Ferhat Ay

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 53

Top Venues

bioRxiv : the preprint server for biology

Nature communications

Genome biology

Science immunology

La Jolla Institute

This page only lists publications with an associated author ORCID identifier.

Affiliation History

La Jolla Institute Jan 04 2016

United States

Assistant Professor

Publications

Todd Lenz, Xu Zhang, Abhijit Chakraborty, Abbas Roayaei Ardakany, Jacques Prudhomme, Ferhat Ay, Kirk Deitsch, Karine G Le Roch
Chromatin structure and var2csa - a tango in regulation of var gene expression in the human malaria parasite, Plasmodium falciparum ? bioRxiv : the preprint server for biology (2024)
Max Mattessich, Joaquin Reyna, Edel Aron, Ferhat Ay, Misha Kilmer, Steven H Kleinstein, Anna Konstorum
nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Non-linear Iterative Partial Least Squares. bioRxiv : the preprint server for biology (2024)
Edahí González-Avalos, Atsushi Onodera, Daniela Samaniego-Castruita, Anjana Rao, Ferhat Ay
Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome biology 25 (1) (2024)
Joaquin Reyna, Kyra Fetter, Romeo Ignacio, Cemil Can Ali Marandi, Nikhil Rao, Zichen Jiang, Daniela Salgado Figueroa, Sourya Bhattacharyya, Ferhat Ay
Loop Catalog: a comprehensive HiChIP database of human and mouse samples. bioRxiv : the preprint server for biology (2024)
Pramod Shinde, Lisa Willemsen, Michael Anderson, Minori Aoki, Saonli Basu, Julie G Burel, Peng Cheng, Souradipto Ghosh Dastidar, Aidan Dunleavy, Tal Einav, Jamie Forschmiedt, Slim Fourati, Javier Garcia, William Gibson, Jason A Greenbaum, Leying Guan, Weikang Guan, Jeremy P Gygi, Brendan Ha, Joe Hou, Jason Hsiao, Yunda Huang, Rick Jansen, Bhargob Kakoty, Zhiyu Kang, James J Kobie, Mari Kojima, Anna Konstorum, Jiyeun Lee, Sloan A Lewis, Aixin Li, Eric F Lock, Jarjapu Mahita, Marcus Mendes, Hailong Meng, Aidan Neher, Somayeh Nili, Lars Rønn Olsen, Shelby Orfield, James A Overton, Nidhi Pai, Cokie Parker, Brian Qian, Mikkel Rasmussen, Joaquin Reyna, Eve Richardson, Sandra Safo, Josey Sorenson, Aparna Srinivasan, Nicky Thrupp, Rashmi Tippalagama, Raphael Trevizani, Steffen Ventz, Jiuzhou Wang, Cheng-Chang Wu, Ferhat Ay, Barry Grant, Steven H Kleinstein, Bjoern Peters
Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes. bioRxiv : the preprint server for biology (2024)
Joaquin Reyna, Kyra Fetter, Romeo Ignacio, Cemil Can Ali Marandi, Nikhil Rao, Zichen Jiang, Daniela Salgado Figueroa, Sourya Bhattacharyya, Ferhat Ay
Loop Catalog: a comprehensive HiChIP database of human and mouse samples. bioRxiv : the preprint server for biology (2024)
Sourya Bhattacharyya, Ferhat Ay
Identifying genetic variants associated with chromatin looping and genome function. Nature communications 15 (1) (2024)
Edahí González-Avalos, Atsushi Onodera, Daniela Samaniego-Castruita, Anjana Rao, Ferhat Ay
Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome biology 25 (1) (2024)
Todd Lenz, Xu Zhang, Abhijit Chakraborty, Abbas Roayaei Ardakany, Jacques Prudhomme, Ferhat Ay, Kirk Deitsch, Karine G Le Roch
Chromatin structure and var2csa - a tango in regulation of var gene expression in the human malaria parasite, Plasmodium falciparum ? bioRxiv : the preprint server for biology (2024)
Max Mattessich, Joaquin Reyna, Edel Aron, Ferhat Ay, Misha Kilmer, Steven H Kleinstein, Anna Konstorum
nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Non-linear Iterative Partial Least Squares. bioRxiv : the preprint server for biology (2024)
