Author

Mohammad Erfan Mowlaei

Temple UniversityORCID 0000-0002-7601-0550Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Organism:human· 2 Approach:transformer / foundation model· 2 Research Focus:dimensionality reduction· 1 Research Focus:genome assembly· 1 Assay:Hi-C· 1 Research Focus:imputation· 1 Organism:mouse· 1

Frequent Co-Authors

Sudhir KumariD· 3 shared Vincenzo CarnevaleiD· 2 shared Xinghua Mindy ShiiD· 2 shared Benyamin Jamialahmadi· 1 shared Chong LiiD· 1 shared Chong LiiD· 1 shared Evan E. EichleriD· 1 shared HGSVC Functional Analysis Working Group· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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3 shared papersBioinformatics

Sudhir KumarORCID

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Author profile →

3 papers

Recent·Most cited

Species phylogenetics using intraprotein residue dependence inferred with protein foundation models

Rohan Ferriols Alibutud, Mohammad Erfan Mowlaei, Sudhir Kumar

This study compares RAM-NJ and SAM-NJ phylogenies using protein foundation models to reconstruct species relationships without conventional substitution models or multiple sequence alignments.

bioRxiv · May 29, 2026 · PreprintBioinformatics

TRUHiC: A TRansformer-embedded U-2 Net to enhance Hi-C data for 3D chromatin structure characterization

Chong Li, Mohammad Erfan Mowlaei, Lingbin Ni, HGSVC Functional Analysis Working Group, Mark Chaisson, Evan E. Eichler, Vincenzo Carnevale, Sudhir Kumar, Xinghua Mindy Shi

TRUHiC enhances low-resolution Hi-C data using deep generative modeling to improve 3D chromatin structure characterization across cell lines and species.

bioRxiv · Mar 29, 2025 · PreprintBioinformatics

Split-Transformer Impute (STI): A Transformer Framework for Genotype Imputation

Mohammad Erfan Mowlaei, Chong Li, Oveis Jamialahmadi, Raquel Dias, Junjie Chen, Benyamin Jamialahmadi, Timothy Richard Rebbeck, Vincenzo Carnevale, Sudhir Kumar, Xinghua Mindy Shi

STI is a transformer-based model for genome-scale genotype imputation that achieves high accuracy and handles multi-allelic variants effectively.

bioRxiv · Mar 5, 2023 · PreprintGenomics