Dr. Amir Ali Abbasi

Professor of Bioinformatics (Comparative Genomics)
National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad,
Pakistan

Designation	Professor
Email	abbasiam@qau.edu.pk
Office Phone	+92-051 9064-4109
Research Area	Bioinformatics, comparative genomics, gene regulation, evo-devo, and evolutionary genomic medicine

International Appointment

CAS-PIFI Visiting Scientist
China National Center for Bioinformation / Beijing Institute of Genomics
Chinese Academy of Sciences, Beijing, China
October 2024 – April 2026

CNCB-NGDC:https://ngdc.cncb.ac.cn/?lang=en

Academic Qualifications

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

Education

I completed my Secondary School Certificate (SSC) and Higher Secondary School Certificate (HSSC) in the Science group from the Federal Board of Intermediate and Secondary Education (FBISE), Islamabad. I pursued my Bachelor’s education in Biological Sciences at IMCB H-9, Islamabad, with the degree awarded by the University of the Punjab, Pakistan.I then obtained M.Sc. and M.Phil. degrees (1999–2003) in Biochemistry/Molecular Biology from the Department of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.During this period, I received academic distinctions, including the President and Chancellor Gold Medals for my M.Sc. performance (1999–2001), securing first position across the Faculty of Biological Sciences and the Faculty of Natural Sciences.My M.Phil. thesis research, supervised by Prof. Dr. Wasim Ahmad (2001–2003), was titled “Linkage Studies of Hearing Impairment Loci in Pakistani Kindreds” and led to my first scientific publication.

Professional Journey

After completing my early academic training, I began my teaching career at Hazara University, Pakistan (2003–2004). I subsequently received a scholarship funded by the Higher Education Commission (HEC), Pakistan, and DAAD, Germany, which supported my doctoral studies at the Center for Human Genetics, Philipps University Marburg, Germany, under the supervision of Prof. Karl-Heinz Grzeschik (2005–2008).My doctoral research focused on the non-coding cis-regulatory architecture of the human/mammalian Gli3 gene, using comparative genomics, transgenic zebrafish and mouse models, and in vitro assays in human cell lines.

After completing my PhD, I joined the National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, as an Assistant Professor in 2008. I was later promoted to Associate Professor in 2015 and Full Professor in 2021.Over the years, I have led a research group working at the interface of functional genomics, molecular phylogenetics, evolutionary developmental biology (evo-devo), comparative genomics, and evolutionary genomic medicine.

A major contribution of our group has been the establishment of Pakistan’s first zebrafish facility dedicated to functional genomic assays of human non-coding cis-regulatory elements.This facility also serves as a training platform for M.Phil. and Ph.D. scholars in zebrafish husbandry, breeding, embryo handling, and reporter-based enhancer assays.It is equipped with essential instrumentation for generating transgenic zebrafish embryos and monitoring reporter gene expression, including GFP expression under the cis-regulatory control of human developmental enhancers.

Our research has produced numerous publications in international peer-reviewed journals, with many contributions led from our laboratory.We have also supervised Ph.D. and M.Phil. scholars, secured national and international research grants, and contributed to capacity building in functional genomics and comparative bioinformatics in Pakistan.

Over the years, our research group has established long-term collaborative bonds with several reputed international research teams and institutes working in gene regulation and evo-devo, big data in health sciences, comparative and conservation genomics, human disease genetics, and evolutionary genomic medicine. These collaborations have strengthened our group’s international research profile and created opportunities for joint publications, data-driven resources, training, and scientific exchange.

Selected Research and Resource Links

Database PAHG:https://www.pahgncb.com
PAHG, Quaid-i-Azam University mirror:http://pahg.qau.edu.pk/
National Genomics Data Center (NGDC):https://ngdc.cncb.ac.cn/?lang=en
Forebrain enhancers:https://bit.ly/4kQ7rWU
GitHub:https://github.com/abbasiam77
ResearchGate:https://www.researchgate.net/profile/Amir_Abbasi3
Google Scholar:https://scholar.google.com/citations?user=t7JMIOEAAAAJ&hl=en
BHBD Alliance:http://bhbd-alliance.org/

Brief Profile Summary

Dr. Amir Ali Abbasi is Professor of Bioinformatics at the National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad. His research focuses on comparative genomics, cis-regulatory evolution, functional genomics, evo-devo, molecular phylogenetics, and evolutionary genomic medicine. His group integrates computational and experimental approaches to study gene regulation, non-coding genomic elements, and disease-associated genomic variation.