Edahí González-Avalos, Atsushi Onodera, Daniela Samaniego-Castruita, Anjana Rao, Ferhat Ay
Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome biology 25 (1) (2024)
Todd Lenz, Xu Zhang, Abhijit Chakraborty, Abbas Roayaei Ardakany, Jacques Prudhomme, Ferhat Ay, Kirk Deitsch, Karine G Le Roch
Chromatin structure and var2csa - a tango in regulation of var gene expression in the human malaria parasite, Plasmodium falciparum ? bioRxiv : the preprint server for biology (2024)
Edahí González-Avalos, Atsushi Onodera, Daniela Samaniego-Castruita, Anjana Rao, Ferhat Ay
Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome biology 25 (1) (2024)
Edahí González-Avalos, Atsushi Onodera, Daniela Samaniego-Castruita, Anjana Rao, Ferhat Ay
Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome biology 25 (1) (2024)
Konstantin Okonechnikov, Aylin Camgöz, Owen Chapman, Sameena Wani, Donglim Esther Park, Jens-Martin Hübner, Abhijit Chakraborty, Meghana Pagadala, Rosalind Bump, Sahaana Chandran, Katerina Kraft, Rocio Acuna-Hidalgo, Derek Reid, Kristin L Sikkink, Monika Mauermann, Edwin F Juarez, Anne Jenseit, James T Robinson, Kristian W Pajtler, Till Milde, Natalie Jäger, Petra Fiesel, Ling Morgan, Sunita Sridhar, Nicole G Coufal, Michael L Levy, Denise Malicki, Charlotte Hobbs, Stephen F Kingsmore, Shareef Nahas, Matija Snuderl, John Crawford, Robert J Wechsler-Reya, Tom Belle Davidson, Jennifer A Cotter, George Michaiel, Gudrun Fleischhack, Stefan Mundlos, Anthony Schmitt, Hannah Carter, Kulandaimanuvel Antony Michealraj, Sachin A Kumar, Michael D Taylor, Jeremy Rich, Frank Buchholz, Jill P Mesirov, Stefan M Pfister, Ferhat Ay, Jesse R Dixon, Marcel Kool, Lukas Chavez
3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nature communications 14 (1) (2023)
Konstantin Okonechnikov, Aylin Camgöz, Owen Chapman, Sameena Wani, Donglim Esther Park, Jens-Martin Hübner, Abhijit Chakraborty, Meghana Pagadala, Rosalind Bump, Sahaana Chandran, Katerina Kraft, Rocio Acuna-Hidalgo, Derek Reid, Kristin L Sikkink, Monika Mauermann, Edwin F Juarez, Anne Jenseit, James T Robinson, Kristian W Pajtler, Till Milde, Natalie Jäger, Petra Fiesel, Ling Morgan, Sunita Sridhar, Nicole G Coufal, Michael L Levy, Denise Malicki, Charlotte Hobbs, Stephen F Kingsmore, Shareef Nahas, Matija Snuderl, John Crawford, Robert J Wechsler-Reya, Tom Belle Davidson, Jennifer A Cotter, George Michaiel, Gudrun Fleischhack, Stefan Mundlos, Anthony Schmitt, Hannah Carter, Kulandaimanuvel Antony Michealraj, Sachin A Kumar, Michael D Taylor, Jeremy Rich, Frank Buchholz, Jill P Mesirov, Stefan M Pfister, Ferhat Ay, Jesse R Dixon, Marcel Kool, Lukas Chavez
3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nature communications 14 (1) (2023)
Konstantin Okonechnikov, Aylin Camgöz, Owen Chapman, Sameena Wani, Donglim Esther Park, Jens-Martin Hübner, Abhijit Chakraborty, Meghana Pagadala, Rosalind Bump, Sahaana Chandran, Katerina Kraft, Rocio Acuna-Hidalgo, Derek Reid, Kristin L Sikkink, Monika Mauermann, Edwin F Juarez, Anne Jenseit, James T Robinson, Kristian W Pajtler, Till Milde, Natalie Jäger, Petra Fiesel, Ling Morgan, Sunita Sridhar, Nicole G Coufal, Michael L Levy, Denise Malicki, Charlotte Hobbs, Stephen F Kingsmore, Shareef Nahas, Matija Snuderl, John Crawford, Robert J Wechsler-Reya, Tom Belle Davidson, Jennifer A Cotter, George Michaiel, Gudrun Fleischhack, Stefan Mundlos, Anthony Schmitt, Hannah Carter, Kulandaimanuvel Antony Michealraj, Sachin A Kumar, Michael D Taylor, Jeremy Rich, Frank Buchholz, Jill P Mesirov, Stefan M Pfister, Ferhat Ay, Jesse R Dixon, Marcel Kool, Lukas Chavez
