Gene Regulation and Vertebrate Evolutionary Development (Evo Devo)

1.

Batool, F., Shireen, H., Malik, M. F., Abrar, M., & Abbasi, A. A. (2025). The combinatorial binding syntax of transcription factors in forebrain-specific enhancers. Biology Open, 14, bio.061751R1. DOI: 10.1242/bio.061751

2.

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

3. 

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

4. 

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. 

5. 

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

6.

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

7.

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.

8.

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.

9.

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.

10. 

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.

11.

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,

12.

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.  

13.

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).

14.

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.

15.

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.

16.

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

17.

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

Vertebrate Gene/Genome Evolution

1.

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

2.

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.

3.

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.

4.

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. Volume 94, Part A, Pages 95-100 

5.

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.  

6.

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.

7.

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. 

8.

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. 

9.

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. 

10.

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.  

11.

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.

12.

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. 

13.

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

14.

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

Molecular/Genomic Basis of Human Evolution

1.

2.

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. 

3.

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

4.

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 

5. 

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

6.

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.

7.

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

8.

Abbasi A.A., (2011) Molecular evolution of HR, a gene that regulates the postnatal cycle of the hair follicle. Sci. Rep. 1, 32; 

Databases

1.

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. 

2. 

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

3. 

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

4.

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

5. 

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

Molecular Evolutionary Basis of Human Infectious Diseases/Darwinian Medicine

1.

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.

2.

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

3.

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.

4. 

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.

Molecular Evolutionary Basis of Neurological Disorders/Darwinian Medicine

1. 

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

2. 

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).

3.

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 19, 72 (2019).

4.

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

Human Diseases Genetics

1.

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

2.

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