Hashem Koohy

Affiliations

MRC Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK. hashem.koohy@rdm.ox.ac.uk.
Alan Turning Fellow in Health and Medicine, University of Oxford, Oxford, UK. hashem.koohy@rdm.ox.ac.uk.

ORCID: http://orcid.org/0000-0002-3640-7043

Publications (21)

Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?

Nature methods

Avec: Benjamin McMaster , Christopher Thorpe , Graham Ogg , Charlotte M Deane , Hashem Koohy

Group A

Science immunology

Avec: Yi-Ling Chen , Jessica Soo Weei Ng , Rosana Ottakandathil Babu , Jeongmin Woo , Janina Nahler , Clare S Hardman , Prathiba Kurupati , Lea Nussbaum , Fei Gao , Tao Dong , Kristin Ladell , David A Price , David A Duncan , David Johnson , Uzi Gileadi , Hashem Koohy , Graham S Ogg

A robust deep learning workflow to predict CD8 + T-cell epitopes.

Genome medicine

Avec: Chloe H Lee , Jaesung Huh , Paul R Buckley , Myeongjun Jang , Mariana Pereira Pinho , Ricardo A Fernandes , Agne Antanaviciute , Alison Simmons , Hashem Koohy

SARS-CoV-2 peptides bind to NKG2D and increase NK cell activity.

Cellular immunology

Avec: Hanna Kim , Jae-Eun Byun , Suk Ran Yoon , Hashem Koohy , Haiyoung Jung , Inpyo Choi

Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors.

Frontiers in immunology

Avec: Chloe H Lee , Mariolina Salio , Giorgio Napolitani , Graham Ogg , Alison Simmons , Hashem Koohy

Can we predict T cell specificity with digital biology and machine learning?

Nature reviews. Immunology

Avec: Dan Hudson , Ricardo A Fernandes , Mark Basham , Graham Ogg , Hashem Koohy

Spatiotemporal analysis of human intestinal development at single-cell resolution.

Cell

Avec: David Fawkner-Corbett , Agne Antanaviciute , Kaushal Parikh , Marta Jagielowicz , Ana Sousa Gerós , Tarun Gupta , Neil Ashley , Doran Khamis , Darren Fowler , Edward Morrissey , Chris Cunningham , Paul R V Johnson , Hashem Koohy , Alison Simmons

HLA-dependent variation in SARS-CoV-2 CD8

Immunology

Avec: Paul R Buckley , Chloe H Lee , Mariana Pereira Pinho , Rosana Ottakandathil Babu , Jeongmin Woo , Agne Antanaviciute , Alison Simmons , Graham Ogg , Hashem Koohy

Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens.

Briefings in bioinformatics

Avec: Paul R Buckley , Chloe H Lee , Ruichong Ma , Isaac Woodhouse , Jeongmin Woo , Vasily O Tsvetkov , Dmitrii S Shcherbinin , Agne Antanaviciute , Mikhail Shughay , Margarida Rei , Alison Simmons , Hashem Koohy

A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses.

Immunotherapy advances

Avec: Paul R Buckley , Chloe H Lee , Agne Antanaviciute , Alison Simmons , Hashem Koohy

Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation.

Cell reports

Avec: Nicholas T Crump , Andreas V Hadjinicolaou , Meng Xia , John Walsby-Tickle , Uzi Gileadi , Ji-Li Chen , Mashiko Setshedi , Lars R Olsen , I-Jun Lau , Laura Godfrey , Lynn Quek , Zhanru Yu , Erica Ballabio , Mike B Barnkob , Giorgio Napolitani , Mariolina Salio , Hashem Koohy , Benedikt M Kessler , Stephen Taylor , Paresh Vyas , James S O McCullagh , Thomas A Milne , Vincenzo Cerundolo

Dual RNA sequencing reveals dendritic cell reprogramming in response to typhoidal Salmonella invasion.