Research Interests

Bioinformatics: Comparative and Functional Genomics

Total Publications

Document

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). Correction: PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 91. https://doi.org/10.1186/s12863-025-01386-3
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). PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 74. https://doi.org/10.1186/s12863-025-01361-y
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, 52, 182–196. 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(2), BIO061751. https://doi.org/10.1242/bio.061751
5 .	Shireen, H., Batool, F., Khatoon, H., Parveen, N., Sehar, N. U., Hussain, I., Ali, S., & Abbasi, A. A. (2025). Predicting genome-wide tissue-specific enhancers via combinatorial transcription factor genomic occupancy analysis. FEBS Letters, 599, 100–119. https://doi.org/10.1002/1873-3468.15030
6 .	Mughal, K. A., Khan, A., Sarwar, A., et al. and Abbasi, A. A. (2024). 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, 79, 2285–2298. https://doi.org/10.1007/s11756-024-01713-6
7 .	Jabeen, M., Shoukat, S., Shireen, H., et al. and 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, 55. https://doi.org/10.1186/s12985-024-02328-8
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, 342, 85–100. https://doi.org/10.1002/jez.b.23246
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. (2024). Identification of ancestral gnathostome Gli3 enhancers with activity in mammals. Development, Growth & Differentiation, 66(1), 75–88. https://doi.org/10.1111/dgd.12901
10 .	Ma, L., Zou, D., Liu, L., Shireen, H., Abbasi, A. A., Bateman, A., Xiao, J., Zhao, W., Bao, Y., & Abbasi, A. A. (2023). Database Commons: A catalog of worldwide biological databases. Genomics, Proteomics & Bioinformatics, 21(5), 1054–1058. https://doi.org/10.1016/j.gpb.2022.12.004
11 .	Khatoon, H., Raza, R. Z., Saleem, S., et al. and Abbasi, A. A. (2023). Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions. BMC Molecular and Cell Biology, 24, 13. https://doi.org/10.1186/s12860-023-00474-5
12 .	Song, S., Li, C., Kang, L., Tian, D., Badar, N., Ma, W., Zhao, S., Jiang, X., Wang, C., Sun, Y., Li, W., Lei, M., Li, S., Qi, Q., Ikram, A., Salman, M., Umair, M., Shireen, H., Batool, F., Zhang, B., Chen, H., Yang, Y.-G., Abbasi, A. A., Li, M., Xue, Y., & Bao, Y. (2021). Genomic epidemiology of SARS-CoV-2 in Pakistan. Genomics, Proteomics & Bioinformatics, 19(5), 727–740. https://doi.org/10.1016/j.gpb.2021.08.007
13 .	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. https://doi.org/10.1016/j.mgene.2021.100872
14 .	Pervaiz, N., Kang, H., Bao, Y., et al. and Abbasi, A. A. (2021). Molecular evolutionary analysis of human primary microcephaly genes. BMC Ecology and Evolution, 21, 76. https://doi.org/10.1186/s12862-021-01801-0
15 .	Ali, S., Arif, I., Iqbal, A., et al. and Abbasi, A. A. (2021). Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Developmental Dynamics, 250, 669–683. https://doi.org/10.1002/dvdy.291
16 .	Khan, A., Zia, T., Suleman, M., Khan, T., Ali, S. S., Abbasi, A. A., Mohammad, A., & Wei, D. (2021). Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Journal of Cellular Physiology, 236, 7045–7057. https://doi.org/10.1002/jcp.30367
17 .	Hussain, I., Raza, R. Z., Ali, S., et al. and Abbasi, A. A. (2021). Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers. Development Genes and Evolution, 231, 21–32. https://doi.org/10.1007/s00427-021-00672-1
18 .	Yong, X., Yi, B., Zhang, Z., Wen, Z., Jing, X., & Shun, H. (2021). China National Center for Bioinformation in 2021. Nucleic Acids Research, 49(D1), D18–D28. https://doi.org/10.1093/nar/gkaa1022
19 .	Batool, F., Pervaiz, N., Khalid, Q., & Abbasi, A. A. (2021). Evolution of Human Multigene Families. eLS, 2, 1–8. https://doi.org/10.1002/9780470015902.a0029116
20 .	Hussain, I., Pervaiz, N., Khan, A., et al. and Abbasi, A. A. (2020). Evolutionary and structural analysis of SARS-CoV-2 specific evasion of host immunity. Genes and Immunity, 21, 409–419. https://doi.org/10.1038/s41435-020-00120-6
21 .	Nawaz, M. S., Asghar, R., Pervaiz, N., et al. and 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, 20, 130. https://doi.org/10.1186/s12862-020-01684-7
22 .	National Genomics Data Center Members and Partners. Database resources of the National Genomics Data Center in 2020. Nucleic Acids Research, 48(D1), D24–D33. https://doi.org/10.1093/nar/gkz913
23 .	Wang, G., Yin, H., Li, B., Yu, C., Wang, F., Xu, X., Cao, J., Bao, Y., Wang, L., & Abbasi, A. A., Bajic, V. B., Ma, L., Zhang, Z. (2019). Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics, 35(17), 2949–2956. https://doi.org/10.1093/bioinformatics/btz008
24 .	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, e82. https://doi.org/10.1002/cpbi.82
25 .	Pervaiz, N., Shakeel, N., Qasim, A., et al. and Abbasi, A. A. (2019). Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals. BMC Evolutionary Biology, 19, 128. https://doi.org/10.1186/s12862-019-1441-0
26 .	Seemab, S., Pervaiz, N., Zehra, R., et al. and Abbasi, A. A. (2019). Molecular evolutionary and structural analysis of familial exudative vitreoretinopathy associated FZD4 gene. BMC Evolutionary Biology, 19, 72. https://doi.org/10.1186/s12862-019-1400-9
27 .	BIG Data Center Members. Database resources of the BIG Data Center in 2019. Nucleic Acids Research, 47(D1), D8–D14. https://doi.org/10.1093/nar/gky993
28 .	Zehra, R., & Abbasi, A. A. (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. https://doi.org/10.1093/gbe/evy052