3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nature communications 14 (1) (2023)
Konstantin Okonechnikov, Aylin Camgöz, Owen Chapman, Sameena Wani, Donglim Esther Park, Jens-Martin Hübner, Abhijit Chakraborty, Meghana Pagadala, Rosalind Bump, Sahaana Chandran, Katerina Kraft, Rocio Acuna-Hidalgo, Derek Reid, Kristin L Sikkink, Monika Mauermann, Edwin F Juarez, Anne Jenseit, James T Robinson, Kristian W Pajtler, Till Milde, Natalie Jäger, Petra Fiesel, Ling Morgan, Sunita Sridhar, Nicole G Coufal, Michael L Levy, Denise Malicki, Charlotte Hobbs, Stephen F Kingsmore, Shareef Nahas, Matija Snuderl, John Crawford, Robert J Wechsler-Reya, Tom Belle Davidson, Jennifer A Cotter, George Michaiel, Gudrun Fleischhack, Stefan Mundlos, Anthony Schmitt, Hannah Carter, Kulandaimanuvel Antony Michealraj, Sachin A Kumar, Michael D Taylor, Jeremy Rich, Frank Buchholz, Jill P Mesirov, Stefan M Pfister, Ferhat Ay, Jesse R Dixon, Marcel Kool, Lukas Chavez
3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nature communications 14 (1) (2023)
Laura Hinojosa-Gonzalez, Jesse L Turner, Takayo Sasaki, Ferhat Ay, David M Gilbert
Brd2 is dispensable for genome compartmentalization and replication timing. bioRxiv : the preprint server for biology (2023)
Laura Hinojosa-Gonzalez, Jesse L Turner, Takayo Sasaki, Ferhat Ay, David M Gilbert
Brd2 is dispensable for genome compartmentalization and replication timing. bioRxiv : the preprint server for biology (2023)
Pramod Shinde, Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Rasmussen, Lisa Willemsen, Mari Kojima, Brendan Ha, Jason A Greenbaum, James A Overton, Hector Guzman-Orozco, Somayeh Nili, Shelby Orfield, Jeremy P Gygi, Ricardo da Silva Antunes, Alessandro Sette, Barry J Grant, Lars Rønn Olsen, Anna Konstorum, Leying Guan, Ferhat Ay, Steven H Kleinstein, Bjoern Peters
A systems vaccinology resource to develop and test computational models of immunity. bioRxiv : the preprint server for biology (2023)
Laura Hinojosa-Gonzalez, Jesse L Turner, Takayo Sasaki, Ferhat Ay, David M Gilbert
Brd2 is dispensable for genome compartmentalization and replication timing. bioRxiv : the preprint server for biology (2023)
Laura Hinojosa-Gonzalez, Jesse L Turner, Takayo Sasaki, Ferhat Ay, David M Gilbert
Brd2 is dispensable for genome compartmentalization and replication timing. bioRxiv : the preprint server for biology (2023)
Konstantin Okonechnikov, Aylin Camgöz, Owen Chapman, Sameena Wani, Donglim Esther Park, Jens-Martin Hübner, Abhijit Chakraborty, Meghana Pagadala, Rosalind Bump, Sahaana Chandran, Katerina Kraft, Rocio Acuna-Hidalgo, Derek Reid, Kristin L Sikkink, Monika Mauermann, Edwin F Juarez, Anne Jenseit, James T Robinson, Kristian W Pajtler, Till Milde, Natalie Jäger, Petra Fiesel, Ling Morgan, Sunita Sridhar, Nicole G Coufal, Michael L Levy, Denise Malicki, Charlotte Hobbs, Stephen F Kingsmore, Shareef Nahas, Matija Snuderl, John Crawford, Robert J Wechsler-Reya, Tom Belle Davidson, Jennifer A Cotter, George Michaiel, Gudrun Fleischhack, Stefan Mundlos, Anthony Schmitt, Hannah Carter, Kulandaimanuvel Antony Michealraj, Sachin A Kumar, Michael D Taylor, Jeremy Rich, Frank Buchholz, Jill P Mesirov, Stefan M Pfister, Ferhat Ay, Jesse R Dixon, Marcel Kool, Lukas Chavez
3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nature communications 14 (1) (2023)
