Dr. Amir Ali Abbasi

Dr. Amir Ali Abbasi

Designation: Professor

National Centre for BioInformatics, Quaid-i-Azam University, Islamabad

Email address: abbasiam@qau.edu.pk

Office Phone: +92-051 9064-4109

Current Position: Visiting Scientist, PIFI Fellow, Chinese Academy of Sciences (CAS), at the Beijing Institute of Genomics and China National Center for Bioinformation (https://www.cncb.ac.cn/?lang=en)

PhD: Philipps University Marburg, Germany
M.Phil: Quaid-i-Azam University, Islamabad
M.Sc: Quaid-i-Azam University, Islamabad (President and Chancellor Gold-Medalist)

Professor of Bioinformatics (Comparative Genomics)

Education

I completed my Secondary (SSC) and Higher Secondary School Certificates (HSSC) in the Science group from The Federal Board of Intermediate & Secondary Education (FBISE),Islamabad. I pursued my Bachelor’s education in Biological Sciences at IMCB H-9, Islamabad, with the degree awarded by Punjab University, Pakistan. I obtained Masters degrees (M.Sc and M.Phil: 1999-2003) in Biochemistry/Molecular Biology from the Department of Biological Sciences at Quaid-i-Azam University, Islamabad, Pakistan. During my academic tenure, I earned recognitions for academic excellence (M.Sc 1999-2001; President and Chancellor Gold Medals), securing the first position across the faculty of Biology and the entire Faculty of Natural Sciences. My M.Phil thesis research, supervised by Prof. Dr. Wasim Ahmad (2001-2003), titled “Linkage Studies of Hearing Impairment Loci in Pakistani Kindreds,” led to my first scientific publication: Dissertation link.

Professional Journey

After completing my academic milestones, I commenced my teaching career at Hazara University, Pakistan (2003-2004). Subsequently, I secured a scholarship funded by HEC Pakistan and DAAD Germany, which facilitated my Ph.D. studies at the Center for Human Genetics, Philipps-Universitt Marburg, under the supervision of Prof. Karl-Heinz Grzeschik (2005-2008). My doctoral research focused on exploring the non-coding cis-regulatory architecture of the human/mammalian Gli3 gene using comparative genomics, transgenic zebrafish/mice models, and in vitro assays in human cell lines. Dissertation link

Upon completing my Ph.D., I joined Quaid-i-Azam University, Islamabad as an Assistant Professor in 2008 at the National Center for Bioinformatics. Over the years, I progressed to the positions of Associate Professor (2015) and Full Professor (2021), leading a dynamic research group focused on functional genomics, molecular phylogenetics, evolutionary developmental biology (evo-devo), and evolutionary genomic medicine. Noteworthy is the establishment of Pakistan’s first Zebrafish facility, aimed at functional genomic assays on human non-coding cis regulatory elements. This facility also serves as a training hub for M.Phil and Ph.D. level scholars in various zebrafish husbandry and breeding techniques. Additionally, the facility is equipped with basic instrumentation relevant to generating transgenic zebrafish embryos and monitoring the reporter gene expression (GFP) under the cis-regulation of human developmental enhancers. My research endeavors have yielded numerous publications in prestigious international journals (the majority as corresponding author) and have successfully supervised both Ph.D. and M.Phil. students. Furthermore, I have secured multiple National and International research grants and established collaborations with various esteemed research groups such as Prof. Axel Visel from DOE Joint Genome Institute; Prof. Neil H. Shubin from the University of Chicago; Prof. Yasuhiko Kawakami from the University of Minnesota, Prof. Yiming Bao from the Beijing Institute of Genomics, and Dr. Muhammad Ali Nawaz from Qatar University.

Other Links:

Database PAHG: https://www.pahgncb.com : http://pahg.qau.edu.pk/

The National Genomics Data Center (NGDC): https://ngdc.cncb.ac.cn/?lang=en

Forebrain enhancers (UCSC Genome Browser; Public track hubs): https://bit.ly/4kQ7rWU