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. https://doi.org/10.1016/j.ympev.2017.02.015
30 .	Ali, S., Amina, B., Anwar, S., Minhas, R., Parveen, N., Nawaz, U., Azam, S. S., & Abbasi, A. A. (2016). Genomic features of human limb specific enhancers. Genomics, 108(3–4), 143–150. https://doi.org/10.1016/j.ygeno.2016.08.003
31 .	Pervaiz, N., & Abbasi, A. A. (2016). Molecular evolution of WDR62, a gene that regulates neocorticogenesis. Meta Gene, 9, 1–9. https://doi.org/10.1016/j.mgene.2016.02.005
32 .	Siddiqui, I., Pervaiz, N., & Abbasi, A. A. (2016). The Parkinson Disease gene SNCA: Evolutionary and structural insights with pathological implication. Scientific Reports, 6, 24475. https://doi.org/10.1038/srep24475
33 .	Hafeez, M., Shabbir, M., Altaf, F., & Abbasi, A. A. (2016). Phylogenomic analysis reveals ancient segmental duplications in the human genome. Molecular Phylogenetics and Evolution, 94(Pt A), 95–100. https://doi.org/10.1016/j.ympev.2015.08.019
34 .	Ali, S., et al. Genomic features of human limb specific enhancers. Genomics (2016). http://dx.doi.org/10.1016/j.ygeno.2016.08.003
35 .	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, 353–357. https://doi.org/10.1007/s00427-015-0518-z
36 .	Anwar, S., Minhas, R., Ali, S., Lambert, N., Kawakami, Y., Elgar, G., Azam, S. S., & 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, 570–580. https://doi.org/10.1111/dgd.12239
37 .	Yousaf, A., Raza, M. S., & Abbasi, A. A. (2015). The evolution of bony vertebrate enhancers at odds with their coding sequence landscape. Genome Biology and Evolution, 7(8), 2333–2343. https://doi.org/10.1093/gbe/evv146
38 .	Minhas, R., Pauls, S., Ali, S., Doglio, L., Khan, M. R., Elgar, G., & Abbasi, A. A. (2015). Cis-regulatory control of human GLI2 expression in the developing neural tube and limb bud. Developmental Dynamics, 244, 681–692. https://doi.org/10.1002/dvdy.24266
39 .	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. https://doi.org/10.1016/j.ympev.2014.09.009
40 .	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. https://doi.org/10.1016/j.ympev.2014.05.002
41 .	Abbasi, A. A., Minhas, R., Schmidt, A., Koch, S., & Grzeschik, K.-H. (2013). Cis-regulatory underpinnings of human GLI3 expression in embryonic craniofacial structures and internal organs. Development, Growth & Differentiation, 55, 699–709. https://doi.org/10.1111/dgd.12076
42 .	Asrar, Z., Haq, F., & 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), 737–747. https://doi.org/10.1016/j.ympev.2012.10.024
43 .	Parveen, N., Masood, A., Iftikhar, N., et al. & Abbasi, A. A. (2013). Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. BMC Genomics, 14, 122. https://doi.org/10.1186/1471-2164-14-122
44 .	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(3), 922–927. https://doi.org/10.1016/j.ympev.2012.02.028
45 .	Abbasi, A. A. (2011). Molecular evolution of HR, a gene that regulates the postnatal cycle of the hair follicle. Scientific Reports, 1, 32. https://doi.org/10.1038/srep00032
46 .	Abbasi, A. A. (2011). Evolution of vertebrate appendicular structures: Insight from genetic and palaeontological data. Developmental Dynamics, 240, 1005–1016. https://doi.org/10.1002/dvdy.22572
47 .	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(2), 836–848. https://doi.org/10.1016/j.ympev.2010.07.021
48 .	Abbasi, A. A., Paparidis, Z., Malik, S., et al. (2010). Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development. BMC Developmental Biology, 10, 44. https://doi.org/10.1186/1471-213X-10-44
49 .	Abbasi, A. A. (2010). Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events. Nature Reviews Genetics, 11, 166. https://doi.org/10.1038/nrg2600-c1
50 .	Abbasi, A. A., Paparidis, Z., Malik, S., 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(Supplement), S209. https://doi.org/10.1016/j.mod.2009.06.521
51 .	Abbasi, A. A., Goode, D. K., Amir, S., & Grzeschik, K.-H. (2009). Evolution and functional diversification of the GLI family of transcription factors in vertebrates. Evolutionary Bioinformatics, 5, EBO-S2322. https://doi.org/10.4137/EBO.S2322
52 .	Abbasi, A. A. (2008). Are we degenerate tetraploids? More genomes, new facts. Biology Direct, 3, 50. https://doi.org/10.1186/1745-6150-3-50
53 .	Abbasi, A. A. (2008). GLI genes: Cis-Acting Regulatory Elements. https://doi.org/10.17192/z2008.0410
54 .	Abbasi, A. A., Grzeschik, K.-H. (2007). An insight into the phylogenetic history of HOX linked gene families in vertebrates. BMC Evolutionary Biology, 7, 239. https://doi.org/10.1186/1471-2148-7-239
55 .	Paparidis, Z., Abbasi, A. A., Malik, S., Goode, D. K., Callaway, H., Elgar, G., DeGraaff, E., Lopez-Rios, J., Zeller, R., & Grzeschik, K.-H. (2007). Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression. Development, Growth & Differentiation, 49, 543–553. https://doi.org/10.1111/j.1440-169X.2007.00954.x
56 .	Abbasi, A. A., Paparidis, Z., Malik, S., Goode, D. K., Callaway, H., Elgar, G., & Grzeschik, K.-H. (2007). Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. PLoS ONE, 2(4), e366. https://doi.org/10.1371/journal.pone.0000366
57 .	Malik, S., Abbasi, A. A., Ansar, M., Ahmad, W., Koch, M., & Grzeschik, K.-H. (2006). Genetic heterogeneity of synpolydactyly: a novel locus SPD3 maps to chromosome 14q11.2-q12. Clinical Genetics, 69, 518–524. https://doi.org/10.1111/j.1399-0004.2006.00620.x
58 .	Wajid, M., Abbasi, A. A., Ansar, M., et al. (2003). DFNB39, a recessive form of sensorineural hearing impairment, maps to chromosome 7q11.22–q21.12. European Journal of Human Genetics, 11, 812–815. https://doi.org/10.1038/sj.ejhg.5201041

