Human Cell Atlas

Publications

Below are the list of papers that are part of the Human Cell Atlas.

HCA Publication Committee is comprised of HCA Organizing Committee members. The committee convenes quarterly and reviews submitted publications to check if the described study section in the publication fits within HCA technical scope. The review by the HCA Publication Committee does not serve as peer review.

  • CloseRead

    Review process

    Any member of the HCA community can submit their publication for review through this google form. The committee will only review papers submitted with a complete draft or a link to a preprint.

    Three committee members will be assigned to each paper and each will vote if the publication should become part of the HCA. If there is no consensus among 3 assigned committee members, the paper will be brought to the entire committee for additional review, to be decided by majority vote.

    To submit your paper for review please complete this form.

    The following statement should be included in the acknowledgement section of the paper:

    This publication is part of the Human Cell Atlas - www.humancellatlas.org/publications/

    Once the paper has been added to bioRXiv, advise publications@humancellatlas.org the bioRXiv DOI to ensure the paper is listed under the bioRXiv HCA channel.

    HCA Membership

    Any individual may become an HCA Member by registering and agreeing to abide by the ethical standards and principles of the HCA, described in the HCA white paper. An HCA member who additionally participates in an HCA project or serves as a member of an HCA group (as defined by the HCA Organizing Committee) will be designated as an HCA Collaborating Member.

    Further details are available on the Join HCA page.

  • CloseRead

    List of Publications

    2017

    • The Human Cell Atlas.

      Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N and Human Cell Atlas Meeting Participants

      eLife 2017;6

    • The Human Cell Atlas: from vision to reality.

      Rozenblatt-Rosen O, Stubbington MJT, Regev A and Teichmann SA

      Nature 2017;550;7677;451-453

    • The Human Cell Atlas White Paper

      Regev, Aviv, Teichmann, Sarah, Rozenblatt-Rosen, Orit, Stubbington, Michael, Ardlie, Kristin, Amit, Ido, Arlotta, Paola, Bader, Gary, Benoist, Christophe, Biton, Moshe, Bodenmiller, Bernd, Bruneau, Benoit, Campbell, Peter, Carmichael, Mary, Carninci, Piero, Castelo-Soccio, Leslie, Clatworthy, Menna, Clevers, Hans, Conrad, Christian, Eils, Roland, Freeman, Jeremy, Fugger, Lars, Goettgens, Berthold, Graham, Daniel, Greka, Anna, Hacohen, Nir, Haniffa, Muzlifah, Helbig, Ingo, Heuckeroth, Robert, Kathiresan, Sekar, Kim, Seung, Klein, Allon, Knoppers, Bartha, Kriegstein, Arnold, Lander, Eric, Lee, Jane, Lein, Ed, Linnarsson, Sten, Macosko, Evan, MacParland, Sonya, Majovski, Robert, Majumder, Partha, Marioni, John, McGilvray, Ian, Merad, Miriam, Mhlanga, Musa, Naik, Shalin, Nawijn, Martijn, Nolan, Garry, Paten, Benedict, Pe'er, Dana, Philippakis, Anthony, Ponting, Chris, Quake, Steve, Rajagopal, Jayaraj, Rajewsky, Nikolaus, Reik, Wolf, Rood, Jennifer, Saeb-Parsy, Kourosh, Schiller, Herbert, Scott, Steve, Shalek, Alex, Shapiro, Ehud, Shin, Jay, Skeldon, Kenneth, Stratton, Michael, Streicher, Jenna, Stunnenberg, Henk, Tan, Kai, Taylor, Deanne, Thorogood, Adrian, Vallier, Ludovic, van Oudenaarden, Alexander, Watt, Fiona, Weicher, Wilko, Weissman, Jonathan, Wells, Andrew, Wold, Barbara, Xavier, Ramnik, Zhuang, Xiaowei, Human Cell Atlas Organizing Committee.

      arXiv.org 2017.

    2018

    • Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations.

      MacParland SA, Liu JC, Ma XZ, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD and McGilvray ID

      Nature communications 2018;9;1;4383

    • Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma.