GitHub: https://github.com/abbasiam77

Research Gate: https://www.researchgate.net/profile/Amir_Abbasi3

Google Scholar: https://scholar.google.com/citations?user=t7JMIOEAAAAJ&hl=en

BHBD Alliance: http://bhbd-alliance.org/

Research Interests:-

  Bioinformatics: Comparative and Functional Genomics

Total Publications:-

  1.  Azhar, R., Malik, M. F., Arif, R., Khokhar, M. W., Abbasi, Y. M., Batool, F., Jalalzai, M. H., Bao, Y., & Abbasi, A. A. (2025). PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 74. https://doi.org/10.1186/s12863-025-01361-y
  2. Azhar, R., Malik, M. F., Arif, R., Khokhar, M. W., Abbasi, Y. M., Batool, F., Jalalzai, M. H., Bao, Y., & Abbasi, A. A. (2025). Correction: PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 91. https://doi.org/10.1186/s12863-025-01386-3
  3. Raza, R. Z., Nazir, F. & Abbasi, A. A. (2025). Genetic Foundations of Human Brain Evolution: A Study of IRX3-Associated Human Accelerated Enhancer and the P422L Mutation. Evolutionary Biology. https://doi.org/10.1007/s11692-025-09654-x

  4. 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

  5. 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
  6. Mughal, K.A., Khan, A., Sarwar, A., Mahmood, R., & Abbasi, A. A. Comparative protein structural analyses of ?-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
  7. 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.
  8. 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
  9. 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.
  10. 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.
  11. 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.
  12. Batool, F., Pervaiz, N., Khalid, Q. & & Abbasi, A.A.(2021). Evolution of Human Multigene Families. https://doi.org/10.1002/9780470015902.a0029116.
  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. Development Genes and Evolution. 2021 Mar;231(1-2):21-32.
  14. 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
  15. 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
  16. 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
  17. 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.
  18. Pervaiz, N., Kang, H., Bao, Y., Abbasi, A. A. Molecular evolutionary analysis of human primary microcephaly genes. BMC Ecol Evo 21, 76 (2021).
  19. 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
  20. 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
  21. 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.
  22. 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).
  23. 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
  24. 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.
  25. 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
  26. 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
  27. 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).
  28. 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.
  29. 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.
  30. 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.
  31. 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
  32. Pervaiz, N., & Abbasi, A. A. (2016). Molecular evolution of WDR62, a gene that regulates neocorticogenesis. Meta gene, 9, 1-9.
  33. Siddiqui, I. J., Pervaiz, N., & Abbasi, A. A. (2016). The Parkinson Disease gene SNCA: Evolutionary and structural insights with pathological implication. Scientific reports , 6.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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,
  41. 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.
  42. 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.
  43. 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.
  44. 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).
  45. Abbasi A.A., (2011) Molecular evolution of HR, a gene that regulates the postnatal cycle of the hair follicle. Sci. Rep. 1, 32;
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. Abbasi A.A., (2008) Are we degenerate tetraploids? More genomes, New facts. Biology Direct 3:50.
  52. 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
  53. 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
  54. Abbasi A.A, Grzeschik KH (2007) An insight into the phylogenetic history of HOX linked gene families in vertebrates. BMC Evol Biol 7:239.
  55. 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
  56. 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

Last Five Years Publications

  1.  Azhar, R., Malik, M. F., Arif, R., Khokhar, M. W., Abbasi, Y. M., Batool, F., Jalalzai, M. H., Bao, Y., & Abbasi, A. A. (2025). PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 74. https://doi.org/10.1186/s12863-025-01361-y
  2. Azhar, R., Malik, M. F., Arif, R., Khokhar, M. W., Abbasi, Y. M., Batool, F., Jalalzai, M. H., Bao, Y., & Abbasi, A. A. (2025). Correction: PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 91. https://doi.org/10.1186/s12863-025-01386-3
  3. Raza, R.Z., Nazir, F. & Abbasi, A.A. Genetic Foundations of Human Brain Evolution: A Study of IRX3-Associated Human Accelerated Enhancer and the P422L Mutation. Evol Biol (2025). https://doi.org/10.1007/s11692-025-09654-x
  4. 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
  5. 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
  6. Mughal, K.A., Khan, A., Sarwar, A., Mahmood, R., & Abbasi, A. A. Comparative protein structural analyses of ?-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
  7. 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.
  8. 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
  9. 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), 7588.
  10. 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.
  11. 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 10541058, 2022.
  12. Batool, F., Pervaiz, N., Khalid, Q. & & Abbasi, A.A.(2021). Evolution of Human Multigene Families. https://doi.org/10.1002/9780470015902.a0029116.
  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. Development Genes and Evolution. 2021 Mar;231(1-2):21-32.
  14. 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
  15. 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), D18D28
  16. 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
  17. 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;113.
  18. Pervaiz, N., Kang, H., Bao, Y., Abbasi, A. A. Molecular evolutionary analysis of human primary microcephaly genes. BMC Ecol Evo 21, 76 (2021).
  19. 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
  20. 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
  21. 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, 409419.
  22. 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).
  23. 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
  24. 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.
  25. 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 D8D14
  26. 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
  27. 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).