Last Five Years Publications

Document


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). Correction: PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 91. https://doi.org/10.1186/s12863-025-01386-3
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). PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 74. https://doi.org/10.1186/s12863-025-01361-y
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, 52, 182–196. 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(2), BIO061751. https://doi.org/10.1242/bio.061751
5 .	Shireen, H., Batool, F., Khatoon, H., Parveen, N., Sehar, N. U., Hussain, I., Ali, S., & Abbasi, A. A. (2025). Predicting genome-wide tissue-specific enhancers via combinatorial transcription factor genomic occupancy analysis. FEBS Letters, 599, 100–119. https://doi.org/10.1002/1873-3468.15030
6 .	Mughal, K. A., Khan, A., Sarwar, A., et al. and Abbasi, A. A. (2024). 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, 79, 2285–2298. https://doi.org/10.1007/s11756-024-01713-6
7 .	Jabeen, M., Shoukat, S., Shireen, H., et al. and 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, 55. https://doi.org/10.1186/s12985-024-02328-8
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, 342, 85–100. https://doi.org/10.1002/jez.b.23246
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. (2024). Identification of ancestral gnathostome Gli3 enhancers with activity in mammals. Development, Growth & Differentiation, 66(1), 75–88. https://doi.org/10.1111/dgd.12901
10 .	Ma, L., Zou, D., Liu, L., Shireen, H., Abbasi, A. A., Bateman, A., Xiao, J., Zhao, W., Bao, Y., & Abbasi, A. A. (2023). Database Commons: A catalog of worldwide biological databases. Genomics, Proteomics & Bioinformatics, 21(5), 1054–1058. https://doi.org/10.1016/j.gpb.2022.12.004
11 .	Khatoon, H., Raza, R. Z., Saleem, S., et al. and Abbasi, A. A. (2023). Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions. BMC Molecular and Cell Biology, 24, 13. https://doi.org/10.1186/s12860-023-00474-5
12 .	Song, S., Li, C., Kang, L., Tian, D., Badar, N., Ma, W., Zhao, S., Jiang, X., Wang, C., Sun, Y., Li, W., Lei, M., Li, S., Qi, Q., Ikram, A., Salman, M., Umair, M., Shireen, H., Batool, F., Zhang, B., Chen, H., Yang, Y.-G., Abbasi, A. A., Li, M., Xue, Y., & Bao, Y. (2021). Genomic epidemiology of SARS-CoV-2 in Pakistan. Genomics, Proteomics & Bioinformatics, 19(5), 727–740. https://doi.org/10.1016/j.gpb.2021.08.007
13 .	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. https://doi.org/10.1016/j.mgene.2021.100872
14 .	Pervaiz, N., Kang, H., Bao, Y., et al. and Abbasi, A. A. (2021). Molecular evolutionary analysis of human primary microcephaly genes. BMC Ecology and Evolution, 21, 76. https://doi.org/10.1186/s12862-021-01801-0
15 .	Ali, S., Arif, I., Iqbal, A., et al. and Abbasi, A. A. (2021). Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Developmental Dynamics, 250, 669–683. https://doi.org/10.1002/dvdy.291
16 .	Khan, A., Zia, T., Suleman, M., Khan, T., Ali, S. S., Abbasi, A. A., Mohammad, A., & Wei, D. (2021). Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Journal of Cellular Physiology, 236, 7045–7057. https://doi.org/10.1002/jcp.30367
17 .	Hussain, I., Raza, R. Z., Ali, S., et al. and Abbasi, A. A. (2021). Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers. Development Genes and Evolution, 231, 21–32. https://doi.org/10.1007/s00427-021-00672-1
18 .	Yong, X., Yi, B., Zhang, Z., Wen, Z., Jing, X., & Shun, H. (2021). China National Center for Bioinformation in 2021. Nucleic Acids Research, 49(D1), D18–D28. https://doi.org/10.1093/nar/gkaa1022
19 .	Batool, F., Pervaiz, N., Khalid, Q., & Abbasi, A. A. (2021). Evolution of Human Multigene Families. eLS, 2, 1–8. https://doi.org/10.1002/9780470015902.a0029116