      Ledergor G, Weiner A, Zada M, Wang SY, Cohen YC, Gatt ME, Snir N, Magen H, Koren-Michowitz M, Herzog-Tzarfati K, Keren-Shaul H, Bornstein C, Rotkopf R, Yofe I, David E, Yellapantula V, Kay S, Salai M, Ben Yehuda D, Nagler A, Shvidel L, Orr-Urtreger A, Halpern KB, Itzkovitz S, Landgren O, San-Miguel J, Paiva B, Keats JJ, Papaemmanuil E, Avivi I, Barbash GI, Tanay A and Amit I

      Nature medicine 2018;24;12;1867-1876

    • Conserved cell types with divergent features between human and mouse cortex

      Rebecca D Hodge, Trygve E Bakken, Jeremy A Miller, Kimberly A Smith, Eliza R Barkan, Lucas T Graybuck, Jennie L Close, Brian Long, Osnat Penn, Zizhen Yao, Jeroen Eggermont, Thomas Hollt, Boaz P Levi, Soraya I Shehata, Brian Aevermann, Allison Beller, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Charles Cobbs, Rachel Dalley, Nick Dee, Song-Lin Ding, Richard G Ellenbogen, Olivia Fong, Emma Garren, Jeff Goldy, Ryder P Gwinn, Daniel Hirschstein, C Dirk Keene, Mohamed Keshk, Andrew L Ko, Kanan Lathia, Ahmed Mahfouz, Zoe Maltzer, Medea McGraw, Thuc Nghi Nguyen, Julie Nyhus, Jeffrey G Ojemann, Aaron Oldre, Sheana Parry, Shannon Reynolds, Christine Rimorin, Nadiya V Shapovalova, Saroja Somasundaram, Aaron Szafer, Elliot R Thomsen, Michael Tieu, Richard H Scheuermann, Rafael Yuste, Susan M Sunkin, Boudewijn Lelieveldt, David Feng, Lydia Ng, Amy Bernard, Michael Hawrylycz, John W. Phillips, Bosiljka Tasic, Hongkui Zeng, Allan R Jones, Christof Koch, Ed S Lein

      bioRxiv 2018

    • Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics

      Roser Vento-Tormo, Mirjana Efremova, Rachel A. Botting, Margherita Y. Turco, Miquel Vento-Tormo, Kerstin B. Meyer, Jongeun Park, Emily Stephenson, Krzysztof Polański, Rebecca P. Payne, Angela Goncalves, Angela Zou, Johan Henriksson, Laura Wood, Steve Lisgo, Andrew Filby, Gavin J. Wright, Michael J. T. Stubbington, Muzlifah Haniffa, Ashley Moffett, Sarah A. Teichmann

      bioRxiv 2018

    • Palantir characterizes cell fate continuities in human hematopoiesis

      Manu Setty, Vaidotas Kiseliovas, Jacob Levine, Adam Gayoso, Linas Mazutis, Dana Pe'er

      bioRxiv 2018

    • Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis.

      Reyfman PA, Walter JM, Joshi N, Anekalla KR, McQuattie-Pimentel AC, Chiu S, Fernandez R, Akbarpour M, Chen CI, Ren Z, Verma R, Abdala-Valencia H, Nam K, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Watanabe S, Williams KJN, Flozak AS, Nicholson TT, Morgan VK, Winter DR, Hinchcliff M, Hrusch CL, Guzy RD, Bonham CA, Sperling AI, Bag R, Hamanaka RB, Mutlu GM, Yeldandi AV, Marshall SA, Shilatifard A, Amaral LAN, Perlman H, Sznajder JI, Argento AC, Gillespie CT, Dematte J, Jain M, Singer BD, Ridge KM, Lam AP, Bharat A, Bhorade SM, Gottardi CJ, Budinger GRS and Misharin AV

      American journal of respiratory and critical care medicine 2018

    • Molecular Architecture of the Mouse Nervous System.

