrenchenko, Angela Lee, Jonathan B. Levitt, Gary R. Lewin, Kaitlyn N. Lewis Hardell, TzuHua D. Lin, Matthew J. Mason, Dan McCloskey, Mary McMahon, Kyoko Miura, Kazutaka Mogi, Vikram Narayan, Timothy P. O’Connor, Kazuo Okanoya, M. Justin O’Riain, Thomas J. Park, Ned J. Place, Katie Podshivalova, Matthew E. Pamenter, Sonja J. Pyott, Jane Reznick, J. Graham Ruby, Adam B. Salmon, Joseph Santos-Sacchi, Diana K. Sarko, Andrei Seluanov, Alyssa Shepard, Megan Smith, Kenneth B. Storey, Xiao Tian, Emily N. Vice, Mélanie Viltard, Akiyuki Watarai, Ewa Wywial, Masanori Yamakawa, Elena D. Zemlemerova, Michael Zions and Ewan St. John Smith

07.26.2021 Commentaries & Reviews Nature Aging
An inflammatory aging clock (iAge) based on deep learning tracks multimorbidity, immunosenescence, frailty and cardiovascular aging

Nazish Sayed, Yingxiang Huang, Khiem Nguyen, Zuzana Krejciova-Rajaniemi, Anissa P. Grawe, Tianxiang Gao, Robert Tibshirani, Trevor Hastie, Ayelet Alpert, Lu Cui, Tatiana Kuznetsova, Yael Rosenberg-Hasson, Rita Ostan, Daniela Monti, Benoit Lehallier, Shai S. Shen-Orr, Holden T. Maecker, Cornelia L. Dekker, Tony Wyss-Coray, Claudio Franceschi, Vladimir Jojic, François Haddad, José G. Montoya, Joseph C. Wu, Mark M. Davis and David Furman

12.30.2020 Commentaries & Reviews Aging
ARDD 2020: from aging mechanisms to interventions

Garik V Mkrtchyan, Kotb Abdelmohsen, Pénélope Andreux, Ieva Bagdonaite, Nir Barzilai, Søren Brunak, Filipe Cabreiro, Rafael de Cabo, Judith Campisi, Ana Maria Cuervo, Marco Demaria, Collin Y Ewald, Evandro Fei Fang, Richard Faragher, Luigi Ferrucci, Adam Freund, Carlos G Silva-García, Anastasia Georgievskaya, Vadim N Gladyshev, David J Glass, Vera Gorbunova, Aubrey de Grey, Wei-Wu He, Jan Hoeijmakers, Eva Hoffmann, Steve Horvath, Riekelt H Houtkooper, Majken K Jensen, Martin Borch Jensen, Alice Kane, Moustapha Kassem, Peter de Keizer, Brian Kennedy, Gerard Karsenty, Dudley W Lamming, Kai-Fu Lee, Nanna MacAulay, Polina Mamoshina, Jim Mellon, Marte Molenaars, Alexey Moskalev, Andreas Mund, Laura Niedernhofer, Brenna Osborne, Heidi H Pak, Andrey Parkhitko, Nuno Raimundo, Thomas A Rando, Lene Juel Rasmussen, Carolina Reis, Christian G Riedel, Anais Franco-Romero, Björn Schumacher, David A Sinclair, Yousin Suh, Pam R Taub, Debra Toiber, Jonas T Treebak, Dario Riccardo Valenzano, Eric Verdin, Jan Vijg, Sergey Young, Lei Zhang, Daniela Bakula, Alex Zhavoronkov and Morten Scheibye-Knudsen

11.19.2020 Publications NPJ Aging and Mechanisms of Disease
NQO1 protects obese mice through improvements in glucose and lipid metabolism

Andrea Di Francesco, Youngshim Choi, Michel Bernier, Yingchun Zhang, Alberto Diaz-Ruiz, Miguel A. Aon, Krystle Kalafut, Margaux R. Ehrlich, Kelsey Murt, Ahmed Ali, Kevin J. Pearson, Sophie Levan, Joshua D. Preston, Alejandro Martin-Montalvo, Jennifer L. Martindale, Kotb Abdelmohsen, Cole R. Michel, Diana M. Willmes, Christine Henke, Placido Navas, Jose Manuel Villalba, David Siegel, Myriam Gorospe, Kristofer Fritz, Shyam Biswal, David Ross and Rafael de Cabo