Subjectwise Publications

Gene Regulation and Vertebrate Evolutionary Development (Evo Devo) 
  1.  Batool, F., Shireen, H., Malik, M. F., Abrar, M., & Abbasi, A. A. The combinatorial binding syntax of transcription factors in forebrain-specific enhancers. Biology Open, 14, bio.061751R1 (2025). 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). DOI
  3. Abrar, M., Ali, S., Hussain, I., Khatoon, H., Batool, F., Ghazanfar, S., Corcoran, D., Kawakami, Y., & Abbasi, A.A. Cis-regulatory control of mammalian Trps1 gene expression. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 342(2), 85-100 (2024).
  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. Identification of ancestral gnathostome Gli3 enhancers with activity in mammals. Development, Growth & Differentiation, 66(1), 75–88 (2023).
  5. Ali, S., Arif, I., Iqbal, I., Hussain, I., Abrar, M., Khan, R. K., Shubin, N., & Abbasi, A.A. Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Developmental Dynamics, 250(5), 669-683 (2020).
  6. Wang, G., Yin, H., Li, B., Abbasi, A.A., & Zhang, Z. Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics. DOI
  7. Ali, S., Amina, B., Anwar, S., Minhas, R., Parveen, N., Nawaz, U., … & Abbasi, A. A. Genomic features of human limb specific enhancers. Genomics, 108(3), 143-150 (2016).
  8. Anwar, S., Minhas, R., Ali, S., Lambert, N., Kawakami, Y., Elgar, G., … & Abbasi, A. A. Identification and functional characterization of novel transcriptional enhancers involved in regulating human GLI3 expression during early development. Development, Growth & Differentiation, 57(8), 570-580 (2015).
  9. Minhas, R., Pauls, S., Ali, S., Doglio, L., Khan, M.R., Elgar, G., and Abbasi, A.A. Cis-regulatory control of human GLI2 expression in the developing neural tube and limb bud. Developmental Dynamics, 244, 681-692 (2015).
  10. Yousaf, A., Raza, M.S., and Abbasi, A.A. The evolution of bony vertebrate enhancers at odds with their coding sequence landscape. Genome Biology and Evolution, evv146 (2015).
  11. Abbasi, A. A., Minhas, R., Schmidt, A., Koch, S. and Grzeschik, K.-H. Cis-regulatory underpinnings of human GLI3 expression in embryonic craniofacial structures and internal organs. Development, Growth & Differentiation, 55(8), 699-709 (2013).
  12. Parveen, N., Masood, A., Iftikhar, N., Minhas, B., Minhas, R., Nawaz, U., & Abbasi, A.A. Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. BMC Genomics, 14(1), 122 (2013).
  13. Abbasi A.A. Evolution of vertebrate appendicular structures: Insight from genetic and palaeontological data. Developmental Dynamics, 240, 1005-1066 (2011).
  14. Abbasi A.A, Paparidis Z, Malik S, Bangs F, Schmidt A, Koch S, Lopez-Rios J, Grzeschik KH Human Intronic Enhancers Control Distinct Sub-domain of Gli3 Expression during Mouse CNS and Limb Development. BMC Developmental Biology, 10:44 (2010).
  15. Abbasi, A. A., Paparidis, Z., Malik, S. M., Weirich, C., & Grzeschik, K. H. Expression patterning in CNS and limb from fish to mammals by GLI3-intronic enhancers. Mechanisms of Development, 126, S209 (2009).
  16. Paparidis Z, Abbasi A.A., Malik S, Goode DK, Callaway H, Elgar G, deGraaff E, Lopez-Rios J, Zeller R, Grzeschik KH Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression. Development Growth & Differentiation, 49, 543-53 (2007).
  17. Abbasi A.A., Paparidis Z, Malik S, Goode DK, Callaway H, Elgar G, Grzeschik KH Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. PLOS ONE, 2:e366 (2007).
Vertebrate Gene/Genome Evolution
1.
Batool, F., Pervaiz, N., Khalid, Q. & Abbasi, A.A. Evolution of Human Multigene Families (2021). DOI
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, 19:128 (2019).
3.
Naz, R., Tahir, S., & Abbasi, A. A. An insight into the evolutionary history of human MHC paralogon. Molecular Phylogenetics and Evolution, 110, 1-6 (2017).
4.
Hafeez, M., Shabbir, M., Altaf, F., and Abbasi, A.A. Phylogenomic analysis reveals ancient segmental duplications in the human genome. Molecular Phylogenetics and Evolution, 94(A), 95-100 (2016).
5.
Abbasi, A. A. 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 (2015).
6.
Ajmal, W., Khan, H., Abbasi, A.A. Phylogenetic investigation of human FGFR-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution. Molecular Phylogenetics and Evolution, 81, 49-60 (2014).
7.
Ambreen S, Khalil F, Abbasi A.A. Integrating large-scale phylogenetic datasets to dissect the ancient evolutionary history of vertebrate genome. Molecular Phylogenetics and Evolution, 78, 1-13 (2014).
8.
Asrar Z, Haq F, Abbasi A.A. Fourfold paralogy regions on human HOX-bearing chromosomes. Molecular Phylogenetics and Evolution, 66(3), 737-747 (2013).
9.
Abbasi A.A, Hanif H Phylogenetic history of paralogous gene quartets on human chromosomes 1, 2, 8 and 20. Molecular Phylogenetics and Evolution, 63, 922-927 (2012).
10.
Abbasi A.A. Piecemeal or big bangs: correlating vertebrate evolution with proposed models of gene expansion events. Nature Reviews Genetics, 11(2), 166 (2010).
11.
Abbasi A.A. Unraveling ancient segmental duplication events in human genome by phylogenetic analysis. Molecular Phylogenetics and Evolution, 57, 836-848 (2010).
