Adam Gayoso

Affiliations

Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Publications (13)

Characterization of cell fate probabilities in single-cell data with Palantir.

Nature biotechnology

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

Cell2location maps fine-grained cell types in spatial transcriptomics.

Nature biotechnology

Avec: Vitalii Kleshchevnikov , Artem Shmatko , Emma Dann , Alexander Aivazidis , Hamish W King , Tong Li , Rasa Elmentaite , Artem Lomakin , Veronika Kedlian , Adam Gayoso , Mika Sarkin Jain , Jun Sung Park , Lauma Ramona , Elizabeth Tuck , Anna Arutyunyan , Roser Vento-Tormo , Moritz Gerstung , Louisa James , Oliver Stegle , Omer Ali Bayraktar

PeakVI: A deep generative model for single-cell chromatin accessibility analysis.

Cell reports methods

Avec: Tal Ashuach , Daniel A Reidenbach , Adam Gayoso , Nir Yosef

Defining and benchmarking open problems in single-cell analysis.

Research square

Avec: Malte Luecken , Scott Gigante , Daniel Burkhardt , Robrecht Cannoodt , Daniel Strobl , Nikolay Markov , Luke Zappia , Giovanni Palla , Wesley Lewis , Daniel Dimitrov , Michael Vinyard , Daniel Magruder , Alma Andersson , Emma Dann , Qian Qin , Dominik Otto , Michal Klein , Olga Botvinnik , Louise Deconinck , Kai Waldrant , Bastian Rieck , Constantin Ahlmann-Eltze , Eduardo da Veiga Beltrame , Andrew Benz , Carmen Bravo González-Blas , Ann Chen , Benjamin DeMeo , Can Ergen , Swann Floc'hlay , Adam Gayoso , Stephanie Hicks , Yuge Ji , Vitalii Kleshchevnikov , Gioele La Manno , Maximilian Lombardo , Romain Lopez , Dario Righelli , Hirak Sarkar , Valentine Svensson , Alexander Tong , Galen Xing , Chenling Xu , Jonathan Bloom , Angela Pisco , Julio Saez-Rodriguez , Drausin Wulsin , Luca Pinello , Yvan Saeys , Fabian Theis , Smita Krishnaswamy

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells.

Nature methods

Avec: Adam Gayoso , Philipp Weiler , Mohammad Lotfollahi , Dominik Klein , Justin Hong , Aaron Streets , Fabian J Theis , Nir Yosef

Author Correction: Characterization of cell fate probabilities in single-cell data with Palantir.

Nature biotechnology

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

Enhancing scientific discoveries in molecular biology with deep generative models.

Molecular systems biology

Avec: Romain Lopez , Adam Gayoso , Nir Yosef

Echinogammarus lusitanicus (Amphipoda), a New Intermediate Host of Echinorhynchus truttae (Acanthocephala: Echinorhynchidae).

Acta parasitologica

Avec: Seila Couso-Pérez , Alberto Gayoso , Elvira Ares-Mazás , Hipólito Gómez-Couso

Interpretable factor models of single-cell RNA-seq via variational autoencoders.

Bioinformatics (Oxford, England)

Avec: Valentine Svensson , Adam Gayoso , Nir Yosef , Lior Pachter

Joint probabilistic modeling of single-cell multi-omic data with totalVI.

Nature methods

Avec: Adam Gayoso , Zoë Steier , Romain Lopez , Jeffrey Regier , Kristopher L Nazor , Aaron Streets , Nir Yosef

Mapping single-cell data to reference atlases by transfer learning.

Nature biotechnology

Avec: Mohammad Lotfollahi , Mohsen Naghipourfar , Malte D Luecken , Matin Khajavi , Maren Büttner , Marco Wagenstetter , Žiga Avsec , Adam Gayoso , Nir Yosef , Marta Interlandi , Sergei Rybakov , Alexander V Misharin , Fabian J Theis

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.

Science (New York, N.Y.)