      Zeisel A, Hochgerner H, Lönnerberg P, Johnsson A, Memic F, van der Zwan J, Häring M, Braun E, Borm LE, La Manno G, Codeluppi S, Furlan A, Lee K, Skene N, Harris KD, Hjerling-Leffler J, Arenas E, Ernfors P, Marklund U and Linnarsson S

      Cell 2018;174;4;999-1014.e22

    • Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis

      Christopher S. Smillie, Moshe Biton, José Ordovas-Montañes, Keri M. Sullivan, Grace Burgin, Daniel B. Graham, Rebecca H. Herbst, Noga Rogel, Michal Slyper, Julia Waldman, Malika Sud, Elizabeth Andrews, Adam L. Haber, Sanja Vickovic, Danielle Dionne, Lan T. Nguyen, Alexandra-Chloé Villani, Matan Hofree, Elizabeth A. Creasey, Hailiang Huang, Orit Rozenblatt Rosen, John J. Garber, Hamed Khalili, A. Nicole Desch, Mark J. Daly, Ashwin N. Ananthakrishnan, Alex K. Shalek, Ramnik J. Xavier, Aviv Regev

      bioRxiv 2018

    • Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

      Jellert T. Gaublomme, Bo Li, Cristin McCabe, Abigail Knecht, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Julia Waldman, Danielle Dionne, Lan Nguyen, Phil De Jager, Bertrand Yeung, Xinfang Zhao, Naomi Habib, Orit Rozenblatt-Rosen, Aviv Regev

      bioRxiv 2018

    2019

    • Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

      Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J. MacCarthy, Adrian Alvarez, Eduard Batlle, Sagar, Dominic Grün, Julia K. Lau, Stéphane C. Boutet, Chad Sanada, Aik Ooi, Robert C. Jones, Kelly Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Itoshi Nikaido, Cornelius Fischer, Sascha Sauer, Timo Trefzer, Christian Conrad, Xian Adiconis, Lan T. Nguyen, Aviv Regev, Joshua Z. Levin, Swati Parekh, Aleksandar Janjic, Lucas E. Wange, Johannes W. Bagnoli, Wolfgang Enard, Marta Gut, Rickard Sandberg, Ivo Gut, Oliver Stegle, Holger Heyn

      bioRxiv 2019

    • Systematic comparative analysis of single cell RNA-sequencing methods

      Jiarui Ding, Xian Adiconis, Sean K. Simmons, Monika S. Kowalczyk, Cynthia C. Hession, Nemanja D. Marjanovic, Travis K. Hughes, Marc H. Wadsworth, Tyler Burks, Lan T. Nguyen, John Y. H. Kwon, Boaz Barak, William Ge, Amanda J. Kedaigle, Shaina Carroll, Shuqiang Li, Nir Hacohen, Orit Rozenblatt-Rosen, Alex K. Shalek, Alexandra-Chloé Villani, Aviv Regev, Joshua Z. Levin

      bioRxiv 2019

    • A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease

      Felipe A Vieira Braga, Gozde Kar, Marijn Berg, Orestes A Carpaij, Krzysztof Polanski, Lukas M Simon, Sharon Brouwer, Tomas Gomes, Laura Hesse, Jian Jiang, Eirini S Fasouli, Mirjana Efremova, Roser Vento-Tormo, Karen Affleck, Subarna Palit, Paulina Strzelecka, Helen V Firth, Krishnaa TA Mahbubani, Ana Cvejic, Kerstin B Meyer, Kourosh Saeb-Parsy, Marjan Luinge, Corry-Anke Brandsma, Wim Timens, Ilias Angelidis, Maximilian Strunz, Gerard H Koppelman, Antoon J van Oosterhout, Herbert B Schiller, Fabian J Theis, Maarten van den Berge, Martijn C Nawijn, Sarah A Teichmann

      bioRxiv 2019

    • A Human Liver Cell Atlas: Revealing Cell Type Heterogeneity and Adult Liver Progenitors by Single-Cell RNA-sequencing

      Nadim Aizarani, Antonio Saviano, Sagar, Laurent Mailly, Sarah Durand, Patrick Pessaux, Thomas F Baumert, Dominic Grün

      bioRxiv 2019

  • CloseRead

    Contact us

    General publication enquiries should be directed to publications@humancellatlas.org.