Dr. Rashid Saif

Research Interests:

Dr. Rashid Saif was awarded ESKAS postdoc fellowship-Molecular Genetics & Bioinformatics from Institute of Genetics-University of Bern, Switzerland, where he was engaged in NGS pooled whole-genome sequencing data for selective sweep analysis in Capra hircus. He earned his PhD-Molecular Biology & Biotechnology from UVAS, Lahore, Pakistan & conducted his doctoral research through IRSIP-HEC from “Lyons Comparative Genomics Lab” at University of Missouri-Columbia, USA, where he got exposure to GWAS by analyzing progressive retinal atrophy & mammary tumor by generating SNP-chip data in Felis catus using PLINK data analysis toolset.

Dr. Rashid’s research interests are detection of genomic selection signatures through different statistical methods using Linux/Galaxy/R & Python scripting in different species. Secondly, bioinformatics pipelines development & optimization using multi-omics NGS data e.g., WG/Exome variant calling, differential gene expression and de-novo genome assembly. His further interest lies in molecular drug development e.g., docking & molecular dynamic simulation approaches. Thirdly, machine/deep learning applications in genomic data science for knowledge extraction from multi-omics datasets e.g., cancer class/variant prediction and devising bioinformatics pipelines for drug prescription as health-care decisions-support for implementing precision medicine. Last but not the least, disease/trait related molecular markers are genotyped for association analysis & genetic testing in human, animals, plants and avian species. He has research connections with University of Bern Switzerland, University of Missouri-Columbia, Washington State University & ARS-USDA, USA for exploring new avenues and collaborative research projects of mutual interests. He has supervised a number of under/post-graduate students of different life sciences disciplines. He has ~50 publications in credit and presented his research at different national and international forums including Japan, USA and Switzerland.

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Honors & Awards:

• Postdoc; Swiss Government Excellence Scholarship
• PhD; IRSIP-HEC, University of Missouri-Columbia, USA
• Summer Institute “Statistical Genetics” award-University of Washington-Seattle, USA
• The Hans-Sigrist Foundation Award, UniBe-Switzerland
• HEC Travel Grants for Pakistani Researcher- ABLS-2017, Kyoto, Japan
• Indigenous PhD Fellowship Program-HEC, Pakistan
• Travel Award from ICNSET 2019, Sapporo, Japan

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Foreign Trainings & Courses:

• Swiss Institute of Bioinformatics (SIB) & UniBe, Switzerland

Training Courses:

• First step with UNIX in life sciences
• Long Read Sequencing & Data Analysis using Nanopore: MinION
• High Performance Computing (HPC) in Life Sciences: Vital-IT Infrastructure Training
• DNA Sequencing & Genetic Variant Analysis: Basics of Sanger & NGS
• NGS bioinformatics Quality Control & Variant Annotation for Cancer Diagnosis
• Cancer Genomics
• Introduction to R Programming and Analyses

• Summer Institute for Statistical Genetics, University of Washington- Seattle, USA

Training Courses:

• Quantitative Genetics
• Integrative Genomics
• Pathway/Network Analysis for Omics Data

• Lyons Comparative Genomics Lab, University of Missouri-Columbia, USA

Training Courses:

• GWAS/SNP-Chip data generation & analysis
• Lab Biosafety

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Research Publications:

• The LCORL Locus is Under Selection in Large-Sized Pakistani Goat Breeds

Rashid Saif, Jan Henkel, Vidhya Jagannathan, Cord Droegmueller, Christine Flury, Tosso Leeb

“Genes” 11 (2) 168 (IF:3.759), https://doi.org/10.3390/genes11020168

• Selection Signatures in Goats Reveal Copy Number Variants Underlying Breed-Defining Coat Color Phenotypes

Jan Henkel, Rashid Saif, Vidhya Jagannathan, Cord Droegmueller, Christine Flury, Tosso Leeb

“PLOS Genetics” doi: 10.1371/journal.pgen.1008536, 15 (12), e1008536 (IF: 5.109)

• Detection of Whole Genome Selection Signatures of Pakistani Teddy Goat

Rashid Saif, Jan Henkel, Tania Mahmood, Aniqa Ejaz, Fraz Ahmad, Saeeda Zia

“Molecular Biology Reports” (IF: 2.316) https://doi.org/10.1007/s11033-021-06726-x