12.
Abbasi A.A, Goode DK, Amir S, Grzeschik KH Evolution and functional diversification of the GLI family of transcription factors in vertebrates. Evolutionary Bioinformatics, 5, 5-13 (2009).
13.
Abbasi A.A. Are we degenerate tetraploids? More genomes, new facts. Biology Direct, 3:50 (2008).
14.
Abbasi A.A, Grzeschik KH An insight into the phylogenetic history of HOX linked gene families in vertebrates. BMC Evolutionary Biology, 7:239 (2007).
Molecular/Genomic Basis of Human Evolution
1.
Raza, R.Z., Nazir, F. & Abbasi, A.A. Genetic Foundations of Human Brain Evolution: A Study of IRX3-Associated Human Accelerated Enhancer and the P422L Mutation. Evol Biol (2025). DOI
2.
Hizran Khatoon, Rabail Zehra Raza, Shoaib Saleem, Fatima Batool, Saba Arshad, Muhammad Abrar, Shahid Ali, Irfan Hussain, Neil H. Shubin & Amir Ali Abbasi Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions. Molecular and Cellular Biology, 24, 13 (2023).
3.
Hussain, I., Zehra, R., Ali, S., Abrar, M & Abbasi, A. A. Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers. Development Genes and Evolution, 231(1-2), 21-32 (2021).
4.
Raza R. Z., Ma, L., Zhang, Z., Bao, Y., Abbasi, A. A. Selection trends on nasal-associated SNP variants across human populations. Meta Gene, 28, 100872 (2021).
5.
Pervaiz, N., Kang, H., Bao, Y., Abbasi, A. A. Molecular evolutionary analysis of human primary microcephaly genes. BMC Ecology and Evolution, 21, 76 (2021).
6.
Rabail Zehra, Amir Ali Abbasi 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 (2018).
7.
Pervaiz, N., & Abbasi, A. A. Molecular evolution of WDR62, a gene that regulates neocorticogenesis. Meta Gene, 9, 1-9 (2016).
8.
Abbasi A.A. Molecular evolution of HR, a gene that regulates the postnatal cycle of the hair follicle. Scientific Reports, 1, 32 (2011).
Databases
  1. Azhar, R., Malik, M. F., Arif, R., Khokhar, M. W., Abbasi, Y. M., Batool, F., Jalalzai, M. H., Bao, Y., & Abbasi, A. A. (2025). PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 74. https://doi.org/10.1186/s12863-025-01361-y
  2. Azhar, R., Malik, M. F., Arif, R., Khokhar, M. W., Abbasi, Y. M., Batool, F., Jalalzai, M. H., Bao, Y., & Abbasi, A. A. (2025). Correction: PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 91. https://doi.org/10.1186/s12863-025-01386-3
  3. 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, 21(5), 1054-1058 (2022).
  4. Zou, D., Mehmood, F., Ali, S., Ali, A., Saleem, S., Hussain, I., Abbasi, A. A., Ma, L. Database Resources of the National Genomics Data Center. Nucleic Acids Research, 49(D1), D18-D28 (2021).
  5. Zhang, Z., Ma, L., Abbasi, A.A., … & Gao, F. Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Research, 48(D1), D24-D33 (2020).
  6. 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, 47(D1), D8-D14 (2019).
  7. 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. Community curation and expert curation of human long noncoding RNAs with LncRNAWiki and LncBook. Current Protocols in Bioinformatics, 67(1):82 (2019).
Molecular Evolutionary Basis of Human Infectious Diseases / Darwinian Medicine
1.
Jabeen, M., Shoukat, S., Shireen, H., Bao, Y., Khan, A., & Abbasi, A. A. Unraveling the genetic variations underlying virulence disparities among SARS-CoV-2 strains across global regions: insights from Pakistan. Virology Journal, 21(1), 55 (2024).
2.
Shuhui Song, Cuiping Li, Lu Kang, Dongmei Tian, Bing Zhang, Hua Chen, Yungui Yang, Amir Ali Abbasi, Mingkun Li, Yongbiao Xue, Yiming Bao. Genomic epidemiology of SARS-CoV-2 in Pakistan. Genomics, Proteomics & Bioinformatics (2021). DOI
3.
Abbas Khan, Tauqir Zia, Muhammad Suleman, Taimoor Khan, Syed Shujait Ali, Amir Ali Abbasi, Anwar Mohammad, Dong-Qing Wei. Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants. Journal of Cellular Physiology (2021).
4.
Hussain, I., Pervaiz, N., Khan, A., Saleem, S., Shireen, H., Wei, D-Q., Labrie, V., Bao, Y., & Abbasi, A. A. Evolutionary and structural analysis of SARS-CoV-2 specific evasion of host immunity. Genes & Immunity, 21, 409-419 (2020).
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). DOI
2.
Nawaz, M.S., Asghar, R., Pervaiz, N., Ali, S., Hussain, Irfan., Peiqi, Xing., Bao, Y., & Abbasi, A. A. Molecular evolutionary and structural analysis of human UCHL1 gene. BMC Evolutionary Biology (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. BMC Evolutionary Biology, 19, 72 (2019).
4.
Siddiqui, I. J., Pervaiz, N., & Abbasi, A. A. The Parkinson Disease gene SNCA: Evolutionary and structural insights with pathological implication. Scientific Reports, 6 (2016).
Human Diseases Genetics
1.
Malik S, Abbasi A.A, Ansar M, Ahmad W, Koch MC, Grzeschik KH Genetic heterogeneity of synpolydactyly: a novel locus SPD3 maps to chromosome 14q11.2-q12. Clinical Genetics, 69, 518-24 (2006).
2.
Wajid M, Abbasi A.A, Ansar M, Pham TL, Yan K, Haque S, Ahmad W, Leal SM DFNB39, a recessive form of sensorineural hearing impairment, maps to chromosome 7q11.22-21.12. European Journal of Human Genetics, 11, 812-815 (2003).

