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Dr. Rashid Saif

Associate Professor, Faculty of Sciences
HOD | Head ORIC
Postdoc (Molecular Genetics & Bioinformatics), University of Bern, Switzerland, 2019
PhD. (Molecular Biology & Biotechnology), UVAS-PAK & University of Missouri-USA, 2015
M.Phil (Molecular Biology & Biotechnology), UVAS-PAK, 2010

Email

[email protected]

Introduction
Research & Publications

Dr. Rashid Saif

Associate Professor | HOD, Faculty of Sciences | Head-ORIC

Dr. Rashid Saif is the Associate Professor and Head-Department of Biotechnology/ORIC at
Qarshi University, Lahore, Pakistan. He holds an esteemed ESKAS postdoc fellowship in
Molecular Genetics & Bioinformatics from the University of Bern, Switzerland, where he
researched selective sweep analysis using NGS whole-genome sequencing data in Capra hircus
at the Institute of Genetics.
Dr. Rashid earned his PhD in Molecular Biology & Biotechnology from UVAS, Lahore, Pakistan
with doctoral research at the University of Missouri-Columbia-USA. His work involved GWAS on
feline progressive retinal atrophy and mammary tumors using SNP-chip data and PLINK. Post-
PhD, he served as an Assistant Professor and later Associate Professor at the Virtual University
of Pakistan and Gulab Devi Educational Complex, Lahore, Pakistan. Dr. Rashid’s research
focuses on detecting genomic selection signatures and validating disease/trait-associated
variants in livestock and human species, developing bioinformatics pipelines for multi-omics
data analysis using Linux, R, and Python platforms/tools. He collaborates with institutions like
Langston University, the University of Missouri-Columbia-USA, the University of Bern-
Switzerland and the Tabuk University-KSA. His mentoring extends to undergraduate and
postgraduate students across diverse biotechnology, biochemistry, zoology, MLT, and
molecular pathology disciplines. Dr. Rashid has a significant scholarly footprint with ~55
publications in peer-reviewed journals of international repute along with 02 monographs He
has also presented his research at various national and international forums, including
conferences/seminars in Pakistan, Japan, USA, and Switzerland.

Education
Postdoc (Molecular Genetics & Bioinformatics) University of Bern, Switzerland

University of Bern, Switzerland, 2019
PhD (Molecular Biology & Biotechnology) UVAS-Pakistan & University of Missouri-USA

UVAS-Pakistan & University of Missouri-USA, 2015
M.Phil (Molecular Biology & Biotechnology) UVAS-Pakistan

UVAS-Pakistan, 2010
Work Experience
Designation/Institution From To
Associate Professor, Department of Biotechnology, Qarshi University Lahore, Pakistan April 2023 Present
Director-Research & Diagnostics, Decode Genomics, Lahore, Pakistan March 2021 April 2023
Associate Professor, Gulab Devi Educational Complex, Lahore, Pakistan August 2017 March 2021
Assistant Professor, Department of Biotechnology, Virtual University of Pakistan (VUP) March 2015 August 2017
Industry Experience
[1] Hatchery Manager, Sadiq Brothers Poultry, Rawalpindi, Pakistan.
[2] Assay Development & NGS Adoption Consultant, Molecular Diagnostics & Medical Lab Industry.

