Nicholas Tatonetti

Affiliations

Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA.

Publications (17)

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions.

bioRxiv : the preprint server for biology

Avec: Daniel J Butler , Christopher Mozsary , Cem Meydan , David Danko , Jonathan Foox , Joel Rosiene , Alon Shaiber , Ebrahim Afshinnekoo , Matthew MacKay , Fritz J Sedlazeck , Nikolay A Ivanov , Maria Sierra , Diana Pohle , Michael Zietz , Undina Gisladottir , Vijendra Ramlall , Craig D Westover , Krista Ryon , Benjamin Young , Chandrima Bhattacharya , Phyllis Ruggiero , Bradley W Langhorst , Nathan Tanner , Justyna Gawrys , Dmitry Meleshko , Dong Xu , Peter A D Steel , Amos J Shemesh , Jenny Xiang , Jean Thierry-Mieg , Danielle Thierry-Mieg , Robert E Schwartz , Angelika Iftner , Daniela Bezdan , John Sipley , Lin Cong , Arryn Craney , Priya Velu , Ari M Melnick , Iman Hajirasouliha , Stacy M Horner , Thomas Iftner , Mirella Salvatore , Massimo Loda , Lars F Westblade , Melissa Cushing , Shawn Levy , Shixiu Wu , Nicholas Tatonetti , Marcin Imielinski , Hanna Rennert , Christopher E Mason

Low Rates of Screening for Celiac Disease Among Family Members.

Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association

Avec: Adam S Faye , Fernanda Polubriaginof , Peter H R Green , David K Vawdrey , Nicholas Tatonetti , Benjamin Lebwohl

ChatGPT and large language models in academia: opportunities and challenges.

BioData mining

Avec: Jesse G Meyer , Ryan J Urbanowicz , Patrick C N Martin , Karen O'Connor , Ruowang Li , Pei-Chen Peng , Tiffani J Bright , Nicholas Tatonetti , Kyoung Jae Won , Graciela Gonzalez-Hernandez , Jason H Moore

TCGA-Reports: A machine-readable pathology report resource for benchmarking text-based AI models.

Patterns (New York, N.Y.)

Avec: Jenna Kefeli , Nicholas Tatonetti

Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps.

bioRxiv : the preprint server for biology

Avec: Jiwoon Park , Jonathan Foox , Tyler Hether , David Danko , Sarah Warren , Youngmi Kim , Jason Reeves , Daniel J Butler , Christopher Mozsary , Joel Rosiene , Alon Shaiber , Ebrahim Afshinnekoo , Matthew MacKay , Yaron Bram , Vasuretha Chandar , Heather Geiger , Arryn Craney , Priya Velu , Ari M Melnick , Iman Hajirasouliha , Afshin Beheshti , Deanne Taylor , Amanda Saravia-Butler , Urminder Singh , Eve Syrkin Wurtele , Jonathan Schisler , Samantha Fennessey , André Corvelo , Michael C Zody , Soren Germer , Steven Salvatore , Shawn Levy , Shixiu Wu , Nicholas Tatonetti , Sagi Shapira , Mirella Salvatore , Massimo Loda , Lars F Westblade , Melissa Cushing , Hanna Rennert , Alison J Kriegel , Olivier Elemento , Marcin Imielinski , Alain C Borczuk , Cem Meydan , Robert E Schwartz , Christopher E Mason

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.