Research Supervision: PhD Thesis Supervised

S.No Researcher’s Name Thesis Title Year
1 Fatima Batool Elucidating Fore-brain Specific Human Enhancers Through Heterotypic Interactions Among Transcriptional Factors 2025
2 Huma Shireen Prediction of Human Forebrain Specific Cis-regulatory Modules by Employing Transcription Factors Cooperativity 2025
3 Muhammad Abrar Human TRSP1 Gene: Endogenous Expression and Cis-acting Regulatory Control 2024
4 Hizran Khatoon Elucidating the Events of Transcription Factor Binding in Human Brain Enhancers 2023
5 Irfan Hussain Roles of Vertebrate Gli3 Gene in Brain Development and Evolution 2021
6 Nashaiman Pervaiz Reconstructing the Evolutionary History of Human MCPH Genes and its Implication in Human Brain Size and Intelligence 2019
7 Shahid Ali Elucidation of Cis-acting Regulatory Control for Human GLI Paralogs 2019
8 Rabail Zehra Brain Enhancers and their Role in Distinguishing Human CNS from Non-Human Primates 2018
9 Nazia Parveen Comparative Studies of Gene Regulatory Networks Involved in Brain Development 2016
10 Rashid Minhas Cis-acting Control of Human Developmental Regulator GLI2 2016