Research & Publications

Honors/Awards
[1] Postdoc Award: Swiss Government Excellence Scholarship.
[2] PhD Award: IRSIP-HEC, University of Missouri-Columbia, USA.
[3] Summer Institute Award in “Statistical Genetics”, University of Washington-Seattle, USA.
[4] The Hans-Sigrist Foundation Award, UniBe-Switzerland.
[5] HEC Travel Grants for Pakistani Researcher – ABLS-2017, Kyoto, Japan.
[6] Indigenous PhD Fellowship Program – HEC, Pakistan.
[7] Keynote/Travel Award, ICNSET 2019, Sapporo, Japan.
Research Publications
[1] Mumtaz, Zilwa, Rashid, Zobia, Saif, Rashid, Yousaf, Muhammad Zubair (2024). Deep Learning Guided Prediction Modeling of Dengue Virus Evolving Serotype. Heliyon. https://doi.org/10.1016/j.heliyon.2024.e32061.
[2] Mumtaz, Zilwa, Zia, Saeeda, Saif, Rashid, Haq, Faheem ul, Yousaf, Muhammad Zubair (2023). Evolutionary Patterns and Heterogeneity of Dengue Virus Serotypes in Pakistan. Evolutionary Biology. https://doi.org/10.1101/2023.09.28.559885.
[3] Saif, Rashid, Raza, Muhammad Hassan, Zafar, Muhammad Osama, Tariq, Wajeeha, Ahmad, Muhammad Danish, Wasim, Muhammad (2023). Genetic Association of MSTN Variant (18:66493737T>C) with Racing Performance & Muscle Development in Pakistani Horses. Futuristic Biotechnology. DOI: https://doi.org/10.54393/fbt.v4i01.89.
[4] Karim, Asma, Saif, Rashid, Ali, Akhtar, Nadeem, Beenish, Ilyas, Hafiza Aqsa, Sajjad, Waseem (2023). DNA Barcoding Application in Study of Icthyo-Biodiversity in Rivers of Pakistan. Inter. J. of Multidisc. Research. DOI: https://doi.org/gtppc6.
[5] Saif, Rashid, Mahmood, Tania, Ejaz, Aniqa, Zia, Saeeda (2023). Genomic Selection Pressure Discovery using Site-Frequency Spectrum & Reduced Local-Variability Statistics in Pakistani Dera-Din-Panah Goat. Trop Anim Health Prod. 55;331 (2023). https://doi.org/10.1007/s11250-023-03758-2.
[6] Yaqub, Hafiz Muhammad Farooq, Firyal, Sehrish, Awan, Ali Raza, Tayyab, Muhammad, Saif, Rashid, Mati-ur-Rehman, Wasim, Muhammad (2022). MicroRNAs hsa-miR-222-3p, hsa-let-7b-5p, hsa-let-7f-5p Regulate their Putative Target Genes HMGA1 and CDKN1B in Pakistani Breast Cancer Patients. Pakistan Journal of Zoology. DOI: https://dx.doi.org/10.17582/journal.pjz/20221124051117.
[7] Jabeen, Sadia, Saif, Rashid, Haq, Rukhama, Hayat, Akbar, Naz, Shagufta (2023). Whole-Genome Sequencing and Variant Discovery of Citrus reticulata “Kinnow” from Pakistan. Functional & Integrative Genomics. 2023 Jul 8;23(3):227. https://doi.org/10.1007/s10142-023-01153-6.
[8] Yaqub, Hafiz Muhammad Farooq, Firyal, Sehrish, Awan, Ali Raza, Tayyab, Muhammad, Saif, Rashid, Mati-ur-Rehman, Wasim, Muhammad (2022). Expression Profiling of microRNAs HSA-222-3P, HSA-LET-7B-5P, HSA-LET-7F-5P and their Putative Targets HMGA1 and CDKN1B Genes in Canine Mammary Tumor. Pakistan J. of Zool., pp 1-7. https://dx.doi.org/10.17582/journal.pjz/20221124051117.
[9] Farhan, Mehroz, Saif, Rashid, Anjum, Iram (2023). In-silico Prediction of Azadirachta indica Compounds as Potential Therapeutic Inhibitor of Lysyl Oxidase to Suppress Canine Mammary Tumor Proliferation. Futuristic Biotechnology, 3;2. https://doi.org/10.54393/fbt.v3i02.42.