Publications

Subject Wise Publications

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(2), BIO061751. https://doi.org/10.1242/bio.061751
2 .	Shireen, H., Batool, F., Khatoon, H., Parveen, N., Sehar, N. U., Hussain, I., Ali, S., & Abbasi, A. A. (2025). Predicting genome-wide tissue-specific enhancers via combinatorial transcription factor genomic occupancy analysis. FEBS Letters, 599, 100–119. 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, 342, 85–100. https://doi.org/10.1002/jez.b.23246
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. (2024). Identification of ancestral gnathostome Gli3 enhancers with activity in mammals. Development, Growth & Differentiation, 66(1), 75–88. https://doi.org/10.1111/dgd.12901
5 .	Ali, S., Arif, I., Iqbal, A., et al. and Abbasi, A. A. (2021). Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Developmental Dynamics, 250, 669–683. https://doi.org/10.1002/dvdy.291
6 .	Wang, G., Yin, H., Li, B., Yu, C., Wang, F., Xu, X., Cao, J., Bao, Y., Wang, L., & Abbasi, A. A., Bajic, V. B., Ma, L., Zhang, Z. (2019). Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics, 35(17), 2949–2956. https://doi.org/10.1093/bioinformatics/btz008
7 .	Ali, S., Amina, B., Anwar, S., Minhas, R., Parveen, N., Nawaz, U., Azam, S. S., & Abbasi, A. A. (2016). Genomic features of human limb specific enhancers. Genomics, 108(3–4), 143–150. https://doi.org/10.1016/j.ygeno.2016.08.003
8 .	Anwar, S., Minhas, R., Ali, S., Lambert, N., Kawakami, Y., Elgar, G., Azam, S. S., & 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, 570–580. https://doi.org/10.1111/dgd.12239
9 .	Yousaf, A., Raza, M. S., & Abbasi, A. A. (2015). The evolution of bony vertebrate enhancers at odds with their coding sequence landscape. Genome Biology and Evolution, 7(8), 2333–2343. https://doi.org/10.1093/gbe/evv146
10 .	Minhas, R., Pauls, S., Ali, S., Doglio, L., Khan, M. R., Elgar, G., & Abbasi, A. A. (2015). Cis-regulatory control of human GLI2 expression in the developing neural tube and limb bud. Developmental Dynamics, 244, 681–692. https://doi.org/10.1002/dvdy.24266
11 .	Abbasi, A. A., Minhas, R., Schmidt, A., Koch, S., & Grzeschik, K.-H. (2013). Cis-regulatory underpinnings of human GLI3 expression in embryonic craniofacial structures and internal organs. Development, Growth & Differentiation, 55, 699–709. https://doi.org/10.1111/dgd.12076
12 .	Parveen, N., Masood, A., Iftikhar, N., et al. & Abbasi, A. A. (2013). Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. BMC Genomics, 14, 122. https://doi.org/10.1186/1471-2164-14-122
13 .	Abbasi, A. A. (2011). Evolution of vertebrate appendicular structures: Insight from genetic and palaeontological data. Developmental Dynamics, 240, 1005–1016. https://doi.org/10.1002/dvdy.22572
14 .	Abbasi, A. A., Paparidis, Z., Malik, S., et al. (2010). Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development. BMC Developmental Biology, 10, 44. https://doi.org/10.1186/1471-213X-10-44
15 .	Abbasi, A. A., Paparidis, Z., Malik, S., 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(Supplement), S209. https://doi.org/10.1016/j.mod.2009.06.521
16 .	Paparidis, Z., Abbasi, A. A., Malik, S., Goode, D. K., Callaway, H., Elgar, G., DeGraaff, E., Lopez-Rios, J., Zeller, R., & Grzeschik, K.-H. (2007). Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression. Development, Growth & Differentiation, 49, 543–553. https://doi.org/10.1111/j.1440-169X.2007.00954.x