Research Supervision: M.Phil Thesis Supervised

S.No Researcher’s Name Thesis Title Year
1 Bushra Fazal Minhas Human CNE-Enhancers and Target Gene Association Through Comparative Syntenic Analysis Across Vertebrates 2011
2 Hafsa Hanif Testing the Validity of Vertebrate Octaploidy Hypothesis by Phylogenetic Re-scrutiny of Proposed Paralogons on Hsa 20(q11-q13), 8(q12-q24), 1(p36-p34) and 2p24/6(q21-q23) 2011
3 Faiza Riaz Characterization of Non-coding Sequence Elements in Tetraodon nigroviridis and Gasterosteus aculeatus through whole genome sequence Comparison 2011
4 Muhammad Azhar Sequence Evolutionary Patterns of the Functionally Defined Human Enhancer Regions 2011
5 Nazia Parveen Defining the Cis-regulatory Networks of Human genes through Comparative Genomic Analysis of Functionally defined CNE-enhancers across tetrapod-teleost Lineages 2012
6 Anam Naz Computationally Predicted Map of Replication Initiation Sites in Human Genome 2012
7 Ayesha Masood Functionally defined Human CNE-enhancers are Associated with their Concerned Genes through Orthology and Paralogy mapping 2012
8 Farhan Haq Molecular Phylogenetic History of Subset of Multi-gene Families with Members Residing on HOX Cluster Paralogons 2012
9 Zainab Asrar Testing the Validity of WGD Hypothesis in the Vertebrates by Phylogenetic Analysis of Gene Families with at least three members Residing on HSA2, HSA7, HSA12, and HSA17 2012
10 Nouman Iftikhar Evolutionary Conserved Syntenic Association of Vertebrate Enhancers and their relevant genes, assists in defining Gene Regulatory Networks in Human Genome 2012
11 Aysha Yousaf Unraveling Evolutionary Patterns of Functionally defined CNEs employing Molecular Phylogenetics 2013
12 Sohail Raza Primate – Specific Impact of Adoptive Evolution of HR Protein 2013
13 Bibi Ameena Deciphering the Regulatory code for Limb Specific CNE Enhancers across Vertebrates by Implying Comparative Genomics Approach 2013
14 Noor Afshan Evolutionary Conserved Cardiac Patterns in the Sequences of Functionally Defined Enhancers 2013
15 Sadaf Ambreen Molecular Phylogenetic Analysis of Multi-gene Families with Members Residing on HOX – cluster Paralogues 2013
16 Faiqa Khalil Testing the Validity of WGD hypothesis in Vertebrates through Phylogenetic Analysis of Multi-gene Families Residing on Human HOX cluster Paralogons 2014
17 Hiba Khan Examining the Authenticity of ‘One–to–Four Model’ in Vertebrates through Phylogenetic Analysis of the Proposed Paralogon; Hsa4, Hsa5, Hsa8 and Hsa10 2014
18 Shahid Ali Elucidating Cis-Acting Regulatory Elements in a Transcriptional Mediator Gene: GLI3 2014
19 Wajya Ajmal Evidence of Ancient Segmental Duplications during Vertebrate Evolution 2014
20 Nashaiman Pervaiz Reconstructing the Evolutionary History of Human WDR62 Gene and its Implication in Human Brain Size and Intelligence 2014
21 Madiha Shabbir Investigating Hypothesis of Vertebrate Genome Duplication through Phylogenetic Analysis of Human Gene Families Residing on FGFR bearing Paralogons 2015
22 Syed Aleem Haider Aging and Longevity in Humans: Functional Annotation of Single Nucleotide Variants in 1000 Genomes 2015
23 Noor us Sehar Elucidating Heterotypic Co-operation of Transcription Factors During Human Forebrain Development 2015
24 Madiha Hafeez Testing the Validity of Vertebrate Whole Genome Duplication Assumption through Molecular Phylogenetic Analysis 2015
25 Fouzia Altaf Insight into Phylogenetic History of Multi-gene Families Residing on Human Paralogon Comprising Hsa 4, 5, 8 and 10 2015
26 Anabia Sohail Molecular Evolution of Mammalian Specific desmoglein Genes 2015
27 Irum Javed Siddiqui Deciphering Evolutionary and Structural Insights of alpha synuclein (SNCA), a Gene Associated with Familial Parkinson’s disease 2015
28 Waqas Khokar Graphical Insight into Evolutionary History of Paralogy Blocks Residing on Vertebrate Genome 2015
29 Amna Farooq Chromosome wide Prediction of Tissue Specific Enhancers Employing Computational and Statistical Approaches 2016
30 Irum Arif Identification of Putative Regulatory Circuit for Human Key Development Gene GLI2 2016
31 Summaira Yasmeen A computational Study to Predict Co-occurring Transcription Factors Binding Sites in Genomic non-Coding DNA of Interest 2016
32 Salma Noreen Annotation of Human Forebrain Specific Cis-acting Gene Regulatory Networks through Comparative Genomic Analysis 2016
33 Sadaf Tahir Testing the Validity of Vertebrate WGD Assumption by Scrutinizing Phylogenetic Histories of Multi-gene Families Residing on Human Paralogon Comprising Hsa 1,6,9, and 19 2016
34 Rozeena Arif Dynamic Framework for Comparative and Interactive Phylogenomic Analysis of Human Paralogy Blocks 2016
35 Roheena Naz Investigating the Polyploidy Hypothesis by Phylogenetic Analysis of Multi-gene Families on MHC Paralogon 2016
36 Ayesha Iqbal Identification of Cis-acting Regulatory Elements in Transcriptional Mediator Gene GLI2 2016
37 Kanwer M. Zeshan Yousaf Functional Analysis of Human Putative Forebrain Enhancer in Transgenic Zebrafish Assay 2017
38 Ayesha Qasim Investigating the Whole Genome Duplication Hypothesis in Vertebrates Through Phylogenomic Analysis of Human Paralogon 1, 2, 8 and 20 2017