[10] Zeeshan, Mouvez, Ashraf, Aqeela, Niamat, Humaira, Mustafa, Muhammad Danyall, Riaz, Laiba, Saif, Rashid (2023). Identification of Vancomycin Resistant Enterococcus Genes in Clinical Isolates. LGU Journal of Life Sciences, 7;3. https://doi.org/10.54692/lgujls.2023.0703290.
[11] Ali, Laraib, Saif, Rashid, Raza, Muhammad Hassan, Zafar, Muhammad Osama, Zia, Saeeda, Shafiq, Mehwish, Ahmad, Tuba, Anjum, Iram (2023). Computational Prediction of Nigella sativa Compounds as Potential Drug Agents for Targeting Spike Protein of SARS-CoV-2. Pakistan BioMedical Journal. https://doi.org/10.54393/pbmj.v6i3.853.
[12] Khalid, Areeb, Ashraf, Hajra, Asim, Hibba, Ayman, Maleeka, Saif, Rashid (2023). Association Analysis of LCORL Genetic Variant (rs657074013A>AT) with Body-Height and Skeletal Frame in Pakistani Goats. Futuristic Biotechnology. DOI: https://doi.org/10.54393/fbt.v3i02.46.
[13] Saif, Rashid, Nadeem, Sadia, Iftekhar, Ali, Khaliq, Alishba, Zia, Saeeda (2022). Mathematical Understandings of Sequence Alignment and Phylogenetics Algorithms: A Comprehensive Review of Computation of Different Methods. Adv. life sci., vol. 9, no. 4, pp. 401-411, Dec 2022. http://www.als-journal.com/945-22/#abs.
[14] Ahmad, Tuba, Saif, Rashid, Raza, Muhammad Hassan, Zafar, Muhammad Osama, Zia, Saeeda, Shafiq, Mehwish, Ali, Laraib, Younas, Hooria (2022). Computational Prediction of Cymbopogon Citratus Compounds as Promising Inhibitors of Main Protease of SARS-CoV-2. Futuristic Biotechnology. DOI: https://doi.org/10.54393/fbt.v2i01.23.
[15] Shafiq, Mehwish, Saif, Rashid, Ali, Laraib, Ahmad, Tuba, Anjum, Iram, Suhail, Anood (2022). Computer-Aided Drug Designing of Ocimum basilicum Compounds as Therapeutic Agents against RdRp of SARS-CoV-2. Futuristic Biotechnology. DOI: https://doi.org/10.54393/fbt.v2i02.5.
[16] Saif, Rashid, Mahmood, Tania, Ejaz, Aniqa, Zia, Saeeda (2022). Pathway Enrichment and Network Analysis of Differentially Expressed Genes in Pashmina Goat. Gene Reports. https://doi.org/10.1016/j.genrep.2022.101606.
[17] Saif, Rashid, Ashfaq, Kanza, Ali, Ghafran, Iftekhar, Ali, Zia, Saeeda, Yousaf, Muhammad Zubair (2022). Computational Prediction of Cassia angustifolia Compounds as a Potential Drug Agents against Main Protease of SARS-nCov-2. Advancement in Life Sciences, vol. 9, no. 1, pp. 36-40, May 2022. http://www.als-journal.com/916-22/.
[18] Saif, Rashid, Henkel, Jan, Mahmood, Tania, Ejaz, Aniqa, Ahmad, Fraz, Zia, Saeeda (2021). Detection of Whole Genome Selection Signatures of Pakistani Teddy Goat. Molecular Biology Reports. https://doi.org/10.1007/s11033-021-06726-x.
[19] Saif, Rashid, Henkel, Jan, Mahmood, Tania, Ejaz, Aniqa, Zia, Saeeda (2021). Whole Genome Selective Sweeps Analysis in Pakistani Kamori Goat. Gene Reports. https://doi.org/10.1016/j.genrep.2021.101429.
[20] Saif, Rashid, Mahmood, Tania, Ejaz, Aniqa, Zia, Saeeda, Qureshi, Abdul Rasheed (2021). Whole Genome Comparison of Pakistani Corona Virus with Chinese and US Strains along with its Predictive Severity of COVID-19. Gene Reports. https://doi.org/10.1016/j.genrep.2021.101139.
