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Publications

Publications and preprints.

Also on Google Scholar.

Journal articles: 6
Conference papers: 5
Preprints: 4

Preprints

4 entries

2026

gRely: Reliability for genome-trained sequence-to-function model predictions

Abdul Muntakim Rafi^†, Gökçen Eraslan, Kipper Fletez-Brant^†

bioRxiv · under review

2026

Evaluation of active learning selection strategies and characterization of informative sequences for sequence-to-expression models

Justin Qian^*, Abdul Muntakim Rafi^*†, Emmanuel Cazottes^*, Carl de Boer^†

bioRxiv · under review

2025

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

Characterizing homology-induced data leakage and memorization in genome-trained sequence models

Abdul Muntakim Rafi^†, Brett Kiyota, Nozomu Yachie, Carl de Boer^†

bioRxiv · under review

Journal articles

6 entries

2025

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 43(8):1373–1383

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

2023

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

2021

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

Conference papers

5 entries

2020

Lung cancer tumor region segmentation using recurrent 3D-DenseUNet

Uday Kamal, Abdul Muntakim Rafi, Rakibul Hoque, Jonathan Wu, Md. Kamrul Hasan

Second International Workshop on Thoracic Image Analysis, MICCAI 2020

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

2019

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 Workshops, Long Beach, United States

2019

Image-based Bengali sign language alphabet recognition for the deaf community

Abdul Muntakim Rafi, Nowshin Nawal, Nur Sultan Nazar Bayev, Lusain Nima, Celia Shahnaz, Shaikh Anowarul Fattah

IEEE Global Humanitarian Technology Conference (GHTC), Seattle, United States

^* Equal contribution · ^† Corresponding author