Nature communications

Avec: Daniel Butler , Christopher Mozsary , Cem Meydan , Jonathan Foox , Joel Rosiene , Alon Shaiber , David Danko , Ebrahim Afshinnekoo , Matthew MacKay , Fritz J Sedlazeck , Nikolay A Ivanov , Maria Sierra , Diana Pohle , Michael Zietz , Undina Gisladottir , Vijendra Ramlall , Evan T Sholle , Edward J Schenck , Craig D Westover , Ciaran Hassan , Krista Ryon , Benjamin Young , Chandrima Bhattacharya , Dianna L Ng , Andrea C Granados , Yale A Santos , Venice Servellita , Scot Federman , Phyllis Ruggiero , Arkarachai Fungtammasan , Chen-Shan Chin , Nathaniel M Pearson , Bradley W Langhorst , Nathan A Tanner , Youngmi Kim , Jason W Reeves , Tyler D Hether , Sarah E Warren , Michael Bailey , Justyna Gawrys , Dmitry Meleshko , Dong Xu , Mara Couto-Rodriguez , Dorottya Nagy-Szakal , Joseph Barrows , Heather Wells , Niamh B O'Hara , Jeffrey A Rosenfeld , Ying Chen , Peter A D Steel , Amos J Shemesh , Jenny Xiang , Jean Thierry-Mieg , Danielle Thierry-Mieg , Angelika Iftner , Daniela Bezdan , Elizabeth Sanchez , Thomas R Campion , John Sipley , Lin Cong , Arryn Craney , Priya Velu , Ari M Melnick , Sagi Shapira , Iman Hajirasouliha , Alain Borczuk , Thomas Iftner , Mirella Salvatore , Massimo Loda , Lars F Westblade , Melissa Cushing , Shixiu Wu , Shawn Levy , Charles Chiu , Robert E Schwartz , Nicholas Tatonetti , Hanna Rennert , Marcin Imielinski , Christopher E Mason

E-Pedigrees: a large-scale automatic family pedigree prediction application.

Bioinformatics (Oxford, England)

Avec: Xiayuan Huang , Nicholas Tatonetti , Katie LaRow , Brooke Delgoffee , John Mayer , David Page , Scott J Hebbring

Plasma Metabolomics Predicts Chemotherapy Response in Advanced Pancreatic Cancer.

Cancers

Avec: Hayato Muranaka , Andrew Hendifar , Arsen Osipov , Natalie Moshayedi , Veronica Placencio-Hickok , Nicholas Tatonetti , Aleksandr Stotland , Sarah Parker , Jennifer Van Eyk , Stephen J Pandol , Neil A Bhowmick , Jun Gong

Using machine learning probabilities to identify effects of COVID-19.

Patterns (New York, N.Y.)

Avec: Vijendra Ramlall , Undina Gisladottir , Jenna Kefeli , Yutaro Tanaka , Benjamin May , Nicholas Tatonetti

Generalizable and Automated Classification of TNM Stage from Pathology Reports with External Validation.

medRxiv : the preprint server for health sciences

Avec: Jenna Kefeli , Nicholas Tatonetti

Benchmark Pathology Report Text Corpus with Cancer Type Classification.

medRxiv : the preprint server for health sciences

Avec: Jenna Kefeli , Nicholas Tatonetti

Prevalence of progressive multifocal leukoencephalopathy (PML) in adults and children with systemic lupus erythematosus.

Lupus science & medicine

Avec: Teja Kapoor , Pooja Mahadeshwar , Joyce Hui-Yuen , Kayla Quinnies , Nicholas Tatonetti , Yevgeniya Gartshteyn , Cathy Guo , Laura Geraldino-Pardilla , Anca D Askanase

KG-LIME: predicting individualized risk of adverse drug events for multiple sclerosis disease-modifying therapy.

Journal of the American Medical Informatics Association : JAMIA

Avec: Jason Patterson , Nicholas Tatonetti

Session Introduction: TOWARDS ETHICAL BIOMEDICAL INFORMATICS: LEARNING FROM OLELO NOEAU, HAWAIIAN PROVERBS.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Avec: Peter Y Washington , Noelani Puniwai , Martina Kamaka , Gamze Gürsoy , Nicholas Tatonetti , Steven E Brenner , Dennis P Wall

Using Time Series Clustering to Segment and Infer Emergency Department Nursing Shifts from Electronic Health Record Log Files.

