Publications
*Equal contribution †Corresponding author
Preprints / In Preparation
Yorzoi: Predicting RNA-seq coverage from DNA sequence in yeast
Timon Schneider, Abdul Muntakim Rafi, Cassandra Jensen, Daniella Liao, Yiren Zhao, Carl de Boer, Tom Ellis
bioRxiv, 2025
Journal Articles
Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae
Zimo Jin, Yueming Dong, Abdul Muntakim Rafi, Mohsin MD Patwary, Catherine Xu, Morten H. Raadam, Carl de Boer, Codruta Ignea
Nucleic Acids Research, 2025
A community effort to optimize sequence-based deep learning models of gene regulation
Abdul Muntakim Rafi†, Daria Nogina, Dmitry Penzar, Dohoon Lee, Danyeong Lee, Nayeon Kim, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il-Youp Kwak, Georgy Meshcheryakov, Andrey Lando, Arsenii Zinkevich, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Eeshit Dhaval Vaishnav, Payman Yadollahpour, Random Promoter DREAM Challenge Consortium, Sun Kim, Jake Albrecht, Aviv Regev, Wuming Gong, Ivan V. Kulakovskiy, Pablo Meyer, Carl de Boer†
Nature Biotechnology, 2024
Biochemical activity is the default DNA state in eukaryotes
Ishika Luthra, Xinyi E Chen, Cassandra Jensen, Asfar Lathif Salaudeen, Abdul Muntakim Rafi, Carl G de Boer
Nature Structural & Molecular Biology, 2024
LegNet: a best-in-class deep learning model for short DNA regulatory regions
Dmitry Penzar, Daria Nogina, Elizaveta Noskova, Arsenii Zinkevich, Georgy Meshcheryakov, Andrey Lando, Abdul Muntakim Rafi, Carl de Boer, Ivan V. Kulakovskiy
Bioinformatics, 2023
GIL: A Python package for designing custom indexing primers
Nicholas Mateyko, Omar Tariq, Xinyi E Chen, Will Cheney, Asfar Lathif Salaudeen, Ishika Luthra, Najmeh Nikpour, Abdul Muntakim Rafi, Hadis Kamali Deghan, Cassandra Jensen, Carl de Boer
Bioinformatics, 2023
RemNet: remnant convolutional neural network for camera model identification
Abdul Muntakim Rafi, Thamidul Islam Tonmoy, Uday Kamal, Jonathan Wu, Md Kamrul Hasan
Neural Computing and Applications, 2021
Conference Papers
Lung cancer tumor region segmentation using recurrent 3D-DenseUNet
Uday Kamal, Abdul Muntakim Rafi, Rakibul Hoque, Jonathan Wu, Md Kamrul Hasan
MICCAI 2020
Understanding Global Reaction to the Recent Outbreaks of COVID-19: Insights from Instagram Data Analysis
Abdul Muntakim Rafi*, Shivang Rana*, Rajwinder Kaur*, Jonathan Wu, Pooya Moradian Zadeh
IEEE International Conference on Systems, Man, and Cybernetics, 2020
L2-Constrained RemNet for Camera Model Identification and Image Manipulation Detection
Abdul Muntakim Rafi, Jonathan Wu, Md. Kamrul Hasan
Advances in Image Manipulation Workshop, ECCV 2020
Application of DenseNet in Camera Model Identification and Post-processing Detection
Abdul Muntakim Rafi, Uday Kamal, Rakibul Hoque, Abid Abrar, Sowmitra Das, Robert Laganiere, Md Kamrul Hasan
CVPR 2019
Image-based Bengali Sign Language Alphabet Recognition for Deaf and Dumb Community
Abdul Muntakim Rafi, Nowshin Nawal, Nur Sultan Nazar Bayev, Lusain Nima, Celia Shahnaz, Shaikh Anowarul Fattah
IEEE GHTC 2019
Selected Awards
Four Year Doctoral Fellowship (4YF)
University of British Columbia
SBME Graduate Support Initiative Entrance Award
School of Biomedical Engineering, UBC
Stem Cell Network International Travel Award
Stem Cell Network, Canada
JXTX + CSHL Biological Data Science Scholarship
Cold Spring Harbor Laboratory