11.18.2020 Publications Nature
A molecular cell atlas of the human lung from single-cell RNA sequencing

Kyle J. Travaglini, Ahmad N. Nabhan, Lolita Penland, Rahul Sinha, Astrid Gillich, Rene V. Sit, Stephen Chang, Stephanie D. Conley, Yasuo Mori, Jun Seita, Gerald J. Berry, Joseph B. Shrager, Ross J. Metzger, Christin S. Kuo, Norma Neff, Irving L. Weissman, Stephen R. Quake and Mark A. Krasnow

11.12.2020 Publications eLife
A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics

Etai Sapoznik, Bo-Jui Chang, Jaewon Huh, Robert J Ju, Evgenia V Azarova, Theresa Pohlkamp, Erik S Welf, David Broadbent, Alexandre F Carisey, Samantha J Stehbens, Kyung-Min Lee, Arnaldo Marín, Ariella B Hanker, Jens C Schmidt, Carlos L Arteaga, Bin Yang, Yoshihiko Kobayashi, Purushothama Rao Tata, Rory Kruithoff, Konstantin Doubrovinski, Douglas P Shepherd, Alfred Millett-Sikking, Andrew G York, Kevin M Dean and Reto P Fiolka

07.01.2020 Publications Nature
Physiological blood-brain transport is impaired with age by a shift in transcytosis

Andrew C. Yang, Marc Y. Stevens, Michelle B. Chen, Davis P. Lee, Daniel Stähli, David Gate, Kévin Contrepois, Winnie Chen, Tal Iram, Lichao Zhang, Ryan T. Vest, Aisling Chaney, Benoit Lehallier, Niclas Olsson, Haley du Bois, Ryan Hsieh, Haley C. Cropper, Daniela Berdnik, Lulin Li, Elizabeth Y. Wang, Gavin M. Traber, Carolyn R. Bertozzi, Jian Luo, Michael P. Snyder, Joshua E. Elias, Stephen R. Quake, Michelle L. James and Tony Wyss-Coray

06.23.2020 Publications Aging
The mitochondrial derived peptide humanin is a regulator of lifespan and healthspan

Kelvin Yen, Hemal H Mehta, Su-Jeong Kim, YanHe Lue, James Hoang, Noel Guerrero, Jenna Port, Qiuli Bi, Gerardo Navarrete, Sebastian Brandhorst, Kaitlyn Noel Lewis, Junxiang Wan, Ronald Swerdloff, Julie A Mattison, Rochelle Buffenstein, Carrie V Breton, Christina Wang, Valter Longo, Gil Atzmon, Douglas Wallace, Nir Barzilai and Pinchas Cohen

07.23.2019 Publications BMC
The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata

Daniele Armaleo, Olaf Müller, François Lutzoni, Ólafur S Andrésson, Guillaume Blanc, Helge B Bode, Frank R Collart, Francesco Dal Grande, Fred Dietrich, Igor V Grigoriev, Suzanne Joneson, Alan Kuo, Peter E Larsen, John M Logsdon Jr, David Lopez, Francis Martin, Susan P May, Tami R McDonald, Sabeeha S Merchant, Vivian Miao, Emmanuelle Morin, Ryoko Oono, Matteo Pellegrini, Nimrod Rubinstein, Maria Virginia Sanchez-Puerta, Elizabeth Savelkoul, Imke Schmitt, Jason C Slot, Darren Soanes, Péter Szövényi, Nicholas J Talbot, Claire Veneault-Fourrey and Basil B Xavier

03.07.2019 Publications Science
Evidence for hormonal control of heart regenerative capacity during endothermy acquisition

Kentaro Hirose, Alexander Y Payumo, Stephen Cutie, Alison Hoang, Hao Zhang, Romain Guyot, Dominic Lunn, Rachel B Bigley, Hongyao Yu, Jiajia Wang, Megan Smith, Ellen Gillett, Sandra E Muroy, Tobias Schmid, Emily Wilson, Kenneth A Field, DeeAnn M Reeder, Malcom Maden, Michael M Yartsev, Michael J Wolfgang, Frank Grützner, Thomas S Scanlan, Luke I Szweda, Rochelle Buffenstein, Guang Hu, Frederic Flamant, Jeffrey E Olgin and Guo N Huang