publications

2025

1. Gene-Gene Interactions Between A LMNA Variant and Common Polymorphisms Drive Early-Onset Atrial Fibrillation

   Asia Owais, Hammad Farooq, Hannah Chen, and 8 more authors

   medRxiv, 2025

   DOI Bib

   @article{owais2025gene,
     title = {Gene-Gene Interactions Between A LMNA Variant and Common Polymorphisms Drive Early-Onset Atrial Fibrillation},
     author = {Owais, Asia and Farooq, Hammad and Chen, Hannah and Thami, Prisca K and DeSantiago, Jaime and Abbas, Talla and Pavel, Arif and Merril, Bradley and Ware, James S and Ng, Fu Siong and others},
     journal = {medRxiv},
     pages = {2025--05},
     year = {2025},
     doi = {10.1101/2025.05.05.25326834},
     publisher = {Cold Spring Harbor Laboratory Press}
   }

2. Effects of Lamina-Chromatin Attachment on Super Long-Range Chromatin Interactions

   Pourya Delafrouz, Hammad Farooq, Lin Du, and 2 more authors

   bioRxiv, 2025

   DOI Bib

   @article{delafrouz2025effects,
     title = {Effects of Lamina-Chromatin Attachment on Super Long-Range Chromatin Interactions},
     author = {Delafrouz, Pourya and Farooq, Hammad and Du, Lin and Ma, Ao and Liang, Jie},
     journal = {bioRxiv},
     doi = {10.1101/2025.02.13.638183},
     year = {2025}
   }

3. Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations

   Lin Du, Hammad Farooq, Pourya Delafrouz, and 1 more author

   Bioinformatics, 2025

   DOI Bib

   @article{du2025structural,
     title = {Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations},
     author = {Du, Lin and Farooq, Hammad and Delafrouz, Pourya and Liang, Jie},
     journal = {Bioinformatics},
     volume = {41},
     number = {2},
     pages = {btaf050},
     year = {2025},
     doi = {10.1093/bioinformatics/btaf050},
     publisher = {Oxford University Press}
   }

2024

1. A New Approach for Discovering Functional Links Connecting Non-Coding Regulatory Variants to Gene Targets

   Hammad Farooq, Lin Du, Pourya Delafrouz, and 3 more authors

   bioRxiv, 2024

   DOI Bib

   @article{farooq2024new,
     title = {A New Approach for Discovering Functional Links Connecting Non-Coding Regulatory Variants to Gene Targets},
     author = {Farooq, Hammad and Du, Lin and Delafrouz, Pourya and Jiang, Wei and Chronis, Constantinos and Liang, Jie},
     journal = {bioRxiv},
     pages = {2024--06},
     year = {2024},
     doi = {10.1101/2024.06.13.598913},
     publisher = {Cold Spring Harbor Laboratory}
   }

2. Low-Cost Histopathological Mitosis Detection for Microscope-acquired Images

   Bilal Shabbir, Saira Saleem, Iffat Aleem, and 4 more authors

   AMIA Summits on Translational Science Proceedings, 2024

   PubMed Bib

   @article{shabbir2024low,
     title = {Low-Cost Histopathological Mitosis Detection for Microscope-acquired Images},
     author = {Shabbir, Bilal and Saleem, Saira and Aleem, Iffat and Babar, Nida and Farooq, Hammad and Loya, Asif and Naveed, Hammad},
     journal = {AMIA Summits on Translational Science Proceedings},
     volume = {2024},
     pages = {409},
     pmid = {38827107},
     year = {2024}
   }

2023

1. An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation

   Khalid H Bhat, Saurabh Priyadarshi, Sarah Naiyer, and 8 more authors

   Nature communications, 2023

   DOI Bib

   @article{bhat2023igh,
     title = {An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation},
     author = {Bhat, Khalid H and Priyadarshi, Saurabh and Naiyer, Sarah and Qu, Xinyan and Farooq, Hammad and Kleiman, Eden and Xu, Jeffery and Lei, Xue and Cantillo, Jose F and Wuerffel, Robert and others},
     journal = {Nature communications},
     volume = {14},
     number = {1},
     pages = {1225},
     year = {2023},
     doi = {10.1038/s41467-023-36414-2},
     publisher = {Nature Publishing Group UK London}
   }

2021

1. Leveraging digital media data for pharmacovigilance

   Hammad Farooq, Junaid Suhail Niaz, Saira Fakhar, and 1 more author

   In AMIA Annual Symposium Proceedings, 2021

   PubMed Bib

   @inproceedings{farooq2021leveraging,
     title = {Leveraging digital media data for pharmacovigilance},
     author = {Farooq, Hammad and Niaz, Junaid Suhail and Fakhar, Saira and Naveed, Hammad},
     booktitle = {AMIA Annual Symposium Proceedings},
     volume = {2020},
     pages = {442},
     pmid = {33936417},
     year = {2021}
   }

2020

1. Predicting the pathogenicity of protein coding mutations using Natural Language Processing

   Naeem Rehmat, Hammad Farooq, Sanjay Kumar, and 2 more authors

   In 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2020

   DOI Bib

   @inproceedings{rehmat2020predicting,
     title = {Predicting the pathogenicity of protein coding mutations using Natural Language Processing},
     author = {Rehmat, Naeem and Farooq, Hammad and Kumar, Sanjay and ul Hussain, Sibt and Naveed, Hammad},
     booktitle = {2020 42nd Annual International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC)},
     pages = {5842--5846},
     year = {2020},
     doi = {10.1109/EMBC44109.2020.9175781},
     organization = {IEEE}
   }

2019

1. Gpadrlex: Grouped phrasal adverse drug reaction lexicon

   Hammad Farooq and Hammad Naveed

   In 2019 IEEE International Conference on Signal Processing, Communications and Computing (ICSPCC), 2019

   DOI Bib

   @inproceedings{farooq2019gpadrlex,
     title = {Gpadrlex: Grouped phrasal adverse drug reaction lexicon},
     author = {Farooq, Hammad and Naveed, Hammad},
     booktitle = {2019 IEEE International Conference on Signal Processing, Communications and Computing (ICSPCC)},
     pages = {1--6},
     year = {2019},
     doi = {10.1109/ICSPCC46631.2019.8960791},
     organization = {IEEE}
   }