Ferhat Ay

16 papers B 1C 1Journal 11Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
<tt>nipalsMCIA</tt> : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares.
Bioinform.
Max Mattessich, Joaquin Reyna, Edel Aron, Ferhat Ay, Misha E. Kilmer, Steven H. Kleinstein, Anna Konstorum
2025 J jnl
Putting computational models of immunity to the test - An invited challenge to predict B.pertussis vaccination responses.
PLoS Comput. Biol.
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, Nicola Thrupp, Rashmi Tippalagama, Raphael Trevizani, Steffen Ventz, Jiuzhou Wang, Cheng-Chang Wu, Ferhat Ay, Barry Grant, Steven H. Kleinstein, Bjoern Peters
2025 J jnl
Soffritto: a deep learning model for predicting high-resolution replication timing.
Bioinform.
Dante Bolzan, Ferhat Ay
2023 J jnl
MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.
Bioinform.
Ali Osman Berk Sapci, Shan Lu, Shuchen Yan, Ferhat Ay, Öznur Tastan, Sündüz Keles
2021 J jnl
ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs.
Bioinform.
Abhijit Chakraborty, Ferhat Ay, Ramana V. Davuluri
2019 J jnl
Selfish: discovery of differential chromatin interactions via a self-similarity measure.
Bioinform.
Abbas Roayaei Ardakany, Ferhat Ay, Stefano Lonardi
2018 J jnl
Identification of copy number variations and translocations in cancer cells from Hi-C data.
Bioinform.
Abhijit Chakraborty, Ferhat Ay
2014 J jnl
A statistical approach for inferring the 3D structure of the genome.
Bioinform.
Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean-Philippe Vert
2012 J jnl
Metabolic network alignment in large scale by network compression.
BMC Bioinform.
Ferhat Ay, Michael Dang, Tamer Kahveci
2011 — conf
A novel framework for large scale metabolic network alignments by compression.
BCB
Michael Dang, Ferhat Ay, Tamer Kahveci
2011 J jnl
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings.
J. Comput. Biol.
Ferhat Ay, Manolis Kellis, Tamer Kahveci
2010 C conf
Finding Dynamic Modules of Biological Regulatory Networks.
BIBE
Ferhat Ay, Thang N. Dinh, My T. Thai, Tamer Kahveci
2010 — conf
Finding steady states of large scale regulatory networks through partitioning.
GENSiPS
Ferhat Ay, Günhan Gülsoy, Tamer Kahveci
2010 — conf
Functional similarities of reaction sets in metabolic pathways.
BCB
Ferhat Ay, Tamer Kahveci
2010 B conf
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings.
RECOMB
Ferhat Ay, Tamer Kahveci
2009 J jnl
A Fast and Accurate Algorithm for Comparative Analysis of metabolic Pathways.
J. Bioinform. Comput. Biol.
Ferhat Ay, Tamer Kahveci, Valérie de Crécy-Lagard