AMIA ... Annual Symposium proceedings. AMIA Symposium

Avec: Amanda J Moy , Kenrick D Cato , Jennifer Withall , Eugene Y Kim , Nicholas Tatonetti , Sarah C Rossetti

Natural Language Processing Can Automate Extraction of Barrett's Esophagus Endoscopy Quality Metrics.

medRxiv : the preprint server for health sciences

Avec: Ali Soroush , Courtney J Diamond , Haley M Zylberberg , Benjamin May , Nicholas Tatonetti , Julian A Abrams , Chunhua Weng

Assessing racial differences in time to subsequent treatment following androgen deprivation therapy among Veterans with prostate cancer.

Research square

Avec: Nadine Friedrich , Nadine Friedrich , Jessica Janes , Joshua Parrish , Amanda De Hoedt , Janis Pruett , Mark Fallick , Raj Gandhi , Agnes Hong , Nicholas Tatonetti , Stephen Freedland

Réseau de co-auteurs

Jenna Kefeli 4 collaborations

Christopher Mozsary 3 collaborations

Cem Meydan 3 collaborations

David Danko 3 collaborations

Jonathan Foox 3 collaborations

Joel Rosiene 3 collaborations

Alon Shaiber 3 collaborations

Ebrahim Afshinnekoo 3 collaborations

Matthew MacKay 3 collaborations

Undina Gisladottir 3 collaborations

Vijendra Ramlall 3 collaborations

Robert E Schwartz 3 collaborations

Arryn Craney 3 collaborations

Priya Velu 3 collaborations

Ari M Melnick 3 collaborations

Iman Hajirasouliha 3 collaborations

Mirella Salvatore 3 collaborations

Massimo Loda 3 collaborations

Lars F Westblade 3 collaborations

Melissa Cushing 3 collaborations

Shawn Levy 3 collaborations

Shixiu Wu 3 collaborations

Marcin Imielinski 3 collaborations

Hanna Rennert 3 collaborations

Christopher E Mason 3 collaborations

Daniel J Butler 2 collaborations

Fritz J Sedlazeck 2 collaborations

Nikolay A Ivanov 2 collaborations

Maria Sierra 2 collaborations

Diana Pohle 2 collaborations

Michael Zietz 2 collaborations

Craig D Westover 2 collaborations

Krista Ryon 2 collaborations

Benjamin Young 2 collaborations

Chandrima Bhattacharya 2 collaborations

Phyllis Ruggiero 2 collaborations

Bradley W Langhorst 2 collaborations

Justyna Gawrys 2 collaborations

Dmitry Meleshko 2 collaborations

Dong Xu 2 collaborations

Peter A D Steel 2 collaborations

Amos J Shemesh 2 collaborations

Jenny Xiang 2 collaborations

Jean Thierry-Mieg 2 collaborations

Danielle Thierry-Mieg 2 collaborations

Angelika Iftner 2 collaborations

Daniela Bezdan 2 collaborations

John Sipley 2 collaborations

Lin Cong 2 collaborations

Thomas Iftner 2 collaborations

Youngmi Kim 2 collaborations

Sagi Shapira 2 collaborations

Benjamin May 2 collaborations

Nadine Friedrich 2 collaborations

Nathan Tanner 1 collaboration

Stacy M Horner 1 collaboration

Adam S Faye 1 collaboration

Fernanda Polubriaginof 1 collaboration

Peter H R Green 1 collaboration

David K Vawdrey 1 collaboration

Benjamin Lebwohl 1 collaboration

Jesse G Meyer 1 collaboration

Ryan J Urbanowicz 1 collaboration

Patrick C N Martin 1 collaboration

Karen O'Connor 1 collaboration

Ruowang Li 1 collaboration

Pei-Chen Peng 1 collaboration

Tiffani J Bright 1 collaboration

Kyoung Jae Won 1 collaboration

Graciela Gonzalez-Hernandez 1 collaboration

Jason H Moore 1 collaboration

Jiwoon Park 1 collaboration