• Whole Genome Selective Sweeps Analysis in Pakistani Kamori Goat

Rashid Saif, Jan Henkel, Tania Mahmood, Aniqa Ejaz, Saeeda Zia

“Gene Reports” (IF 0.72), https://doi.org/10.1016/j.genrep.2021.101429

• Applications and Efficiencies of the First Cat 63K DNA Array

Barbara Gandolfi et.al.,

“Scientific Reports” DOI:10.1038/s41598-018-25438-0 (IF: 3.998)

• 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

Hafiz Muhammad Farooq Yaqub, Sehrish Firyal, Ali Raza Awan, Muhammad Tayyab,

Rashid Saif, Mati-ur-Rehman, Muhammad Wasim 

“Pakistan J. of Zool.”, pp 1-7, 2022, https://dx.doi.org/10.17582/journal.pjz/20221124051117

• Whole Genome Comparison of Pakistani Corona Virus with Chinese and US Strains along with its Predictive Severity of COVID-19

Rashid Saif, Tania Mahmood, Aniqa Ejaz, Saeeda Zia, Abdul Rasheed Qureshi

“Gene Reports” IF 0.72: 23, June 2021, 101139 (https://doi.org/10.1016/j.genrep.2021.101139)

• Single Nucleotide Somatic Variants of Tp53 Gene in Widespread Neoplasms of Canis Familiaris

Rashid Saif, Ali Raza Awan, Leslie Lyon, Barbara Gandolfi, Muhammad Wasim

“Journal of Animal and Plant Sciences”, 28 (5) 2018: 1329-1338 (IF:0.490)

• Expression Profiling of Hspb1 and Tp53 Genes through RT-qPCR in Different Cancer Types of Canis familiaris

Rashid Saif, Ali Raza Awan, Muhammad Tayyab, Masroor Ellahi Babar, Saeeda Zia, Muhammad Wasim

“Iranian Journal of Biotechnology”, doi: 10.15171/IJB.1505 (IF 0.973)

• Exploration of Novel Somatic Hspb1 mutations in Widespread Neoplasms of Canis Familiaris

Rashid Saif, Ali Raza Awan, Leslie A. Lyons, Barbara Gandolfi, Muhammad Wasim

“International Journal of Biosciences” (IF 0.553) doi: http://dx.doi.org/10.12692/ijb/10.5.265-272

• Mammary Tumor Associated Hspb1 Mutation and Screening of Eight Cat Populations of the World

Rashid Saif, Leslie Lyons, Barbara Gandolfi, Ali Raza Awan, Muhammad Tayyab, Masroor Ellahi Babar, Muhammad Wasim

“Iranian Journal of Veterinary Research” 17(4);231-236, https://doi.org/10.22099/ijvr.2016.3907

• Hspb1 and Tp53 Mutation and Expression Analysis in Cat Mammary Tumors

Rashid Saif, Ali Raza Awan, Leslie Lyons, Barbara Gandolfi, Muhammad Tayyab, Masroor Ellahi Babar, Asim Khalid Mehmood, Zia Ullah, Muhammad Wasim     

“Iranian Journal of Biotechnology” (IF 0.309), DOI: 10.15171/IJB.1480

• Genetic Contribution of BDNF Gene in Obsessive Compulsive Disorder in Pakistani Punjabi Population

Javeria, Masroor Ellahi Babar, Tanveer Hussain, Rashid Saif, Sadaf Rashid, Hanan Sarfraz , Abbas Ali Shah , Muhammad Wasim1 and Muhammad Abdullah

“Pakistan Journal of Zoology (IF 0.491), doi: http://dx.doi.org/10.17582/journal.pjz/2017.49.4.sc7

• DNA Fingerprinting of Pakistani Buffalo Breeds (Nili-Ravi, Kundi) Using Microsatellite and Cytochrome b Gene Markers

Rashid Saif, Masroor Ellahi Babar, Ali Raza Awan, Asif Nadeem, Abu Saeed Hashmi, Tanveer Hussain

“Molecular Biology Reports” doi: 10.1007/s11033/011-0808-0 (IF 1.828)

• Molecular Phylogeny of Pakistani Riverine Buffalo Based on Genetic Variability of Mitochondrial Cytochrome b

Rashid Saif, Muhammad Wasim, Masroor Ellahi Babar

“Molecular Biology Reports” doi: 10.1007/s11033-012-1835-1 (IF 1.828)

• Pathway Enrichment and Network Analysis of Differentially Expressed Genes in Pashmina Goat

Rashid Saif, Tania Mahmood, Aniqa Ejaz, Saeeda Zia

“Gene Reports” https://doi.org/10.1016/j.genrep.2022.101606

• Dog Coat Color Genetics: A Review

Rashid Saif, Ali Iftekhar, Fatima Asif, Mohammad Suliman Alghanem

“Advancements in Life Sciences” 7 (4), 215-224

• Molecular Expression of Cyclin Dependent Kinase Inhibitor (P21) in Canine Tumors

