- MaCroDNA: Accurate integration of single-cell DNA and RNA data for a deeper understanding of tumor heterogeneity
Mohammadamin Edrisi, Xiru Huang, Huw A. Ogilvie, Luay Nakhleh
Accepted for publication at Nature Communications, 2023.
- MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks Mohammadamin Edrisi, Huw A. Ogilvie, Meng Li, Luay Nakhleh
RECOMB International Workshop on Comparative Genomics, 232-247, 2023.
- NestedBD: Bayesian Inference of Phylogenetic Trees from Single-Cell DNA Copy Number Profile Data Under a Birth-Death Model
Yushu Liu, Mohammadamin Edrisi, Huw A. Ogilvie, Luay Nakhleh
Under review at PLOS Computational Biology, 2023.
- Phylovar: Towards scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data
Mohammadamin Edrisi, Monica V. Valecha, Sunkara B.V. Chowdary, Sergio Robledo, Huw A. Ogilvie, David Posada, Hamim Zafar, Luay Nakhleh,
In proceedings of the 30th annual conference on Intelligent Systems for Molecular Biology (ISMB), Bioinformatics 38 (Supplement_1): i195-i202, 2022.
- Current progress and open challenges for applying deep learning across the biosciences Nicolae Nicolae Sapoval, Amirali Aghazadeh, Michael G. Nute, Dinler A. Antunes, Advait Balaji, Richard Baraniuk, C. J. Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, R. A. Leo Elworth, Bryce Kille, Anastasios Kyrillidis, Luay Nakhleh, Cameron R. Wolfe, Zhi Yan, Vicky Yao and Todd J. Treangen
Nature Communications, 13 (1): 1728, 2022.
- Methods for Copy Number Aberration Detection from Single-cell DNA Sequencing Data
Xian F Mallory, Mohammadamin Edrisi, Nicholas Navin, Luay Nakhleh
Genome Biology, 21 (1): 208, 2020.
- Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data
Xian F Mallory, Mohammadamin Edrisi, Nicholas Navin, Luay Nakhleh
PLoS Computational Biology, 16 (7): 1–24, 2020.
- Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine
Medhat Mahmoud, Alejandro Rafael Gener, Michael M. Khayat, [and 43 authors including Mohammadamin Edrisi]
F1000Research, 9:1141, 2020.
- A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference
Mohammadamin Edrisi, Hamim Zafar, Luay Nakhleh
19th International Workshop on Algorithms in Bioinformatics (WABI 2019) (Vol. 143, p. 22:1-22:13). Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, 2019.
- Meta-aligner: Long-read alignment based on genome statistics
Damoun Nashta-ali, Ali Alyari, Mohammadamin Edrisi, Ahmad Ahmadian Moghadam, Seyed Abolfazl Motahari, Babak Hossein Khalaj,
BMC Bioinformatics, BMC Bioinformatics, 18 (1): 126, 2017.