Vertebrate Gene/Genome Evolution

1 .	Batool, F., Pervaiz, N., Khalid, Q., & Abbasi, A. A. (2021). Evolution of Human Multigene Families. eLS, 2, 1–8. https://doi.org/10.1002/9780470015902.a0029116
2 .	Pervaiz, N., Shakeel, N., Qasim, A., et al. and Abbasi, A. A. (2019). Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals. BMC Evolutionary Biology, 19, 128. https://doi.org/10.1186/s12862-019-1441-0
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. https://doi.org/10.1016/j.ympev.2017.02.015
4 .	Hafeez, M., Shabbir, M., Altaf, F., & Abbasi, A. A. (2016). Phylogenomic analysis reveals ancient segmental duplications in the human genome. Molecular Phylogenetics and Evolution, 94(Pt A), 95–100. https://doi.org/10.1016/j.ympev.2015.08.019
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, 353–357. https://doi.org/10.1007/s00427-015-0518-z
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. https://doi.org/10.1016/j.ympev.2014.09.009
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. https://doi.org/10.1016/j.ympev.2014.05.002
8 .	Asrar, Z., Haq, F., & 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), 737–747. https://doi.org/10.1016/j.ympev.2012.10.024
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(3), 922–927. https://doi.org/10.1016/j.ympev.2012.02.028
10 .	Abbasi, A. A. (2010). Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events. Nature Reviews Genetics, 11, 166. https://doi.org/10.1038/nrg2600-c1
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(2), 836–848. https://doi.org/10.1016/j.ympev.2010.07.021
12 .	Abbasi, A. A., Goode, D. K., Amir, S., & Grzeschik, K.-H. (2009). Evolution and functional diversification of the GLI family of transcription factors in vertebrates. Evolutionary Bioinformatics, 5, EBO-S2322. https://doi.org/10.4137/EBO.S2322
13 .	Abbasi, A. A. (2008). Are we degenerate tetraploids? More genomes, new facts. Biology Direct, 3, 50. https://doi.org/10.1186/1745-6150-3-50
14 .	Abbasi, A. A., Grzeschik, K.-H. (2007). An insight into the phylogenetic history of HOX linked gene families in vertebrates. BMC Evolutionary Biology, 7, 239. https://doi.org/10.1186/1471-2148-7-239

Molecular/Genetic Basis of Human Evolution

1 .	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, 52, 182–196. https://doi.org/10.1007/s11692-025-09654-x
2 .	Khatoon, H., Raza, R. Z., Saleem, S., et al. and Abbasi, A. A. (2023). Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions. BMC Molecular and Cell Biology, 24, 13. https://doi.org/10.1186/s12860-023-00474-5
3 .	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. https://doi.org/10.1016/j.mgene.2021.100872
4 .	Hussain, I., Raza, R. Z., Ali, S., et al. and Abbasi, A. A. (2021). Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers. Development Genes and Evolution, 231, 21–32. https://doi.org/10.1007/s00427-021-00672-1
5 .	Pervaiz, N., Kang, H., Bao, Y., et al. and Abbasi, A. A. (2021). Molecular evolutionary analysis of human primary microcephaly genes. BMC Ecology and Evolution, 21, 76. https://doi.org/10.1186/s12862-021-01801-0
6 .	Zehra, R., & Abbasi, A. A. (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. https://doi.org/10.1093/gbe/evy052
7 .	Pervaiz, N., & Abbasi, A. A. (2016). Molecular evolution of WDR62, a gene that regulates neocorticogenesis. Meta Gene, 9, 1–9. https://doi.org/10.1016/j.mgene.2016.02.005
8 .	Abbasi, A. A. (2011). Molecular evolution of HR, a gene that regulates the postnatal cycle of the hair follicle. Scientific Reports, 1, 32. https://doi.org/10.1038/srep00032

