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. 

https://doi.org/10.1101/2021.06.24.21255875

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. 2022. https://doi.org/10.1016/j.gpb.2022.12.004

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. BMC Mol and Cell Biol 24, 13 . https://doi.org/10.1186/s12860-023-00474-5

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. DOI: https://doi.org/10.1002/jcp.30367. J Cell Physiol. 2021;1–13.

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. DOI: 10.1007/s00427-021-00672-1. Development Genes and Evolution.*Corresponding Author

Raza R. Z., Ma, L., Zhang, Z., Bao, Y., Abbasi ,A. A., (2021) Selection trends on nasal-associated SNP variants across human populations https://doi.org/10.1016/j.mgene.2021.100872 Meta Gene, 28, 100872

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.doi: 10.1093/nar/gkaa1022 Nucleic Acids Research, 49(DI), D18–D28

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. DOI: 10.1002/dvdy.291.Developmental Dynamics.*Corresponding Author

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. *Corresponding Author

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). *Corresponding Author

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

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. (2019) 19:128. BMC Evolutionary Biology

Seemab, S., Pervaiz, N., Zehra, R., Anwar, S.,Yiming Bao & Abbasi, A.A. Molecular evolutionary and structural analysis of familial exudative vitreoretinopathy associated FZD4 gene. (2019) 19:72. BMC Evolutionary Biology

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. 67, e82. doi: 10.1002/cpbi.82. Current Protocols in Bioinformatics

Wang, G., Yin, H., Li, B., Abbasi, A.A., … & Zhang, Z. (2019). Characterization and identification of long non-coding RNAs based on feature relationship. doi: 10.1093/bioinformatics/btz008. Bioinformatics

Zhang, Z., Zhao, W., Xiao, J., Bao, Y., Wang, F., Abbasi, A.A*., ... & Tang, B. Database Resources of the BIG Data Center in 2019. doi:10.1093/nar/gky993.2019. Nucleic Acids Research.

Rabail Zehra, Amir Ali Abbasi (2018). Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population. Genome Biology and Evolution, 10 (3), 956-966.

Naz, R., Tahir, S., & Abbasi, A. A. (2017). An insight into the evolutionary history of human MHC paralogon. Molecular Phylogenetics and Evolution, 110, 1-6.

Ali, S., Amina, B., Anwar, S., Minhas, R., Parveen, N., Nawaz, U., ... & Abbasi, A. A. (2016). Genomic features of human limb specific enhancers. Genomics, 108(3), 143-150.

Siddiqui, I. J., Pervaiz, N., & Abbasi, A. A*. (2016). The Parkinson Disease gene SNCA: Evolutionary and structural insights with pathological implication. Scientific reports, 6. *Corresponding Author 

Pervaiz, N., & Abbasi, A. A*. (2016). Molecular evolution of WDR62, a gene that regulates neocorticogenesis. Meta gene, 9, 1-9. *Corresponding Author

Hafeez, M., Shabbir, M., Altaf, F., and Abbasi, A.A*. (2016). Phylogenomic analysis reveals ancient segmental duplications in the human genome. Molecular Phylogenetics and Evolution. doi:10.1016/j.ympev.2016 *Corresponding Author

Abbasi, A. A. (2015). Diversification of four human HOX gene clusters by step-wise evolution rather than ancient whole-genome duplications. Development genes and evolution, 225(6), 353-357. 

Anwar, S., Minhas, R., Ali, S., Lambert, N., Kawakami, Y., Elgar, G., ... & Abbasi, A. A*. (2015). Identification and functional characterization of novel transcriptional enhancers involved in regulating human GLI3 expression during early development. Development, growth & differentiation, 57(8), 570-580. *Corresponding Author

Minhas, R., Pauls, S., Ali, S., Doglio, L., Khan, M.R., Elgar, G., and Abbasi, A.A*. (2015). Cis-regulatory control of human GLI2 expression in the developing neural tube and limb bud. Developmental Dynamics.  244, 681-692. *Corresponding Author

Yousaf, A., Raza, M.S., and Abbasi, A.A*. (2015). The evolution of bony vertebrate enhancers at odds with their coding sequence landscape. Genome Biology and Evolution. evv146. *Corresponding Author

Ajmal, W., Khan, H., Abbasi, A.A*., (2014). Phylogenetic investigation of human FGFR-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution. Molecular Phylogenetics and Evolution. 81, 49-60. *Corresponding Author

