publications

2025

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

   Asia Owais, Hammad Farooq, Hannah Chen, Prisca K Thami, Jaime DeSantiago, Talla Abbas, and 5 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, Ao Ma, and Jie Liang

   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 Jie Liang

   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}
   }

4. ChromPolymerDB: a high-resolution database of single-cell 3D chromatin structures for functional genomics

   Min Chen, Lin Du, Siyuan Zhao, Bowei Ye, Pourya Delafrouz, Hammad Farooq, and 5 more authors

   Nucleic Acids Research, 2025

   DOI Bib

   @article{chen2025chrompolymerdb,
     title = {ChromPolymerDB: a high-resolution database of single-cell 3D chromatin structures for functional genomics},
     author = {Chen, Min and Du, Lin and Zhao, Siyuan and Ye, Bowei and Delafrouz, Pourya and Farooq, Hammad and Chattopadhyay, Debaleena and Marai, G Elisabeta and Shao, Zhifeng and Liang, Jie and others},
     journal = {Nucleic Acids Research},
     pages = {gkaf1233},
     year = {2025},
     doi = {10.1093/nar/gkaf1233},
     publisher = {Oxford University Press}
   }

5. Exuberant long noncoding RNA expression may sculpt Igh locus topology

   Ellen Brandenburg Drake, Sarah Naiyer, Xinyan Qu, Khalid Bhat, Hammad Farooq, Mark Maienschein-Cline, and 2 more authors

   Frontiers in Immunology, 2025

   DOI Bib

   @article{drake16exuberant,
     title = {Exuberant long noncoding RNA expression may sculpt Igh locus topology},
     author = {Drake, Ellen Brandenburg and Naiyer, Sarah and Qu, Xinyan and Bhat, Khalid and Farooq, Hammad and Maienschein-Cline, Mark and Liang, Jie and Kenter, Amy L},
     journal = {Frontiers in Immunology},
     volume = {16},
     pages = {1678105},
     year = {2025},
     doi = {10.3389/fimmu.2025.1678105},
     publisher = {Frontiers}
   }

2024

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

   Hammad Farooq, Lin Du, Pourya Delafrouz, Wei Jiang, Constantinos Chronis, and Jie Liang

   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, Nida Babar, Hammad Farooq, Asif Loya, and 1 more author

   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, Xinyan Qu, Hammad Farooq, Eden Kleiman, and 5 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 Hammad Naveed

   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, Sibt Hussain, and Hammad Naveed

   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}
   }