39 Nazia Shakeel Phylogenetic Investigation of Paralogy Blocks Residing on Human Chromosome 1, 2 8 and 20 2017
40 Huma Shireen Employing the Transcription Factors Co-operativity in Predicting the Human Forebrain Specific Enhancers 2017
41 Neenish Rana Genome-wide Mapping of Duplication on Human Paralogy Blocks to Infer Their Impact on Vertebrate Evolution 2017
42 Erum Yasmeen Cloning and Functional Analysis of Human GLI3 Specific Putative Enhancer Region 2017
43 Suman Seemab Investigating the Whole Genome Duplications in Vertebrates 2018
44 Qanta Khalid Whole Genome Analysis of Segmentally Duplicated Regions Residing on Human Paralogy Blocks to Scrutinize their Impact on Vertebrate’s Origin 2018
45 Asfia Shahid Prediction of Forebrain Specific Super Enhancers in Human Genome 2018
46 Saima Ghulam Nabi Molecular Evolutionary Basis for the Etiology of Parkinson’s disease 2018
47 Saba Arshad Invitro Validation of Human Forebrain Specific Transcription Factor Motifs 2018
48 Alia Rafique Evolutionary and Structural underpinnings of Neurodegenerative Disease Associated Gene 2018
49 Aniza Aziz Implementation of Phylogenetic features in Client-server Environment Using Multiple Developmental Platforms 2018
50 Raza Muhammad GLI3 Expression Profiling in Zebrafish by Whole Mount in situ Hybridization 2019
51 Sardar Syed Muhammad Junaid Evolutionary and Structural Analysis of Parkinson’s Disease Causing Proteins 2019
52 Farah Nazir Identifying Evolutionary Patterns on Brain Genes Associated with Enhancers 2019
53 Sidra Younas Development of Heuristic Searches for Character-Based Methods of Phylogenetic Inference 2019
54 Mansoor Khan Molecular Phylogenetics of Human EPH Multigene Family 2019
55 Maria Khalid Unveiling of Polymorphism in STRs and SNPs Forensic Markers in Pakhtoon and Gilgit Baltistan Samples 2019
56 Muhammad Saqib Nawaz Phylogenetic and Evolutionary Insight into Parkinson Disease Causing Gene 2019
57 Ayesha Maqsood Molecular Evolution and Structural Insight of CHCHD Gene Family Linked to Neurodegenerative Diseases 2019
58 Saher Musrrat Evolutionary and Phylogenetic Analysis of Human Multigene Families Involved in AD 2019
59 Shoaib Saleem Protein Structure Prediction and Diseased Mutational Analysis of Human Developmentally Important GLI3 Gene 2020
60 Hadiqa Yasmeen PhyloEdit: A Web-based interactive Visualization and Manipulation of Phylogenetic Trees 2020
61 Washaakh Ahmad Computational Prediction of Human Limb Specific Enhancers Utilizing the Transcription Factors Cooperativity 2020
62 Hadia Haider Abbasi Chromosome Wide Prediction of Human Limb Specific Cis- Regulatory Module Employing Computational and Statistical Approaches 2020
63 Raheela Habib Comparative and Structure Analysis of Human-Octopus FZD4 Orthologs 2020
64 Itfa Safdar Prediction and Functional Analysis of Forebrain Specific Enhancers in Zebrafish 2020
65 Rida Mahmood Investigating the phylogenetic and evolutionary aspects of Parkinson’s disease associated genes 2021
66 Amina Sarwar Protein structural and mutational analysis of Parkinson’s disease associated human genes. 2021
67 Kashifa Akhtar Mughal Deciphering the role of SNCA mutants by employing comparative genomics and proteomics approaches 2022
68 Momina Jabeen Evolutionary and structural analysis of SARS-CoV-2 Macrodomains of Pakistan’s Isolates 2022
69 Shifa Shoukat Comparative sequence analysis of SARS-CoV-2 pp1ab of Pakistan’s isolates 2022
70 Aiman Khan Comparative structural modeling of mutants and protein-protein interactions of SNCA 2022
71 Arshiya Qayyum Recruiting Transcription Factor Heterotypic cooperativity to design computational approach for chromosome-wide prediction of human limb-specific enhancers 2022
72 Ramsha Azhar PhyloEasy: A python framework for phylogeny inference and its integration into the PAHG database 2022
73 Aleena Murtaza Comparative analysis and population genetics of human TBX4 associated human limb-specific enhancer 2022
74 Atika khan Functional investigation of human limb specific enhancer in Transgenic zebrafish assay 2023
75 Ayesha Ikram Denovo genome assembly and annotation of Capra Falconeri (Markhor) 2023
76 Jaweria Hafeez Molecular sequence evolutionary analyses of the EGLN1 gene in Capra falconeri (Markhor), a gene involved in high altitude adaptation. 2023
77 Muhammad Faizan Malik Interactive view of 220 human multigene families spread across human genome available at PAHG database 2023
78 Syed Nouman Nasir Genomic variant analysis of SARS-CoV-2 macrodomain from globally sampled population of virus 2023
79 Areej Naveed Abbasi Comparative and Structural Analysis of Parkinson’s disease Associated Human Proteins 2024
80 Sania Mustafa Comparative Sequence and Protein Structural Analysis of Parkinson’s Disease-Causing Genes 2024
81 Noor Afshan Molecular Evolution of EPAS1 Gene in Panthera Uncia 2022
82 Shahab Ahmad Estimation of Genetic Diversity in Markhor Species in Pakistan 2023
83 Ijaz ul Haq Phylogenetic Human History of Multigene Families and Their Relevance to Vertebrate Genome Evolution 2023
84 Muhammad Awais NA 2023
85 Aiza Khan NA 2023
86 Tehmeena Asghar NA 2023
Research Supervision: M.Phil Currently Under Supervision
S.No Researcher’s Name Thesis Title Year
1 Hifsa NA Spring 2023
2 Muqadas NA Fall 2022
3 ABC NAn Spring 2023