[21] Saif, Rashid, Ali, Ghafran, Ashfaq, Kanza, Zia, Saeeda, Qureshi, Abdul Rasheed (2021). Computational Prediction of Olea europaea Compounds as Inhibitors of Main-Peptidase of SARS-CoV-2. Advancement in Life Sciences, 8(2), 133-136. http://submission.als-journal.com/index.php/ALS/article/view/1040/519.
[22] Saif, Rashid, Henkel, Jan, Jagannathan, Vidhya, Droegmueller, Cord, Flury, Christine, Leeb, Tosso (2020). The LCORL Locus is Under Selection in Large-Sized Pakistani Goat Breeds. Genes. https://doi.org/10.3390/genes11020168.
[23] Saif, Rashid, Ejaz, A., Mehmood, T., Asif, F., Alghanem, S.M., Ahmad, T.S. (2020). Introduction to Galaxy Platform for NGS Variant Calling Pipeline. Advancements in Life Sciences, 7(3), 129-134.
[24] Saif, Rashid, Iftekhar, Ali, Asif, Fatima, Alghanem, Mohammad Suliman (2020). Dog Coat Color Genetics: A Review. Advancements in Life Sciences, 7(4), 215-224.
[25] Henkel, Jan, Saif, Rashid, Jagannathan, Vidhya, Droegmueller, Cord, Flury, Christine, Leeb, Tosso (2019). Selection Signatures in Goats Reveal Copy Number Variants Underlying Breed-Defining Coat Color Phenotypes. PLOS Genetics. https://doi.org/10.1371/journal.pgen.1008536.
[26] Saif, Rashid, Qazi, Kinza, Zia, Saeeda, Mahmood, Tania, Ejaz, Aniqa, Tamseel, Talha, Alghanem, Suliman Mohammad, Khaliq, Adnan (2019). First Step with R for Life Sciences: Learning Basics of this Supporting Tool for NGS Data Analysis. Advancement in Life Sciences, 6(4), 187-194.
[27] Manzoor, Saba, Saif, Rashid, Sadia, Haleema, Firyal, Sehrish, Tayyab, Muhammad, Mansha, Muhammad, Mehmood, Asim Khalid, Hashmi, Abu Saeed, Wasim, Muhammad (2019). Molecular Expression of Cyclin Dependent Kinase Inhibitor (P21) in Canine Tumors. Journal of Animal and Plant Sciences. https://doi.org/10.36899/JAPS.2019.4.0257.
[28] Ali, Akhtar, Baig, Zukhruf, Babar, Masroor Ellahi, Nadeem, Asif, Hussain, Tanveer, Saif, Rashid, Javed, Maryam (2019). A Novel SNP (c.258+43C>T) in LPL Gene and Association with Milk Production in Buffaloes. Buffalo Bulletin. https://kuojs.lib.ku.ac.th/index.php/BufBu/article/view/1045.
[29] Karim, Asma, Saif, Rashid, Ali, Faisal Salamat, Gil, Zohaib, Ali, Wajid (2019). Use of CO1 Gene Sequences for Computing Genetic Diversity Between Cirrhinus mrigala from Two Different Habitats (Farm and River). Journal of Fisheries and Life Sciences, 3(2), 54-57.
[31] Tahir, Hafsa, Ejaz, Aniqa, Mehmood, Tania, Riaz, Sidra, Saif, Rashid (2019). An Overview of Genome-Wide Association Studies for Genetics Novices: A Review. Advancements in Life Sciences, 6(3), 88-96.
[32] Gandolfi, Barbara, Alhaddad, Hasan, Abdi, Mona, Bach, Leslie H., Creighton, Erica K., Davis, Brian W., Decker, Jared E., Dodman, Nicholas H., Grahn, Jennifer C., Grahn, Robert A., Waud, Bianca, Haggstrom, Jens, Hamilton, Michael J., Helps, Christopher R., Kurushima, Jennifer D., Lohi, Hannes, Longeri, Maria, Malik, Richard, Meurs, Kathryn M., Montague, Michael J., Mullikin, James C., Murphy, William J., Nilson, Sara M., Pedersen, Niels C., Peterson, Carlyn B., Rusbridge, Clare, Saif, Rashid, Shelton, Diane G., Warren, Wesley C., Wasim, Muhammad, Lyons, Leslie A. (2018). Applications and Efficiencies of the First Cat 63K DNA Array. Scientific Reports. https://doi.org/10.1038/s41598-018-25438-0.