Communications biology

Avec: Anna Aulicino , Agne Antanaviciute , Joe Frost , Ana Sousa Geros , Esther Mellado , Moustafa Attar , Marta Jagielowicz , Philip Hublitz , Julia Sinz , Lorena Preciado-Llanes , Giorgio Napolitani , Rory Bowden , Hashem Koohy , Hal Drakesmith , Alison Simmons

HLA variants have different preferences to present proteins with specific molecular functions which are complemented in frequent haplotypes.

Frontiers in immunology

Avec: Vadim Karnaukhov , Wayne Paes , Isaac B Woodhouse , Thomas Partridge , Annalisa Nicastri , Simon Brackenridge , Dmitrii Shcherbinin , Dmitry M Chudakov , Ivan V Zvyagin , Nicola Ternette , Hashem Koohy , Persephone Borrow , Mikhail Shugay

A comparison of clustering models for inference of T cell receptor antigen specificity.

Immunoinformatics (Amsterdam, Netherlands)

Avec: Dan Hudson , Alex Lubbock , Mark Basham , Hashem Koohy

Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains.

Frontiers in immunology

Avec: Chloe H Lee , Mariana Pereira Pinho , Paul R Buckley , Isaac B Woodhouse , Graham Ogg , Alison Simmons , Giorgio Napolitani , Hashem Koohy

Discovery of a CD10-negative B-progenitor in human fetal life identifies unique ontogeny-related developmental programs.

Blood

Avec: Sorcha O'Byrne , Natalina Elliott , Siobhan Rice , Gemma Buck , Nicholas Fordham , Catherine Garnett , Laura Godfrey , Nicholas T Crump , Gary Wright , Sarah Inglott , Peng Hua , Bethan Psaila , Benjamin Povinelli , David J H F Knapp , Antonio Agraz-Doblas , Clara Bueno , Ignacio Varela , Phillip Bennett , Hashem Koohy , Suzanne M Watt , Anastasios Karadimitris , Adam J Mead , Phillip Ancliff , Paresh Vyas , Pablo Menendez , Thomas A Milne , Irene Roberts , Anindita Roy

Colonic epithelial cell diversity in health and inflammatory bowel disease.

Nature

Avec: Kaushal Parikh , Agne Antanaviciute , David Fawkner-Corbett , Marta Jagielowicz , Anna Aulicino , Christoffer Lagerholm , Simon Davis , James Kinchen , Hannah H Chen , Nasullah Khalid Alham , Neil Ashley , Errin Johnson , Philip Hublitz , Leyuan Bao , Joanna Lukomska , Rajinder Singh Andev , Elisabet Björklund , Benedikt M Kessler , Roman Fischer , Robert Goldin , Hashem Koohy , Alison Simmons

Single-cell atlas of colonic CD8

Nature medicine

Avec: Daniele Corridoni , Agne Antanaviciute , Tarun Gupta , David Fawkner-Corbett , Anna Aulicino , Marta Jagielowicz , Kaushal Parikh , Emmanouela Repapi , Steve Taylor , Dai Ishikawa , Ryo Hatano , Taketo Yamada , Wei Xin , Hubert Slawinski , Rory Bowden , Giorgio Napolitani , Oliver Brain , Chikao Morimoto , Hashem Koohy , Alison Simmons

HLA binding of self-peptides is biased towards proteins with specific molecular functions.

bioRxiv : the preprint server for biology

Avec: Vadim Karnaukhov , Wayne Paes , Isaac B Woodhouse , Thomas Partridge , Annalisa Nicastri , Simon Brackenridge , Dmitrii Scherbinin , Dmitry M Chudakov , Ivan V Zvyagin , Nicola Ternette , Hashem Koohy , Persephone Borrow , Mikhail Shugay

Decitabine increases neoantigen and cancer testis antigen expression to enhance T-cell-mediated toxicity against glioblastoma.

Neuro-oncology

Avec: Ruichong Ma , Margarida Rei , Isaac Woodhouse , Katherine Ferris , Sophie Kirschner , Anandhakumar Chandran , Uzi Gileadi , Ji-Li Chen , Mariana Pereira Pinho , Yoanna Ariosa-Morejon , Skirmantas Kriaucionis , Nicola Ternette , Hashem Koohy , Olaf Ansorge , Graham Ogg , Puneet Plaha , Vincenzo Cerundolo

Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitis.