Ambreen S , Khalil F ,  Abbasi A.A*. (2014). Integrating large-scale phylogenetic datasets to dissect the ancient evolutionary history of vertebrate genome. Molecular Phylogenetics and Evolution. 78: 1-13. Corresponding Author*

Abbasi, A. A., Minhas, R., Schmidt, A., Koch, S. and Grzeschik, K.-H. (2013), Cis-regulatory underpinnings of human GLI3 expression in embryonic craniofacial structures and internal organs. Development, Growth & Differentiation. 55(8):699-709, *Corresponding Author

Parveen, N., Masood, A., Iftikhar, N., Minhas, B., Minhas, R., Nawaz, U., & Abbasi, A.A*. (2013). Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. BMC Genomics, 14(1), 122. *Corresponding Author

Asrar Z ,HaqF, Abbasi A.A*. (2013). Fourfold paralogy regions on human HOX-bearing chromosomes: Role of ancient segmental duplications in the evolution of vertebrate genome, Molecular Phylogenetics and Evolution. 66(3), Pages 737–747. *Corresponding Author

Abbasi A.A*, Hanif H (2012). Phylogenetic history of paralogous gene quartets on human chromosomes 1, 2, 8 and 20 provides no evidence in favor of the vertebrate octoploidy hypothesis. Molecular Phylogenetics and Evolution. 63:922-927. *Corresponding Author

Abbasi A.A.*, (2011) Molecular evolution of HR, a gene that regulates the postnatal cycle of the hair follicle. Sci. Rep. 1, 32; DOI:10.1038/srep00032. *Corresponding Author

Abbasi A.A.*, (2011) Evolution of vertebrate appendicular structures: Insight from genetic and palaeontological data.Developmental Dynamics, 240:1005-1066. (Special issue on limb development). *Corresponding Author

Abbasi A.A.*, (2010) Unraveling ancient segmental duplication events in human genome by phylogenetic analysis of multigene families residing on HOX cluster paralogons. Molecular Phylogenetics and Evolution., 57: 836-848.*Corresponding Author

Abbasi A.A*, Paparidis Z, Malik S, Bangs F, Schmidt A, Koch S, Lopez-Rios J, Grzeschik KH (2010): Human Intronic Enhancers Control Distinct Sub-domain of Gli3 Expression during Mouse CNS and Limb Development. BMC Developmental Biology. 2010, 10:44. (Highly accessed) .*Corresponding Author

Abbasi A.A.*, (2010) Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events. Nat Rev Genet 11(2):166. *Corresponding Author

Abbasi A.A*, Goode DK, Amir S, Grzeschik KH (2009). Evolution and functional diversification of the GLI family of transcription factors in vertebrates. Evolutionary Bioinformatics 5: 5-13. *Corresponding Author

Abbasi, A. A., Paparidis, Z., Malik, S. M., Weirich, C., & Grzeschik, K. H. (2009). 13- P048  Expression patterning in CNS and limb from fish to mammals by GLI3-intronic enhancers. Mechanisms of Development, 126, S209.

Abbasi A.A*., (2008) Are we degenerate tetraploids? More genomes, New facts. Biology Direct 3:50 (Highly accessed).*Corresponding Author

Abbasi A.A*, Grzeschik KH (2007) An insight into the phylogenetic history of HOX linked gene families in vertebrates. BMC Evol Biol 7:239. *Corresponding Author

Abbasi A.A., Paparidis Z, Malik S, Goode DK, Callaway H, Elgar G, Grzeschik KH (2007) Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. PLoS ONE 2:e366

Paparidis Z, Abbasi A.A., Malik S, Goode DK, Callaway H, Elgar G, deGraaff E, Lopez-Rios J, Zeller R, Grzeschik KH (2007)Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression. Dev Growth Differ 49:543-53

Malik S, Abbasi A.A, Ansar M, Ahmad W, Koch MC, Grzeschik KH (2006) Genetic heterogeneity of synpolydactyly: a novel locus SPD3 maps to chromosome 14q11.2-q12. Clin Genet 69:518-24

Wajid M, Abbasi A.A, Ansar M, Pham TL, Yan K, Haque S, Ahmad W, Leal SM (2003) DFNB39, a recessive form of sensorineural hearing impairment, maps to chromosome 7q11.22-21.12. Eur J Hum Genet 11:812-5