Avec: Auteur inconnu , Robert C Jones , Jim Karkanias , Mark A Krasnow , Angela Oliveira Pisco , Stephen R Quake , Julia Salzman , Nir Yosef , Bryan Bulthaup , Phillip Brown , William Harper , Marisa Hemenez , Ravikumar Ponnusamy , Ahmad Salehi , Bhavani A Sanagavarapu , Eileen Spallino , Ksenia A Aaron , Waldo Concepcion , James M Gardner , Burnett Kelly , Nikole Neidlinger , Zifa Wang , Sheela Crasta , Saroja Kolluru , Maurizio Morri , Angela Oliveira Pisco , Serena Y Tan , Kyle J Travaglini , Chenling Xu , Marcela Alcántara-Hernández , Nicole Almanzar , Jane Antony , Benjamin Beyersdorf , Deviana Burhan , Kruti Calcuttawala , Matthew M Carter , Charles K F Chan , Charles A Chang , Stephen Chang , Alex Colville , Sheela Crasta , Rebecca N Culver , Ivana Cvijović , Gaetano D'Amato , Camille Ezran , Francisco X Galdos , Astrid Gillich , William R Goodyer , Yan Hang , Alyssa Hayashi , Sahar Houshdaran , Xianxi Huang , Juan C Irwin , SoRi Jang , Julia Vallve Juanico , Aaron M Kershner , Soochi Kim , Bernhard Kiss , Saroja Kolluru , William Kong , Maya E Kumar , Angera H Kuo , Rebecca Leylek , Baoxiang Li , Gabriel B Loeb , Wan-Jin Lu , Sruthi Mantri , Maxim Markovic , Patrick L McAlpine , Antoine de Morree , Maurizio Morri , Karim Mrouj , Shravani Mukherjee , Tyler Muser , Patrick Neuhöfer , Thi D Nguyen , Kimberly Perez , Ragini Phansalkar , Angela Oliveira Pisco , Nazan Puluca , Zhen Qi , Poorvi Rao , Hayley Raquer-McKay , Nicholas Schaum , Bronwyn Scott , Bobak Seddighzadeh , Joe Segal , Sushmita Sen , Shaheen Sikandar , Sean P Spencer , Lea C Steffes , Varun R Subramaniam , Aditi Swarup , Michael Swift , Kyle J Travaglini , Will Van Treuren , Emily Trimm , Stefan Veizades , Sivakamasundari Vijayakumar , Kim Chi Vo , Sevahn K Vorperian , Wanxin Wang , Hannah N W Weinstein , Juliane Winkler , Timothy T H Wu , Jamie Xie , Andrea R Yung , Yue Zhang , Angela M Detweiler , Honey Mekonen , Norma F Neff , Rene V Sit , Michelle Tan , Jia Yan , Gregory R Bean , Vivek Charu , Erna Forgó , Brock A Martin , Michael G Ozawa , Oscar Silva , Serena Y Tan , Angus Toland , Venkata N P Vemuri , Shaked Afik , Kyle Awayan , Olga Borisovna Botvinnik , Ashley Byrne , Michelle Chen , Roozbeh Dehghannasiri , Angela M Detweiler , Adam Gayoso , Alejandro A Granados , Qiqing Li , Gita Mahmoudabadi , Aaron McGeever , Antoine de Morree , Julia Eve Olivieri , Madeline Park , Angela Oliveira Pisco , Neha Ravikumar , Julia Salzman , Geoff Stanley , Michael Swift , Michelle Tan , Weilun Tan , Alexander J Tarashansky , Rohan Vanheusden , Sevahn K Vorperian , Peter Wang , Sheng Wang , Galen Xing , Chenling Xu , Nir Yosef , Marcela Alcántara-Hernández , Jane Antony , Charles K F Chan , Charles A Chang , Alex Colville , Sheela Crasta , Rebecca Culver , Les Dethlefsen , Camille Ezran , Astrid Gillich , Yan Hang , Po-Yi Ho , Juan C Irwin , SoRi Jang , Aaron M Kershner , William Kong , Maya E Kumar , Angera H Kuo , Rebecca Leylek , Shixuan Liu , Gabriel B Loeb , Wan-Jin Lu , Jonathan S Maltzman , Ross J Metzger , Antoine de Morree , Patrick Neuhöfer , Kimberly Perez , Ragini Phansalkar , Zhen Qi , Poorvi Rao , Hayley Raquer-McKay , Koki Sasagawa , Bronwyn Scott , Rahul Sinha , Hanbing Song , Sean P Spencer , Aditi Swarup , Michael Swift , Kyle J Travaglini , Emily Trimm , Stefan Veizades , Sivakamasundari Vijayakumar , Bruce Wang , Wanxin Wang , Juliane Winkler , Jamie Xie , Andrea R Yung , Steven E Artandi , Philip A Beachy , Michael F Clarke , Linda C Giudice , Franklin W Huang , Kerwyn Casey Huang , Juliana Idoyaga , Seung K Kim , Mark Krasnow , Christin S Kuo , Patricia Nguyen , Stephen R Quake , Thomas A Rando , Kristy Red-Horse , Jeremy Reiter , David A Relman , Justin L Sonnenburg , Bruce Wang , Albert Wu , Sean M Wu , Tony Wyss-Coray

