1.

Shireen, H., Batool, F., Khatoon, H., Parveen, N., Sehar, N.U., Noor U.S., Hussain, I., Ali, S., Abbasi, A. A. Predicting genome-wide tissue-specific enhancers via combinatorial transcription factor genomic occupancy analysis. FEBS Letters (2024). https://doi.org/10.1002/1873-3468.15030

2.

Mughal, K.A., Khan, A., Sarwar, A., Mahmood, R., & Abbasi, A. A. Comparative protein structural analyses of α-synuclein linked pathogenic variants reveal the role of N-terminally located critical region in Parkinson’s disease pathogenesis. Biologia (2024). https://doi.org/10.1007/s11756-024-01713-6

3. 

Jabeen, M., Shoukat, S., Shireen, H., Bao, Y., Khan, A., & Abbasi, A. A., (2024).Unraveling the genetic variations underlying virulence disparities among SARS-CoV-2 strains across global regions: insights from Pakistan. Virology journal, 21(1), 55.

4. 

Abrar, M., Ali, S., Hussain, I., Khatoon, H., Batool, F., Ghazanfar, S., Corcoran, D., Kawakami, Y., && Abbasi, A.A.(2024).Cis-regulatory control of mammalian Trps1 gene expression. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Volume342, Issue2, March 2024, Pages 85-100

5.

Ali, S., Abrar, M., Hussain, I., Batool, F., Raza, R. Z., Khatoon, H., Zoia, M., Visel, A., Shubin, N. H., Osterwalder, M., && Abbasi, A.A.(2023). Identification of ancestral gnathostome Gli3 enhancers with activity in mammals. Development, Growth & Differentiation, 66(1), 75–88.

6.

Hizran Khatoon, Rabail Zehra Raza, Shoaib Saleem, Fatima Batool, Saba Arshad, Muhammad Abrar,  Shahid Ali, Irfan Hussain, Neil H. Shubin & Amir Ali Abbasi (2023). Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions. Mol and Cell Biol 24, 13. 

7.

Lina Ma, Dong Zou, Lin Liu, Huma Shireen, Amir A. Abbasi, Alex Bateman, Jingfa Xiao, Wenming Zhao, Yiming Bao, Zhang Zhang. Database Commons: A Catalog of Worldwide Biological Databases. Genomics, Proteomics & Bioinformatics. Volume 21, Issue 5, Pages 1054–1058, 2022. 

8.

Batool, F., Pervaiz, N., Khalid, Q. & & Abbasi, A.A.(2021). Evolution of Human Multigene Families. https://doi.org/10.1002/9780470015902.a0029116.

9. 

 Hussain, I., Zehra, R., Ali, S., Abrar, M &Abbasi, A. A. (2021). Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers. Development Genes and Evolution. 2021 Mar;231(1-2):21-32.

10. 

Raza R. Z., Ma, L., Zhang, Z., Bao, Y., Abbasi ,A. A., (2021) Selection trends on nasal-associated SNP variants across human populations. Meta Gene, 28, 100872

11.

Zou1, D., Mehmood, F., Ali, S., Ali, A., Saleem, S., Hussain, I., Abbasi, A. A., Ma, L......., Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021.Nucleic Acids Research, 49(DI), D18–D28

12.

Shuhui Song., Cuiping Li., Lu Kang., Dongmei Tian.,….., Bing Zhang., Hua Chen., Yungui Yang., Amir Ali Abbasi Mingkun Li., Yongbiao Xue., Yiming Bao., (2021).Genomic epidemiology of SARS-CoV-2 in Pakistan. Genomics, Proteomics & Bioinformatics. doi: https://doi.org/10.1101/2021.06.24.21255875

13.

Abbas Khan, Tauqir Zia, Muhammad Suleman, Taimoor Khan, Syed Shujait Ali, Amir Ali Abbasi, Anwar Mohammad, Dong‐Qing Wei. 2021. Higher infectivity of the SARS‐CoV‐2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. J Cell Physiol. 2021;1–13.

14. 

Pervaiz, N., Kang, H., Bao, Y., Abbasi, A. A. Molecular evolutionary analysis of human primary microcephaly genes. BMC Ecol Evo 21, 76 (2021).

15. 

Ali, S., Arif, I., Iqbal, I., Hussain., I., Abrar., M., Khan, R. K., Shubin., N., & Abbasi, A.A. (2020).Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Developmental Dynamics. Volume 250, Issue 5 p. 669-683

16. 

Zhang, Z., Ma, L.,....Abbasi, A.A., ... & Gao, F. (2020). Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Research, 48(D1), D24-D33

17. 

Hussain, I., Pervaiz, N., Khan, A., Saleem, S., Shireen, H., Wei, D-Q., Labrie, V., Bao, Y., & Abbasi, A. A (2020). Evolutionary and structural analysis of SARS-CoV-2 specific evasion of host immunity. Genes Immun 21, 409–419.

18.

Nawaz, M.S., Asghar, R., Pervaiz, N., Ali, S., Hussain, Irfan., Peiqi, Xing., Bao, Y., & Abbasi, A. A. (2020) Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson's disease and other neurological disorders. BMC Evolutionary Biology, 130 (2020).

19.

Wang, G., Yin, H., Li, B.,Abbasi, A.A., … & Zhang, Z. (2019). Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics doi: https://doi.org/10.1101/327882

20.

Pervaiz, N., Shakeel, N., Qasim, A., Zehra, R., Anwar, S., Rana, N., Xue,Y., Zhang, Z., Bao,Y., & Abbasi, A.A. Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals. BMC Evolutionary Biology (2019) 19:128.

21. 

Zhang, Z., Zhao, W., Xiao, J., Bao, Y., Wang, F., Abbasi, A.A., ... & Tang, B. Database Resources of the BIG Data Center in 2019.Nucleic Acids Research. Volume 47, Issue D1, Pages D8–D14

22. 

Ma, L., Cao, J., Liu, L., Li, Z., Shireen, H., Pervaiz, N., Batool, F., Raza, R. Z., Zou, D., Bao, Y., Abbasi, A. A., & Zhang, Z. (2019). Community curation and expert curation of human long noncoding RNAs with LncRNAWiki and LncBook. Current Protocols in Bioinformatics 67(1):82

23.