Konstantin Okonechnikov, Aylin Camgöz, Owen Chapman, Sameena Wani, Donglim Esther Park, Jens-Martin Hübner, Abhijit Chakraborty, Meghana Pagadala, Rosalind Bump, Sahaana Chandran, Katerina Kraft, Rocio Acuna-Hidalgo, Derek Reid, Kristin L Sikkink, Monika Mauermann, Edwin F Juarez, Anne Jenseit, James T Robinson, Kristian W Pajtler, Till Milde, Natalie Jäger, Petra Fiesel, Ling Morgan, Sunita Sridhar, Nicole G Coufal, Michael L Levy, Denise Malicki, Charlotte Hobbs, Stephen F Kingsmore, Shareef Nahas, Matija Snuderl, John Crawford, Robert J Wechsler-Reya, Tom Belle Davidson, Jennifer A Cotter, George Michaiel, Gudrun Fleischhack, Stefan Mundlos, Anthony Schmitt, Hannah Carter, Kulandaimanuvel Antony Michealraj, Sachin A Kumar, Michael D Taylor, Jeremy Rich, Frank Buchholz, Jill P Mesirov, Stefan M Pfister, Ferhat Ay, Jesse R Dixon, Marcel Kool, Lukas Chavez
3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nature communications 14 (1) (2023)
Abhijit Chakraborty, Jeffrey G Wang, Ferhat Ay
dcHiC detects differential compartments across multiple Hi-C datasets. Nature communications 13 (1) (2022)
Mariko Kashiwagi, Daniela Salgado Figueroa, Ferhat Ay, Bruce A Morgan, Katia Georgopoulos
A double-negative thymocyte-specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and β-selection. Nature immunology 23 (11) (2022)
Benjamin J Schmiedel, Cristian Gonzalez-Colin, Vicente Fajardo, Job Rocha, Ariel Madrigal, Ciro Ramírez-Suástegui, Sourya Bhattacharyya, Hayley Simon, Jason A Greenbaum, Bjoern Peters, Grégory Seumois, Ferhat Ay, Vivek Chandra, Pandurangan Vijayanand
Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type-dependent effects of disease-risk variants. Science immunology 7 (68) (2022)
Simon Eschweiler, Ciro Ramírez-Suástegui, Yingcong Li, Emma King, Lindsey Chudley, Jaya Thomas, Oliver Wood, Adrian von Witzleben, Danielle Jeffrey, Katy J McCann, Hayley Simon, Monalisa Mondal, Alice Wang, Martina Dicker, Elena Lopez-Guadamillas, Ting-Fang Chou, Nicola A Dobbs, Louisa Essame, Gary Acton, Fiona Kelly, Gavin Halbert, Joseph J Sacco, Andrew Graeme Schache, Richard J Shaw, James Anthony McCaul, Claire Paterson, Joseph H Davies, Peter A Brennan, Rabindra P Singh, Paul M Loadman, William Wilson, Allan Hackshaw, Grégory Seumois, Klaus Okkenhaug, Gareth J Thomas, Terry M Jones, Ferhat Ay, Greg Friberg, Mitchell Kronenberg, Bart Vanhaesebroeck, Pandurangan Vijayanand, Christian Hermann Ottensmeier
Intermittent PI3Kδ inhibition sustains anti-tumour immunity and curbs irAEs. Nature 605 (7911) (2022)
Yichen Wang, Lin Jia, Cong Wang, Zhonghua Du, Shilin Zhang, Lei Zhou, Xue Wen, Hui Li, Huiling Chen, Yuanyuan Nie, Dan Li, Shanshan Liu, Daniela Salgado Figueroa, Ferhat Ay, Wei Xu, Songling Zhang, Wei Li, Jiuwei Cui, Andrew R Hoffman, Hui Guo, Ji-Fan Hu
Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture. The Journal of cell biology 221 (4) (2022)
Simon Eschweiler, James Clarke, Ciro Ramírez-Suástegui, Bharat Panwar, Ariel Madrigal, Serena J Chee, Ioannis Karydis, Edwin Woo, Aiman Alzetani, Somaia Elsheikh, Christopher J Hanley, G J Thomas, Peter S Friedmann, Tilman Sanchez-Elsner, Ferhat Ay, Christian Hermann Ottensmeier, Pandurangan Vijayanand
Intratumoral follicular regulatory T cells curtail anti-PD-1 treatment efficacy. Nature immunology 22 (8) (2021)
Benjamin J Schmiedel, Job Rocha, Cristian Gonzalez-Colin, Sourya Bhattacharyya, Ariel Madrigal, Christian Hermann Ottensmeier, Ferhat Ay, Vivek Chandra, Pandurangan Vijayanand
COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types. Nature communications 12 (1) (2021)
Rinkesh K Gupta, Donald T Gracias, Daniela Salgado Figueroa, Haruka Miki, Jacqueline Miller, Kai Fung, Ferhat Ay, Linda Burkly, Michael Croft
TWEAK functions with TNF and IL-17 on keratinocytes and is a potential target for psoriasis therapy. Science immunology 6 (65) (2021)
Jing Xia, Aarthi Venkat, Rachel E Bainbridge, Michael L Reese, Karine G Le Roch, Ferhat Ay, Jon P Boyle
Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants. Genome research 31 (5) (2021)
Mariko Takahashi, Chan-Wang Jerry Lio, Anaamika Campeau, Martin Steger, Ferhat Ay, Matthias Mann, David J Gonzalez, Mohit Jain, Sonia Sharma
The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway. Nature immunology 22 (4) (2021)
Ivelisse Cajigas, Abhijit Chakraborty, Madison Lynam, Kelsey R Swyter, Monique Bastidas, Linden Collens, Hao Luo, Ferhat Ay, Jhumku D Kohtz
Sox2-Evf2 lncRNA-mediated mechanisms of chromosome topological control in developing forebrain. Development (Cambridge, England) 148 (6) (2021)
Anthony Kusnadi, Ciro Ramírez-Suástegui, Vicente Fajardo, Serena J Chee, Benjamin J Meckiff, Hayley Simon, Emanuela Pelosi, Grégory Seumois, Ferhat Ay, Pandurangan Vijayanand, Christian Hermann Ottensmeier
Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells. Science immunology 6 (55) (2021)
Bharat Panwar, Benjamin J Schmiedel, Shu Liang, Brandie White, Enrique Rodriguez, Kenneth Kalunian, Andrew J McKnight, Rachel Soloff, Gregory Seumois, Pandurangan Vijayanand, Ferhat Ay
Multi-cell type gene coexpression network analysis reveals coordinated interferon response and cross-cell type correlations in systemic lupus erythematosus. Genome research 31 (4) (2021)
Chan-Wang Jerry Lio, Vipul Shukla, Daniela Samaniego-Castruita, Edahi González-Avalos, Abhijit Chakraborty, Xiaojing Yue, David G Schatz, Ferhat Ay, Anjana Rao
TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the Aicda superenhancer. Science immunology 4 (34) (2020)
Benjamin J Schmiedel, Vivek Chandra, Job Rocha, Cristian Gonzalez-Colin, Sourya Bhattacharyya, Ariel Madrigal, Christian H Ottensmeier, Ferhat Ay, Pandurangan Vijayanand
COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types. bioRxiv : the preprint server for biology (2020)
Vivek Chandra, Sourya Bhattacharyya, Benjamin J Schmiedel, Ariel Madrigal, Cristian Gonzalez-Colin, Stephanie Fotsing, Austin Crinklaw, Grégory Seumois, Pejman Mohammadi, Mitchell Kronenberg, Bjoern Peters, Ferhat Ay, Pandurangan Vijayanand
Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants. Nature genetics 53 (1) (2020)
Arya Kaul, Sourya Bhattacharyya, Ferhat Ay
Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2. Nature protocols 15 (3) (2020)
Abbas Roayaei Ardakany, Halil Tuvan Gezer, Stefano Lonardi, Ferhat Ay
Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation. Genome biology 21 (1) (2020)
Evelien M Bunnik, Aarthi Venkat, Jianlin Shao, Kathryn E McGovern, Gayani Batugedara, Danielle Worth, Jacques Prudhomme, Stacey A Lapp, Chiara Andolina, Leila S Ross, Lauren Lawres, Declan Brady, Photini Sinnis, Francois H Nosten, David A Fidock, Emma H Wilson, Rita Tewari, Mary R Galinski, Choukri Ben Mamoun, Ferhat Ay, Karine G Le Roch
Comparative 3D genome organization in apicomplexan parasites. Proceedings of the National Academy of Sciences of the United States of America 116 (8) (2019)