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). Correction: PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 91. https://doi.org/10.1186/s12863-025-01386-3
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). PAHG: the database of human multi-gene families. BMC Genomic Data, 26(1), 74. https://doi.org/10.1186/s12863-025-01361-y
3 .	Ma, L., Zou, D., Liu, L., Shireen, H., Abbasi, A. A., Bateman, A., Xiao, J., Zhao, W., Bao, Y., & Abbasi, A. A. (2023). Database Commons: A catalog of worldwide biological databases. Genomics, Proteomics & Bioinformatics, 21(5), 1054–1058. https://doi.org/10.1016/j.gpb.2022.12.004
4 .	Yong, X., Yi, B., Zhang, Z., Wen, Z., Jing, X., & Shun, H. (2021). China National Center for Bioinformation in 2021. Nucleic Acids Research, 49(D1), D18–D28. https://doi.org/10.1093/nar/gkaa1022
5 .	National Genomics Data Center Members and Partners. Database resources of the National Genomics Data Center in 2020. Nucleic Acids Research, 48(D1), D24–D33. https://doi.org/10.1093/nar/gkz913
6 .	Wang, G., Yin, H., Li, B., Yu, C., Wang, F., Xu, X., Cao, J., Bao, Y., Wang, L., & Abbasi, A. A., Bajic, V. B., Ma, L., Zhang, Z. (2019). Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics, 35(17), 2949–2956. https://doi.org/10.1093/bioinformatics/btz008
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. (2019). Community curation and expert curation of human long noncoding RNAs with LncRNAWiki and LncBook. Current Protocols in Bioinformatics, 67, e82. https://doi.org/10.1002/cpbi.82

Molecular Evolutionary Basis of Human Infectious Diseases/Darwinian Medicine

1 .	Jabeen, M., Shoukat, S., Shireen, H., et al. and 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, 55. https://doi.org/10.1186/s12985-024-02328-8
2 .	Song, S., Li, C., Kang, L., Tian, D., Badar, N., Ma, W., Zhao, S., Jiang, X., Wang, C., Sun, Y., Li, W., Lei, M., Li, S., Qi, Q., Ikram, A., Salman, M., Umair, M., Shireen, H., Batool, F., Zhang, B., Chen, H., Yang, Y.-G., Abbasi, A. A., Li, M., Xue, Y., & Bao, Y. (2021). Genomic epidemiology of SARS-CoV-2 in Pakistan. Genomics, Proteomics & Bioinformatics, 19(5), 727–740. https://doi.org/10.1016/j.gpb.2021.08.007
3 .	Khan, A., Zia, T., Suleman, M., Khan, T., Ali, S. S., Abbasi, A. A., Mohammad, A., & Wei, D. (2021). Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Journal of Cellular Physiology, 236, 7045–7057. https://doi.org/10.1002/jcp.30367
4 .	Hussain, I., Pervaiz, N., Khan, A., et al. and Abbasi, A. A. (2020). Evolutionary and structural analysis of SARS-CoV-2 specific evasion of host immunity. Genes and Immunity, 21, 409–419. https://doi.org/10.1038/s41435-020-00120-6

Molecular Evolutionary Basis of Neurological Disorders/Darwinian Medicine

1 .	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, 52, 182–196. https://doi.org/10.1007/s11692-025-09654-x
2 .	Mughal, K. A., Khan, A., Sarwar, A., et al. and Abbasi, A. A. (2024). 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, 79, 2285–2298. https://doi.org/10.1007/s11756-024-01713-6
3 .	Nawaz, M. S., Asghar, R., Pervaiz, N., et al. and 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, 20, 130. https://doi.org/10.1186/s12862-020-01684-7
4 .	Seemab, S., Pervaiz, N., Zehra, R., et al. and Abbasi, A. A. (2019). Molecular evolutionary and structural analysis of familial exudative vitreoretinopathy associated FZD4 gene. BMC Evolutionary Biology, 19, 72. https://doi.org/10.1186/s12862-019-1400-9
5 .	Siddiqui, I., Pervaiz, N., & Abbasi, A. A. (2016). The Parkinson Disease gene SNCA: Evolutionary and structural insights with pathological implication. Scientific Reports, 6, 24475. https://doi.org/10.1038/srep24475

Clinical Genetics

1 .	Malik, S., Abbasi, A. A., Ansar, M., Ahmad, W., Koch, M., & Grzeschik, K.-H. (2006). Genetic heterogeneity of synpolydactyly: a novel locus SPD3 maps to chromosome 14q11.2-q12. Clinical Genetics, 69, 518–524. https://doi.org/10.1111/j.1399-0004.2006.00620.x
2 .	Wajid, M., Abbasi, A. A., Ansar, M., et al. (2003). DFNB39, a recessive form of sensorineural hearing impairment, maps to chromosome 7q11.22–q21.12. European Journal of Human Genetics, 11, 812–815. https://doi.org/10.1038/sj.ejhg.5201041