Tyler Hether 1 collaboration

Sarah Warren 1 collaboration

Jason Reeves 1 collaboration

Yaron Bram 1 collaboration

Vasuretha Chandar 1 collaboration

Heather Geiger 1 collaboration

Afshin Beheshti 1 collaboration

Deanne Taylor 1 collaboration

Amanda Saravia-Butler 1 collaboration

Urminder Singh 1 collaboration

Eve Syrkin Wurtele 1 collaboration

Jonathan Schisler 1 collaboration

Samantha Fennessey 1 collaboration

André Corvelo 1 collaboration

Michael C Zody 1 collaboration

Soren Germer 1 collaboration

Steven Salvatore 1 collaboration

Alison J Kriegel 1 collaboration

Olivier Elemento 1 collaboration

Alain C Borczuk 1 collaboration

Daniel Butler 1 collaboration

Evan T Sholle 1 collaboration

Edward J Schenck 1 collaboration

Ciaran Hassan 1 collaboration

Dianna L Ng 1 collaboration

Andrea C Granados 1 collaboration

Yale A Santos 1 collaboration

Venice Servellita 1 collaboration

Scot Federman 1 collaboration

Arkarachai Fungtammasan 1 collaboration

Chen-Shan Chin 1 collaboration

Nathaniel M Pearson 1 collaboration

Nathan A Tanner 1 collaboration

Jason W Reeves 1 collaboration

Tyler D Hether 1 collaboration

Sarah E Warren 1 collaboration

Michael Bailey 1 collaboration

Mara Couto-Rodriguez 1 collaboration

Dorottya Nagy-Szakal 1 collaboration

Joseph Barrows 1 collaboration

Heather Wells 1 collaboration

Niamh B O'Hara 1 collaboration

Jeffrey A Rosenfeld 1 collaboration

Ying Chen 1 collaboration

Elizabeth Sanchez 1 collaboration

Thomas R Campion 1 collaboration

Alain Borczuk 1 collaboration

Charles Chiu 1 collaboration

Xiayuan Huang 1 collaboration

Katie LaRow 1 collaboration

Brooke Delgoffee 1 collaboration

John Mayer 1 collaboration

David Page 1 collaboration

Scott J Hebbring 1 collaboration

Hayato Muranaka 1 collaboration

Andrew Hendifar 1 collaboration

Arsen Osipov 1 collaboration

Natalie Moshayedi 1 collaboration

Veronica Placencio-Hickok 1 collaboration

Aleksandr Stotland 1 collaboration

Sarah Parker 1 collaboration

Jennifer Van Eyk 1 collaboration

Stephen J Pandol 1 collaboration

Neil A Bhowmick 1 collaboration

Jun Gong 1 collaboration

Yutaro Tanaka 1 collaboration

Teja Kapoor 1 collaboration

Pooja Mahadeshwar 1 collaboration

Joyce Hui-Yuen 1 collaboration

Kayla Quinnies 1 collaboration

Yevgeniya Gartshteyn 1 collaboration

Cathy Guo 1 collaboration

Laura Geraldino-Pardilla 1 collaboration

Anca D Askanase 1 collaboration

Jason Patterson 1 collaboration

Peter Y Washington 1 collaboration

Noelani Puniwai 1 collaboration

Martina Kamaka 1 collaboration

Gamze Gürsoy 1 collaboration

Steven E Brenner 1 collaboration

Dennis P Wall 1 collaboration

Amanda J Moy 1 collaboration

Kenrick D Cato 1 collaboration

Jennifer Withall 1 collaboration

Eugene Y Kim 1 collaboration

Sarah C Rossetti 1 collaboration

Ali Soroush 1 collaboration

Courtney J Diamond 1 collaboration

Haley M Zylberberg 1 collaboration

Julian A Abrams 1 collaboration

Chunhua Weng 1 collaboration

Jessica Janes 1 collaboration

Joshua Parrish 1 collaboration

Amanda De Hoedt 1 collaboration

Janis Pruett 1 collaboration

Mark Fallick 1 collaboration

Raj Gandhi 1 collaboration

Agnes Hong 1 collaboration

Stephen Freedland 1 collaboration