An empirical Bayes method for differential expression analysis of single cells with deep generative models.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Pierre Boyeau , Jeffrey Regier , Adam Gayoso , Michael I Jordan , Romain Lopez , Nir Yosef

Réseau de co-auteurs

Nir Yosef 9 collaborations

Romain Lopez 4 collaborations

Angela Oliveira Pisco 4 collaborations

Chenling Xu 3 collaborations

Sheela Crasta 3 collaborations

Kyle J Travaglini 3 collaborations

Antoine de Morree 3 collaborations

Michael Swift 3 collaborations

Manu Setty 2 collaborations

Vaidotas Kiseliovas 2 collaborations

Jacob Levine 2 collaborations

Linas Mazutis 2 collaborations

Dana Pe'er 2 collaborations

Vitalii Kleshchevnikov 2 collaborations

Emma Dann 2 collaborations

Valentine Svensson 2 collaborations

Galen Xing 2 collaborations

Mohammad Lotfollahi 2 collaborations

Aaron Streets 2 collaborations

Fabian J Theis 2 collaborations

Jeffrey Regier 2 collaborations

Stephen R Quake 2 collaborations

Julia Salzman 2 collaborations

Saroja Kolluru 2 collaborations

Maurizio Morri 2 collaborations

Serena Y Tan 2 collaborations

Marcela Alcántara-Hernández 2 collaborations

Jane Antony 2 collaborations

Charles K F Chan 2 collaborations

Charles A Chang 2 collaborations

Alex Colville 2 collaborations

Camille Ezran 2 collaborations

Astrid Gillich 2 collaborations

Yan Hang 2 collaborations

Juan C Irwin 2 collaborations

SoRi Jang 2 collaborations

Aaron M Kershner 2 collaborations

William Kong 2 collaborations

Maya E Kumar 2 collaborations

Angera H Kuo 2 collaborations

Rebecca Leylek 2 collaborations

Gabriel B Loeb 2 collaborations

Wan-Jin Lu 2 collaborations

Patrick Neuhöfer 2 collaborations

Kimberly Perez 2 collaborations

Ragini Phansalkar 2 collaborations

Zhen Qi 2 collaborations

Poorvi Rao 2 collaborations

Hayley Raquer-McKay 2 collaborations

Bronwyn Scott 2 collaborations

Sean P Spencer 2 collaborations

Aditi Swarup 2 collaborations

Emily Trimm 2 collaborations

Stefan Veizades 2 collaborations

Sivakamasundari Vijayakumar 2 collaborations

Sevahn K Vorperian 2 collaborations

Wanxin Wang 2 collaborations

Juliane Winkler 2 collaborations

Jamie Xie 2 collaborations

Andrea R Yung 2 collaborations

Angela M Detweiler 2 collaborations

Michelle Tan 2 collaborations

Bruce Wang 2 collaborations

Artem Shmatko 1 collaboration

Alexander Aivazidis 1 collaboration

Hamish W King 1 collaboration

Tong Li 1 collaboration

Rasa Elmentaite 1 collaboration

Artem Lomakin 1 collaboration

Veronika Kedlian 1 collaboration

Mika Sarkin Jain 1 collaboration

Jun Sung Park 1 collaboration

Lauma Ramona 1 collaboration

Elizabeth Tuck 1 collaboration

Anna Arutyunyan 1 collaboration

Roser Vento-Tormo 1 collaboration

Moritz Gerstung 1 collaboration

Louisa James 1 collaboration

Oliver Stegle 1 collaboration

Omer Ali Bayraktar 1 collaboration

Tal Ashuach 1 collaboration