[33] Karim, Asma, Saif, Rashid, Gill, Zohaib, Salamat, Faisal, Ali, Akhtar, Razzaq, Asem (2018). CO1 Gene Based Identification and Phylogenetic Analysis of Two Freshwater Fish Species Labeo gonius and Cirrhinus mrigala (Family: Cyprinidae) from River Ravi, Punjab, Pakistan. MRJ of Agricultural Science and Soil Sciences, 6(3), 24-31. https://doi.org/10.15739/mrjasss.06.03.004.
[34] Saif, Rashid, Naz, Naila, Tariq, Beenish, Iftekhar, Ali (2018). Molecular Characterization of EGLN1 Gene in Fast and Slow-Moving Animals of Diversified Terrain. Advancements in Life Sciences, 5(4), 171-178.
[35] Saif, Rashid, Awan, Ali Raza, Lyon, Leslie, Gandolfi, Barbara, Wasim, Muhammad (2018). Single Nucleotide Somatic Variants of Tp53 Gene in Widespread Neoplasms of Canis Familiaris. Journal of Animal and Plant Sciences, 28(5), 1329-1338. https://doi.org/10.36899/JAPS.2018.5.0235.
[36] Saif, Rashid, Zia, Saeeda, Qazi, Kinza, Asif, Fatima, Ejaz, Aniqa, Mehmood, Tania, Tamseel, Talha (2018). Computational Proteomic Data Mining of Heat Shock Protein β1 Using Mathematica Software. Merit Res. J. Microbiol. Biol. Sci., 6(4), 043-053.
[37] Saif, Rashid, Tariq, Beenish, Naz, Naila (2018). Sequence Diversity of MAOA Gene within Wild and Docile Animal Species. Advancements in Life Sciences, 5(3), 135-142.
[38] Tahir, Hafsa, Saif, Rashid, Tamseel, Talha, Ahmad, Fraz (2018). Targeted Pinpoint Gene Editing Tool, CRISPR/Cas9: A Review. International Journal of Biosciences. http://dx.doi.org/10.12692/ijb/12.5.101-117.
[39] Saif, Rashid, Awan, Ali Raza, Tayyab, Muhammad, Babar, Masroor Ellahi, Zia, Saeeda, Wasim, Muhammad (2018). Expression Profiling of Hspb1 and Tp53 Genes through RT-qPCR in Different Cancer Types of Canis familiaris. Iranian Journal of Biotechnology. https://doi.org/10.15171/ijb.1505.
[40] Saif, Rashid, Lyons, Leslie, Gandolfi, Barbara, Ahmad, Hafiza Maleeha, Ejaz, Ramlah, Wasim, Muhammad (2017). Genome-Wide Association Study of Cat Mammary Tumor Using 63,000 SNP Chip through PLINK Data Analysis Tool Set. International Journal of Biosciences. http://dx.doi.org/10.12692/ijb/11.1.75-82.
[41] Saif, Rashid, Qazi, Kinza, Tamseel, Talha, Zia, Saeeda (2017). Genomic Data Mining through Python Language. International Journal of Biosciences. http://dx.doi.org/10.12692/ijb/11.3.116-125.
[42] Hassan, Syeda Aamna, Akhlaq, Farwa, Tayyab, Muhammad, Awan, Ali Raza, Firyal, Sehrish, Khan, Waqas Ahmad, Saif, Rashid, Wasim, Muhammad (2017). Glyphosate: Cancerous or Not; Perspectives from Both Ends of the Debate. Advancements in Life Sciences, 4(4), 108-112.
[43] Javeria, Babar, Masroor Ellahi, Hussain, Tanveer, Saif, Rashid, Rashid, Sadaf, Sarfraz, Hanan, Shah, Abbas Ali, Wasim, Muhammad, Abdullah, Muhammad (2017). Genetic Contribution of BDNF Gene in Obsessive Compulsive Disorder in Pakistani Punjabi Population. Pakistan Journal of Zoology. http://dx.doi.org/10.17582/journal.pjz/2017.49.4.sc7.