Cancer cell

Avec: Tarun Gupta , Agne Antanaviciute , Chloe Hyun-Jung Lee , Rosana Ottakandathil Babu , Anna Aulicino , Zoe Christoforidou , Paulina Siejka-Zielinska , Caitlin O'Brien-Ball , Hannah Chen , David Fawkner-Corbett , Ana Sousa Geros , Esther Bridges , Colleen McGregor , Nicole Cianci , Eve Fryer , Nasullah Khalid Alham , Marta Jagielowicz , Ana Mafalda Santos , Martin Fellermeyer , Simon J Davis , Kaushal Parikh , Vincent Cheung , Lulia Al-Hillawi , Sarah Sasson , Stephanie Slevin , Oliver Brain , Auteur inconnu , Ricardo A Fernandes , Hashem Koohy , Alison Simmons

Réseau de co-auteurs

Alison Simmons 11 collaborations

Agne Antanaviciute 9 collaborations

Graham Ogg 6 collaborations

Chloe H Lee 6 collaborations

Paul R Buckley 5 collaborations

Giorgio Napolitani 5 collaborations

Marta Jagielowicz 5 collaborations

Mariana Pereira Pinho 4 collaborations

David Fawkner-Corbett 4 collaborations

Kaushal Parikh 4 collaborations

Anna Aulicino 4 collaborations

Rosana Ottakandathil Babu 3 collaborations

Jeongmin Woo 3 collaborations

Uzi Gileadi 3 collaborations

Ricardo A Fernandes 3 collaborations

Tarun Gupta 3 collaborations

Isaac B Woodhouse 3 collaborations

Nicola Ternette 3 collaborations

Mariolina Salio 2 collaborations

Dan Hudson 2 collaborations

Mark Basham 2 collaborations

Neil Ashley 2 collaborations

Ruichong Ma 2 collaborations

Isaac Woodhouse 2 collaborations

Margarida Rei 2 collaborations

Nicholas T Crump 2 collaborations

Ji-Li Chen 2 collaborations

Laura Godfrey 2 collaborations

Benedikt M Kessler 2 collaborations

Paresh Vyas 2 collaborations

Thomas A Milne 2 collaborations

Vincenzo Cerundolo 2 collaborations

Ana Sousa Geros 2 collaborations

Philip Hublitz 2 collaborations

Rory Bowden 2 collaborations

Vadim Karnaukhov 2 collaborations

Wayne Paes 2 collaborations

Thomas Partridge 2 collaborations

Annalisa Nicastri 2 collaborations

Simon Brackenridge 2 collaborations

Dmitry M Chudakov 2 collaborations

Ivan V Zvyagin 2 collaborations

Persephone Borrow 2 collaborations

Mikhail Shugay 2 collaborations

Nasullah Khalid Alham 2 collaborations

Oliver Brain 2 collaborations

Benjamin McMaster 1 collaboration

Christopher Thorpe 1 collaboration

Charlotte M Deane 1 collaboration

Yi-Ling Chen 1 collaboration

Jessica Soo Weei Ng 1 collaboration

Janina Nahler 1 collaboration

Clare S Hardman 1 collaboration

Prathiba Kurupati 1 collaboration

Lea Nussbaum 1 collaboration

Fei Gao 1 collaboration

Tao Dong 1 collaboration

Kristin Ladell 1 collaboration

David A Price 1 collaboration

David A Duncan 1 collaboration

David Johnson 1 collaboration

Graham S Ogg 1 collaboration

Jaesung Huh 1 collaboration

Myeongjun Jang 1 collaboration

Hanna Kim 1 collaboration

Jae-Eun Byun 1 collaboration

Suk Ran Yoon 1 collaboration

Haiyoung Jung 1 collaboration

Inpyo Choi 1 collaboration

Ana Sousa Gerós 1 collaboration

Doran Khamis 1 collaboration

Darren Fowler 1 collaboration

Edward Morrissey 1 collaboration

Chris Cunningham 1 collaboration