Research Supervision: PhD Thesis Supervised

S.No	Student’s Name	Thesis title	Completion 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: PhD candidates under supervision

S.No	Student’s Name	Thesis title	Year enrolled
1	Mohsin Majeed	In Progress	Fall 2025

M.Phil Thesis Supervised

Research Supervision: M. Phil Thesis Supervised

S.No	Student 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	Human 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: AWeb-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 (HIF2a) in panthera uncia (snow leopard), a gene involved in High altitude adaptation	2024
82	Ijazul Haq	Phylogenetic History of Human Multigene Families and Their Relevance to Vertebrate Genome Evolution	2025
83	Shahab Ahmad	Estimation of Genetic Diversity in Markhor Species in Pakistan Using Standard Microsatellite, Exome and Mitochondrial Genetic Markers	2025
84	Tehmeena Asghar	Comparative Structural Analysis of Protein Encoded by Human PHC 1 Gene Associated with Primary Microcephaly-11, a Disease Condition Resulting in Reduced Brain Size	2025
85	Muhammad Shoaib Khan	Phylogenetic Analysis of Human Multigene Families to Test the Validity of the Vertebrate Whole Genome Duplication Hypothesis	2025
86	Izza Khan	Molecular Evolutionary Sequence Analysis of the Human PHC1 Gene Associated with Primary Microcephaly-11, A Disease Condition Resulting in Reduced Brain Size	2025
87	Muhammad Awais	Genetic diversity analysis of Capra falocneri (Markhor) in Pakistan based on exonic DNA, mitochondrial DNA, and microsatellite markers	2025
88	Hina Iqbal	Molecular Sequence and Protein Structural Analysis of Human SLC25A19 Gene Associated with Microcephaly and Evolutionary Brain Enlargement	2026

Research Supervision: M.Phil Currently Under Supervision

S.No	Researcher’s Name	Thesis Title	Year
1	Hifsa	Elucidating Gene Duplication Mechanisms and Evolutionary Trajectories of Selected Multigene Families Through Comparative Phylogenomic Approaches	Fall 2024
2	Muqadas	Molecular Phylogenetic Investigation of Human Multigene Families to Elucidate the Mechanisms Shaping Vertebrates Genome Evolution	Fall 2024

Research Projects Completed

Total Projects: 9

S.No	Project Title	Sponsoring Agency	Duration
1	CAS-PIFI Visiting Scientist Fellowship at CNCB–Beijing	Chinese Academy of Sciences (P2025PVA0027_Y1 and 2025PVA0027_Y)	Oct 2024 - April 2026
2	The Global Biodiversity and Health Big Data Alliance	Professional Association of the Alliance of International Science Organizations (ANSO-PA-2020-07)	2020 - 2022
3	The Open Biodiversity and Health Big Data Program	The International Union of Biological Sciences (IUBS)	2020 - 2022
4	The Global Life Omics Data Sharing Program	National Key Research & Development Program of China (2016YFE0206600)	2017 - 2022
5	The Global Health Big Data Sharing Program	Chinese Academy of Sciences (153F11KYSB20160008)	2016 - 2022
6	Characterization of non-coding sequence elements in Tetraodon nigroviridis and Gasterosteus aculeatus through whole genome sequence comparisons	Higher Education Commission of Pakistan (No.20-2562/R&D/NRPU/HEC)	2015 - 2019
7	Elucidation of cis-acting gene regulatory network of human GLI gene paralogs by employing computational and functional approaches	Higher Education Commission of Pakistan (No.20-2085/NRPU/R&D/HEC)	2014 - 2018
8	Estimation of Missing Values for Microarray Data	Higher Education Commission of Pakistan (IPFP/HRD/HEC/2012/3544)	2012 - 2013
9	Identification of human GLI3 gene enhancer regions by reporter expression analysis in zebrafish	Higher Education Commission of Pakistan (PM-IPFP/HRD/HEC/2010/1811)	2010 - 2011

Research Projects in Progress

S.No	Project Title	Principal Investigator	Sponsoring Agency	Duration
1	Markhor Genome Sequencing and Phylogenetics	Principal Investigator	Snow Leopard Foundation	2024 – Continue
2	Global Biodiversity and Health Big Data	Co-Principal Investigator	Alliance (Project No. ANSO-PA-2023-07)	2023 – Continue
3	Generation of Zebrafish Models for BCR-ABL-Induced Leukemogenesis and Development of Fast and Robust Real-Time Assay for its Diagnosis and Mutation Detection Based to Pakistani Population	Principal Investigator	Pakistan Science Foundation (PSF/Res/C-QU/Biotech 241)	2022 – Continue
4	Whole Genome Sequencing and Conservation Genomics of the Pakistani Markhor (Capra falconeri) Population	Principal Investigator	HEC/NRPU (Project No. 14888)	2022 – Continue