[44] Saif, Rashid, Awan, Ali Raza, Lyons, Leslie A., Gandolfi, Barbara, Wasim, Muhammad (2017). Exploration of Novel Somatic Hspb1 Mutations in Widespread Neoplasms of Canis Familiaris. International Journal of Biosciences. http://dx.doi.org/10.12692/ijb/10.5.265-272.
[45] Saif, Rashid, Lyons, Leslie, Gandolfi, Barbara, Awan, Ali Raza, Tayyab, Muhammad, Babar, Masroor Ellahi, Wasim, Muhammad (2016). Mammary Tumor Associated Hspb1 Mutation and Screening of Eight Cat Populations of the World. Iranian Journal of Veterinary Research, 17(4), 231-236. https://doi.org/10.22099/ijvr.2016.3907.
[46] Saif, Rashid, Awan, Ali Raza, Lyons, Leslie, Gandolfi, Barbara, Tayyab, Muhammad, Babar, Masroor Ellahi, Mehmood, Asim Khalid, Ullah, Zia, Wasim, Muhammad (2016). Hspb1 and Tp53 Mutation and Expression Analysis in Cat Mammary Tumors. Iranian Journal of Biotechnology. https://doi.org/10.15171/IJB.1480.
[47] Saif, Rashid, Khan, Ezza, Azhar, Arooj, Choudhry, Shahnaz, Husaain, Tanveer, Babar, Masroor Ellahi, Awan, Ali Raza, Tayyab, Muhammad, Zia, Saeeda, Wasim, Muhammad (2016). Insight of Tp53 Mutants and Its Effect on Protein in Different Feline and Canine Neoplasms. Advancements in Life Sciences, 3(2), 42-50.
[48] Saif, Rashid, Azhar, Arooj, Khan, Ezza, Choudhry, Shahnaz, Husaain, Tanveer, Babar, Masroor Ellahi, Awan, Ali Raza, Tayyab, Muhammad, Wasim, Muhammad (2016). In Silico Characterization of Hspb1 Mutant Protein in Canine and Feline Cancers. Pak J. of Bioch. Mol. Bio., 49(1), 18-28.
[49] Shahzad, Muhammad, Yaqub, Atif, Sheeraz, Muhammad, Saif, Rashid (2016). Exposure and Vulnerability: Health-Related Symptoms, Attitude, and Practices Towards Handling Agricultural Pesticides Among Vendors of Central Punjab, Pakistan. BIOLOGIA (Pakistan), 62(1), 57-67.
[50] Hussain, Tanveer, Babar, M. E., Mustafa, M. M., Saif, Rashid, Hussain, Fiaz, Aqeel, M., Naveed, N., Pervez, M. T., Khan, W. A., Ziaullah, Shahzad, S., Yaqub, A. (2015). Mitochondrial ATP6 & ATP8 Genes Based Molecular Diversity and Phylogenetic Analysis in Punjab Urial (Ovis vignei punjabiensis). Journal of Animal and Plant Sciences, 25(3 Supp. 2), 311-317. https://doi.org/10.36899/JAPS.2015.SpecialIssue2.0154.
[51] Khan, Waqas Ahmad, Hussain, Tanveer, Babar, Masroor Ellahi, Nadeem, Asif, Awan, Ali Raza, Fatima, Ambrin, Saif, Rashid (2015). Polymorphic Status of PRKAA2 Gene in Pakistani Buffaloes. International Journal of Agriculture and Biology. https://doi.org/10.17957/IJAB/15.0149.
[52] Hussain, Tanveer, Babar, Masroor Ellahi, Nadeem, Asif, Saif, Rashid, Ali, Wajid (2015). Genomic Exploration of Pakistani Buffalo – Our Black Gold. Buffalo Bulletin, 32(Sp. Issue 2), 658-661.
[53] Saif, Rashid, Babar, Masroor Ellahi, Awan, Ali Raza, Nadeem, Asif, Hashmi, Abu Saeed, Hussain, Tanveer (2011). DNA Fingerprinting of Pakistani Buffalo Breeds (Nili-Ravi, Kundi) Using Microsatellite and Cytochrome b Gene Markers. Molecular Biology Reports. https://doi.org/10.1007/s11033-011-0808-0.
[54] Saif, Rashid, Wasim, Muhammad, Babar, Masroor Ellahi (2012). Molecular Phylogeny of Pakistani Riverine Buffalo Based on Genetic Variability of Mitochondrial Cytochrome b. Molecular Biology Reports. https://doi.org/10.1007/s11033-012-1835-1.