Paul R V Johnson 1 collaboration

Vasily O Tsvetkov 1 collaboration

Dmitrii S Shcherbinin 1 collaboration

Mikhail Shughay 1 collaboration

Andreas V Hadjinicolaou 1 collaboration

Meng Xia 1 collaboration

John Walsby-Tickle 1 collaboration

Mashiko Setshedi 1 collaboration

Lars R Olsen 1 collaboration

I-Jun Lau 1 collaboration

Lynn Quek 1 collaboration

Zhanru Yu 1 collaboration

Erica Ballabio 1 collaboration

Mike B Barnkob 1 collaboration

Stephen Taylor 1 collaboration

James S O McCullagh 1 collaboration

Joe Frost 1 collaboration

Esther Mellado 1 collaboration

Moustafa Attar 1 collaboration

Julia Sinz 1 collaboration

Lorena Preciado-Llanes 1 collaboration

Hal Drakesmith 1 collaboration

Dmitrii Shcherbinin 1 collaboration

Alex Lubbock 1 collaboration

Sorcha O'Byrne 1 collaboration

Natalina Elliott 1 collaboration

Siobhan Rice 1 collaboration

Gemma Buck 1 collaboration

Nicholas Fordham 1 collaboration

Catherine Garnett 1 collaboration

Gary Wright 1 collaboration

Sarah Inglott 1 collaboration

Peng Hua 1 collaboration

Bethan Psaila 1 collaboration

Benjamin Povinelli 1 collaboration

David J H F Knapp 1 collaboration

Antonio Agraz-Doblas 1 collaboration

Clara Bueno 1 collaboration

Ignacio Varela 1 collaboration

Phillip Bennett 1 collaboration

Suzanne M Watt 1 collaboration

Anastasios Karadimitris 1 collaboration

Adam J Mead 1 collaboration

Phillip Ancliff 1 collaboration

Pablo Menendez 1 collaboration

Irene Roberts 1 collaboration

Anindita Roy 1 collaboration

Christoffer Lagerholm 1 collaboration

Simon Davis 1 collaboration

James Kinchen 1 collaboration

Hannah H Chen 1 collaboration

Errin Johnson 1 collaboration

Leyuan Bao 1 collaboration

Joanna Lukomska 1 collaboration

Rajinder Singh Andev 1 collaboration

Elisabet Björklund 1 collaboration

Roman Fischer 1 collaboration

Robert Goldin 1 collaboration

Daniele Corridoni 1 collaboration

Emmanouela Repapi 1 collaboration

Steve Taylor 1 collaboration

Dai Ishikawa 1 collaboration

Ryo Hatano 1 collaboration

Taketo Yamada 1 collaboration

Wei Xin 1 collaboration

Hubert Slawinski 1 collaboration

Chikao Morimoto 1 collaboration

Dmitrii Scherbinin 1 collaboration

Katherine Ferris 1 collaboration

Sophie Kirschner 1 collaboration

Anandhakumar Chandran 1 collaboration

Yoanna Ariosa-Morejon 1 collaboration

Skirmantas Kriaucionis 1 collaboration

Olaf Ansorge 1 collaboration

Puneet Plaha 1 collaboration

Chloe Hyun-Jung Lee 1 collaboration

Zoe Christoforidou 1 collaboration

Paulina Siejka-Zielinska 1 collaboration

Caitlin O'Brien-Ball 1 collaboration

Hannah Chen 1 collaboration

Esther Bridges 1 collaboration

Colleen McGregor 1 collaboration

Nicole Cianci 1 collaboration

Eve Fryer 1 collaboration

Ana Mafalda Santos 1 collaboration

Martin Fellermeyer 1 collaboration

Simon J Davis 1 collaboration

Vincent Cheung 1 collaboration

Lulia Al-Hillawi 1 collaboration

Sarah Sasson 1 collaboration

Stephanie Slevin 1 collaboration

None None 1 collaboration