Priscillia Lhoumaud, Sana Badri, Javier Rodriguez-Hernaez, Theodore Sakellaropoulos, Gunjan Sethia, Andreas Kloetgen, MacIntosh Cornwell, Sourya Bhattacharyya, Ferhat Ay, Richard A Bonneau, Aristotelis Tsirigos, Jane A Skok
NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains. Nature communications 10 (1) (2019)
Ryan K Nelson, Howard Brickner, Bharat Panwar, Ciro Ramírez-Suástegui, Sara Herrera-De la Mata, Neiman Liu, Damaris Diaz, Laura E Crotty Alexander, Ferhat Ay, Pandurangan Vijayanand, Grégory Seumois, Praveen Akuthota
Human Eosinophils Express a Distinct Gene Expression Program in Response to IL-3 Compared with Common β-Chain Cytokines IL-5 and GM-CSF. Journal of immunology (Baltimore, Md. : 1950) 203 (2) (2019)
Sourya Bhattacharyya, Vivek Chandra, Pandurangan Vijayanand, Ferhat Ay
Identification of significant chromatin contacts from HiChIP data by FitHiChIP. Nature communications 10 (1) (2019)
James Clarke, Bharat Panwar, Ariel Madrigal, Divya Singh, Ravindra Gujar, Oliver Wood, Serena J Chee, Simon Eschweiler, Emma V King, Amiera S Awad, Christopher J Hanley, Katy J McCann, Sourya Bhattacharyya, Edwin Woo, Aiman Alzetani, Grégory Seumois, Gareth J Thomas, Anusha-Preethi Ganesan, Peter S Friedmann, Tilman Sanchez-Elsner, Ferhat Ay, Christian Hermann Ottensmeier, Pandurangan Vijayanand
Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer. The Journal of experimental medicine 216 (9) (2019)
Evelien M Bunnik, Kate B Cook, Nelle Varoquaux, Gayani Batugedara, Jacques Prudhomme, Anthony Cort, Lirong Shi, Chiara Andolina, Leila S Ross, Declan Brady, David A Fidock, Francois H Nosten, Rita Tewari, Photini Sinnis, Ferhat Ay, Jean-Philippe Vert, William Stafford Noble, Karine G Le Roch
Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nature communications 9 (1) (2018)
Jesse R Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T Le, Galip Gürkan Yardımcı, Abhijit Chakraborty, Darrin V Bann, Yanli Wang, Royden Clark, Lijun Zhang, Hongbo Yang, Tingting Liu, Sriranga Iyyanki, Lin An, Christopher Pool, Takayo Sasaki, Juan Carlos Rivera-Mulia, Hakan Ozadam, Bryan R Lajoie, Rajinder Kaul, Michael Buckley, Kristen Lee, Morgan Diegel, Dubravka Pezic, Christina Ernst, Suzana Hadjur, Duncan T Odom, John A Stamatoyannopoulos, James R Broach, Ross C Hardison, Ferhat Ay, William Stafford Noble, Job Dekker, David M Gilbert, Feng Yue
Integrative detection and analysis of structural variation in cancer genomes. Nature genetics 50 (10) (2018)
Zhonghua Du, Lin Jia, Yichen Wang, Cong Wang, Xue Wen, Jingcheng Chen, Yanbo Zhu, Dehai Yu, Lei Zhou, Naifei Chen, Shilin Zhang, Ilkay Celik, Ferhat Ay, Sujun Gao, Songling Zhang, Wei Li, Andrew R Hoffman, Jiuwei Cui, Ji-Fan Hu
Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming. Scientific data 5 (2018)
Umut Eser, Devon Chandler-Brown, Ferhat Ay, Aaron F Straight, Zhijun Duan, William Stafford Noble, Jan M Skotheim
Form and function of topologically associating genomic domains in budding yeast. Proceedings of the National Academy of Sciences of the United States of America 114 (15) (2017)
Laura S Burrack, Hannah F Hutton, Kathleen J Matter, Shelly Applen Clancey, Ivan Liachko, Alexandra E Plemmons, Amrita Saha, Erica A Power, Breanna Turman, Mathuravani Aaditiyaa Thevandavakkam, Ferhat Ay, Maitreya J Dunham, Judith Berman
Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome. PLoS genetics 12 (9) (2016)

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Publication Activity (10 Years)

Top Topics

Top Venues

Ferhat Ay