Daniel A Reidenbach 1 collaboration

Malte Luecken 1 collaboration

Scott Gigante 1 collaboration

Daniel Burkhardt 1 collaboration

Robrecht Cannoodt 1 collaboration

Daniel Strobl 1 collaboration

Nikolay Markov 1 collaboration

Luke Zappia 1 collaboration

Giovanni Palla 1 collaboration

Wesley Lewis 1 collaboration

Daniel Dimitrov 1 collaboration

Michael Vinyard 1 collaboration

Daniel Magruder 1 collaboration

Alma Andersson 1 collaboration

Qian Qin 1 collaboration

Dominik Otto 1 collaboration

Michal Klein 1 collaboration

Olga Botvinnik 1 collaboration

Louise Deconinck 1 collaboration

Kai Waldrant 1 collaboration

Bastian Rieck 1 collaboration

Constantin Ahlmann-Eltze 1 collaboration

Eduardo da Veiga Beltrame 1 collaboration

Andrew Benz 1 collaboration

Carmen Bravo González-Blas 1 collaboration

Ann Chen 1 collaboration

Benjamin DeMeo 1 collaboration

Can Ergen 1 collaboration

Swann Floc'hlay 1 collaboration

Stephanie Hicks 1 collaboration

Yuge Ji 1 collaboration

Gioele La Manno 1 collaboration

Maximilian Lombardo 1 collaboration

Dario Righelli 1 collaboration

Hirak Sarkar 1 collaboration

Alexander Tong 1 collaboration

Jonathan Bloom 1 collaboration

Angela Pisco 1 collaboration

Julio Saez-Rodriguez 1 collaboration

Drausin Wulsin 1 collaboration

Luca Pinello 1 collaboration

Yvan Saeys 1 collaboration

Fabian Theis 1 collaboration

Smita Krishnaswamy 1 collaboration

Philipp Weiler 1 collaboration

Dominik Klein 1 collaboration

Justin Hong 1 collaboration

Seila Couso-Pérez 1 collaboration

Alberto Gayoso 1 collaboration

Elvira Ares-Mazás 1 collaboration

Hipólito Gómez-Couso 1 collaboration

Lior Pachter 1 collaboration

Zoë Steier 1 collaboration

Kristopher L Nazor 1 collaboration

Mohsen Naghipourfar 1 collaboration

Malte D Luecken 1 collaboration

Matin Khajavi 1 collaboration

Maren Büttner 1 collaboration

Marco Wagenstetter 1 collaboration

Žiga Avsec 1 collaboration

Marta Interlandi 1 collaboration

Sergei Rybakov 1 collaboration

Alexander V Misharin 1 collaboration

None None 1 collaboration

Robert C Jones 1 collaboration

Jim Karkanias 1 collaboration

Mark A Krasnow 1 collaboration

Bryan Bulthaup 1 collaboration

Phillip Brown 1 collaboration

William Harper 1 collaboration

Marisa Hemenez 1 collaboration

Ravikumar Ponnusamy 1 collaboration

Ahmad Salehi 1 collaboration

Bhavani A Sanagavarapu 1 collaboration

Eileen Spallino 1 collaboration

Ksenia A Aaron 1 collaboration

Waldo Concepcion 1 collaboration

James M Gardner 1 collaboration

Burnett Kelly 1 collaboration

Nikole Neidlinger 1 collaboration

Zifa Wang 1 collaboration

Nicole Almanzar 1 collaboration

Benjamin Beyersdorf 1 collaboration

Deviana Burhan 1 collaboration

Kruti Calcuttawala 1 collaboration

Matthew M Carter 1 collaboration

Stephen Chang 1 collaboration

Rebecca N Culver 1 collaboration

Ivana Cvijović 1 collaboration