Research Projects Completed

Sr. NoProject TitleSponsoring AgencyDuration
1Characterization of non-coding sequence elements in Tetraodon nigroviridis and Gasterosteus aculeatus through whole genome sequence comparisonsHigher Education Commission of Pakistan (No.20-2562/R&D/NRPU/HEC)2015 – 2019
2Elucidation of cis-acting gene regulatory network of human GLI gene paralogs by employing computational and functional approachesHigher Education Commission of Pakistan (No.20-2085/NRPU/R&D/HEC)2014 – 2018
3Estimation of Missing Values for Microarray DataHigher Education Commission of Pakistan (IPFP/HRD/HEC/2012/3544)2012 – 2013
4Identification of human GLI3 gene enhancer regions by reporter expression analysis in zebrafishHigher Education Commission of Pakistan (PM-IPFP/HRD/HEC/2010/1811)2010 – 2011
5The Global Health Big Data Sharing ProgramChinese Academy of Sciences (153F11KYSB20160008)2016 – 2022
6The Global Life Omics Data Sharing ProgramNational Key Research & Development Program of China (2016YFE0206600)2017 – 2022
7The Global Biodiversity and Health Big Data AllianceProfessional Association of the Alliance of International Science Organizations (ANSO-PA-2020-07)2020 – 2022
8The Open Biodiversity and Health Big Data ProgramThe International Union of Biological Sciences (IUBS)2020 – 2022
9German Academic Exchange Service (DAAD) Equipment GrantFederal Ministry for Economic Cooperation and Development (BMZ), Germany (PKZ302969)2017 – 2021

Research Projects in Progress

Sr. NoProject TitlePrincipal InvestigatorSponsoring AgencyDuration
1Generation of Zebrafish Models for BCR-ABL-Induced Leukemogenesis and Development of fast real-time diagnostic assay for Pakistani populationPrincipal InvestigatorPakistan Science Foundation2022 – Continue
2Whole Genome Sequencing and Conservation Genomics of the Pakistani Markhor (Capra falconeri) PopulationPrincipal InvestigatorHEC / NRPU2022 – Continue
3Global Biodiversity and Health Big DataCo-Principal InvestigatorAlliance (Project No. ANSO-PA-2023-07)2023 – Continue

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