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

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

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

Document

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	Year enrolled
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

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	2011
3	Faiza Riaz	Characterization of Non-coding Sequence Elements in Tetraodon nigroviridis	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	2012
6	Anam Naz	Computationally Predicted Map of Replication Initiation Sites in Human Genome	2012
7	Ayesha Masood	Functionally defined Human CNE-enhancers	2012
8	Farhan Haq	Molecular Phylogenetic History of Subset of Multi-gene Families	2012
9	Zainab Asrar	Testing the Validity of WGD Hypothesis in Vertebrates	2012
10	Nouman Iftikhar	Evolutionary Conserved Syntenic Association	2012
11	Aysha Yousaf	Unraveling Evolutionary Patterns of Functionally defined CNEs	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	2013
14	Noor Afshan	Evolutionary Conserved Cardiac Patterns	2013
15	Sadaf Ambreen	Molecular Phylogenetic Analysis of Multi-gene Families	2013
16	Faiqa Khalil	Testing the Validity of WGD hypothesis in Vertebrates	2014
17	Hiba Khan	Examining the Authenticity of One-to-Four Model	2014
18	Shahid Ali	Elucidating Cis-Acting Regulatory Elements in GLI3	2014
19	Wajya Ajmal	Evidence of Ancient Segmental Duplications	2014
20	Nashaiman Pervaiz	Evolutionary History of Human WDR62 Gene	2014
21	Madiha Shabbir	Genome Duplication through Phylogenetic Analysis	2015
22	Syed Aleem Haider	Aging and Longevity in Humans	2015
23	Noor us Sehar	Heterotypic Co-operation of Transcription Factors	2015
24	Madiha Hafeez	Testing Vertebrate Whole Genome Duplication	2015
25	Fouzia Altaf	Phylogenetic History of Multi-gene Families	2015
26	Anabia Sohail	Molecular Evolution of Mammalian desmoglein Genes	2015
27	Irum Javed Siddiqui	Evolutionary and Structural Insights of alpha synuclein	2015
28	Waqas Khokar	Graphical Insight into Evolutionary History	2015
29	Amna Farooq	Prediction of Tissue Specific Enhancers	2016
30	Irum Arif	Identification of Putative Regulatory Circuit for GLI2	2016
31	Summaira Yasmeen	Predict Co-occurring Transcription Factors	2016
32	Salma Noreen	Annotation of Human Forebrain Specific Networks	2016
33	Sadaf Tahir	Testing the Validity of Vertebrate WGD	2016
34	Rozeena Arif	Comparative and Interactive Phylogenomic Analysis	2016
35	Roheena Naz	Investigating the Polyploidy Hypothesis	2016
36	Ayesha Iqbal	Identification of Cis-acting Regulatory Elements	2016
37	Kanwer M.Zeshan Yousaf	Functional Analysis in Transgenic Zebrafish	2017
38	Ayesha Qasim	Investigating Whole Genome Duplication	2017
39	Nazia Shakeel	Phylogenetic Investigation of Paralogy Blocks	2017
40	Human Shireen	Predicting Human Forebrain Specific Enhancers	2017
41	Neenish Rana	Genome-wide Mapping of Duplication	2017
42	Erum Yasmeen	Functional Analysis of Human GLI3	2017
43	Suman Seemab	Investigating Whole Genome Duplications	2018
44	Qanta Khalid	Whole Genome Analysis of Segmentally Duplicated Regions	2018
45	Asfia Shahid	Prediction of Forebrain Specific Super Enhancers	2018
46	Saima Ghulam Nabi	Molecular Evolutionary Basis for Parkinson’s disease	2018
47	Saba Arshad	Validation of Human Forebrain Specific Motifs	2018
48	Alia Rafique	Evolutionary and Structural underpinnings	2018
49	Aniza Aziz	Implementation of Phylogenetic features	2018
50	Raza Muhammad	GLI3 Expression Profiling in Zebrafish	2019
51	Sardar Syed Muhammad Junaid	Evolutionary and Structural Analysis	2019
52	Farah Nazir	Identifying Evolutionary Patterns	2019
53	Sidra Younas	Development of Heuristic Searches	2019
54	Mansoor Khan	Molecular Phylogenetics of Human EPH	2019
55	Maria Khalid	Polymorphism in STRs and SNPs	2019
56	Muhammad Saqib Nawaz	Evolutionary Insight into Parkinson Disease	2019
57	Ayesha Maqsood	Molecular Evolution and Structural Insight	2019
58	Saher Musrrat	Evolutionary and Phylogenetic Analysis	2019
59	Shoaib Saleem	Protein Structure Prediction	2020
60	Hadiqa Yasmeen	PhyloEdit: Web-based Visualization	2020
61	Washaakh Ahmad	Prediction of Human Limb Specific Enhancers	2020
62	Hadia Haider Abbasi	Prediction of Human Limb Specific Modules	2020
63	Raheela Habib	Comparative and Structure Analysis	2020
64	Itfa Safdar	Prediction and Functional Analysis	2020
65	Rida Mahmood	Phylogenetic and evolutionary aspects	2021
66	Amina Sarwar	Protein structural and mutational analysis	2021
67	Kashifa Akhtar Mughal	Role of SNCA mutants	2022
68	Momina Jabeen	Evolutionary and structural analysis of SARS-CoV-2	2022
69	Shifa Shoukat	Comparative sequence analysis of SARS-CoV-2	2022
70	Aiman Khan	Comparative structural modeling of mutants	2022
71	Arshiya Qayyum	Transcription Factor Heterotypic cooperativity	2022
72	Ramsha Azhar	PhyloEasy: Python framework	2022
73	Aleena Murtaza	Comparative analysis and population genetics	2022
74	Atika Khan	Functional investigation in zebrafish assay	2023
75	Ayesha Ikram	Denovo genome assembly of Markhor	2023
76	Jaweria Hafeez	Evolutionary analyses of EGLN1 gene	2023
77	Muhammad Faizan Malik	Interactive view of human multigene families	2023
78	Syed Nouman Nasir	Genomic variant analysis of SARS-CoV-2	2023
79	Areej Naveed Abbasi	Comparative and Structural Analysis	2024
80	Sania Mustafa	Protein Structural Analysis of Parkinson’s Genes	2024
81	Noor Afshan	Molecular evolution of EPAS1	2024
82	Ijazul Haq	Phylogenetic History of Human Multigene Families	2025
83	Shahab Ahmad	Estimation of Genetic Diversity in Markhor	2025
84	Tehmeena Asghar	Comparative Structural Analysis of PHC1	2025
85	Muhammad Shoaib Khan	Phylogenetic Analysis of Human Multigene Families	2025
86	Izza Khan	Molecular Evolutionary Sequence Analysis	2025
87	Muhammad Awais	Genetic diversity analysis of Markhor	2025
88	Hina Iqbal	Protein Structural Analysis of Human SLC25A19	2026

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

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 / Co-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 diagnosis and mutation detection based on Pakistani population	Principal Investigator	Pakistan Science Foundation Project No. 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