Gaetano D'Amato 1 collaboration

Francisco X Galdos 1 collaboration

William R Goodyer 1 collaboration

Alyssa Hayashi 1 collaboration

Sahar Houshdaran 1 collaboration

Xianxi Huang 1 collaboration

Julia Vallve Juanico 1 collaboration

Soochi Kim 1 collaboration

Bernhard Kiss 1 collaboration

Baoxiang Li 1 collaboration

Sruthi Mantri 1 collaboration

Maxim Markovic 1 collaboration

Patrick L McAlpine 1 collaboration

Karim Mrouj 1 collaboration

Shravani Mukherjee 1 collaboration

Tyler Muser 1 collaboration

Thi D Nguyen 1 collaboration

Nazan Puluca 1 collaboration

Nicholas Schaum 1 collaboration

Bobak Seddighzadeh 1 collaboration

Joe Segal 1 collaboration

Sushmita Sen 1 collaboration

Shaheen Sikandar 1 collaboration

Lea C Steffes 1 collaboration

Varun R Subramaniam 1 collaboration

Will Van Treuren 1 collaboration

Kim Chi Vo 1 collaboration

Hannah N W Weinstein 1 collaboration

Timothy T H Wu 1 collaboration

Yue Zhang 1 collaboration

Honey Mekonen 1 collaboration

Norma F Neff 1 collaboration

Rene V Sit 1 collaboration

Jia Yan 1 collaboration

Gregory R Bean 1 collaboration

Vivek Charu 1 collaboration

Erna Forgó 1 collaboration

Brock A Martin 1 collaboration

Michael G Ozawa 1 collaboration

Oscar Silva 1 collaboration

Angus Toland 1 collaboration

Venkata N P Vemuri 1 collaboration

Shaked Afik 1 collaboration

Kyle Awayan 1 collaboration

Olga Borisovna Botvinnik 1 collaboration

Ashley Byrne 1 collaboration

Michelle Chen 1 collaboration

Roozbeh Dehghannasiri 1 collaboration

Alejandro A Granados 1 collaboration

Qiqing Li 1 collaboration

Gita Mahmoudabadi 1 collaboration

Aaron McGeever 1 collaboration

Julia Eve Olivieri 1 collaboration

Madeline Park 1 collaboration

Neha Ravikumar 1 collaboration

Geoff Stanley 1 collaboration

Weilun Tan 1 collaboration

Alexander J Tarashansky 1 collaboration

Rohan Vanheusden 1 collaboration

Peter Wang 1 collaboration

Sheng Wang 1 collaboration

Rebecca Culver 1 collaboration

Les Dethlefsen 1 collaboration

Po-Yi Ho 1 collaboration

Shixuan Liu 1 collaboration

Jonathan S Maltzman 1 collaboration

Ross J Metzger 1 collaboration

Koki Sasagawa 1 collaboration

Rahul Sinha 1 collaboration

Hanbing Song 1 collaboration

Steven E Artandi 1 collaboration

Philip A Beachy 1 collaboration

Michael F Clarke 1 collaboration

Linda C Giudice 1 collaboration

Franklin W Huang 1 collaboration

Kerwyn Casey Huang 1 collaboration

Juliana Idoyaga 1 collaboration

Seung K Kim 1 collaboration

Mark Krasnow 1 collaboration

Christin S Kuo 1 collaboration

Patricia Nguyen 1 collaboration

Thomas A Rando 1 collaboration

Kristy Red-Horse 1 collaboration

Jeremy Reiter 1 collaboration

David A Relman 1 collaboration

Justin L Sonnenburg 1 collaboration

Albert Wu 1 collaboration

Sean M Wu 1 collaboration

Tony Wyss-Coray 1 collaboration

Pierre Boyeau 1 collaboration

Michael I Jordan 1 collaboration