Saba Manzoor, Rashid Saif, Haleema Sadia, Sehrish Firyal, Muhammad Tayyab, Muhammad Mansha, Asim Khalid Mehmood, Abu Saeed Hashmi, Muhammad Wasim

“Journal of Animal and Plant Sciences” (IF 0.529) 29 (4) 2019: 1127-1134

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Professional Academic/Industry Experiences:

• Associate Professor-Biotechnology
• Gulab Devi Educational Complex, Lahore, Pakistan
• Assistant Professor-Biotechnology

Virtual University of Pakistan, Lahore, Pakistan

• Visiting Faculty-Kinnaird College for Women, Lahore, Pakistan
• Visiting Faculty-NUR International University, Lahore, Pakistan
• Co-Supervisory: Mathematical Genomics & Biological Modeling

National University of Computer & Emerging Sciences (FAST), Lahore, Pakistan

• Director-Research & Diagnostics

Decode Genomics, Lahore, Pakistan

• Hatchery Manager, Sadiq Brother’s Poultry, Rawalpindi, Pakistan

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Books & Monographs:

• Bioinformatics: Multi-Omics Applications in Food Science

Rashid Saif, Ali Iftekhar

• Evolutionary Dynamics and Biodiversity in Pakistani Livestock Species

Pakistan Research Repository-HEC (As major contributor)

• Insight to Integrative Genomics

Rashid Saif, “Lambert Academic Publishing”

ISBN: 978-613-9-85813-2

• DNA Polymorphism: A Tool for Molecular Characterization

Rashid Saif “VDM Verlag Dr. Müller GmbH & Co. Germany

ISBN: 978-3-639-32567-6

• The 99 Business Ideas in Biotechnology (In-progress)

Rashid Saif, Ali Iftekhar

• Multi-Omics Data Analysis: A Bioinformatics Pipeline Manual (In-progress)
• Rashid Saif, Tania Mahmood, Aniqa Ejaz

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Project Completed:

As Team Member

• Genomic Selection Signatures in Pakistani & Swiss Goat Breeds

“In collaboration with University of Bern & SNSF-Switzerland”

• Applications and Efficiencies of the First Cat 63K DNA Array

“In collaboration with University of Missouri-Columbia-USA”

Funded Projects:

As PI

• Splenic Expression Profiling of Immunity Related IL-6, 10, 1β Genes in Different Chicken Lines

“Funded by VUP”

Projects Submitted to NRPU/PARC/NIG/IsDB/Fulbright Foundation (2015-2020):

As PI:

• Pan-genome Assembly of Indigenous Goats in Pakistan

Fulbright Foundation; in collaboration with Washington State University & ARS-USDA, USA

• Identification of Milk Production Genomic Selection Signatures in Pakistani Goats

Submitted to IsDB; in collaboration with WSU-USA & McGill University, Canada

• Genetic and Epigenetic Insight: Hi-C Genome Scanning and Selection Signature in Cats

Submitted to National Institute of Genetics (NIG)-DDBJ, Japan

• Transcriptome and Sequence Diversity Analysis of Xenobiotic-Metabolizing and Disease Resistance Set of Genes in Desi and Broiler Chicken Lines

Submitted to NRPU-HEC, Pakistan

• Immunity Related Selective Sweeps Analysis in Pakistani Indigenous Chicken

University of Maryland, USA 

• Allele-Specific Expression Profiling for Predicting the Predisposition of Colorectal Cancer

Georgia Institute of Technology, Georgia, USA

• Sex and Immunity Specific Whole Transcriptome Alternative Polyadenylation Site Sequencing in Chicken

Washington State University, Washington, USA

• Identification of Milk Production Genomic Selection Signatures in Pakistani Goats

In collaboration with Washington State University, Washington, USA

On-going Projects:

As PI

• Identification of Genomic Selection Signatures for Valued Traits in Pakistani Goats
• Genetic Association of AIP Gene Variant (c.910C>T) with Pituitary Adenoma Patients from Pakistan
• Assessing the CYP1A2 Gene Variant (rs762551) Association with Hypertension Susceptibility in Pakistan
• Molecular Docking & Dynamic Simulations of Olea Europaea & Curcuma Longa Compounds as Potential Drug Agents for Targeting Main-Protease of SARS-nCoV2
• Genetic Association of SLC47A1, UMOD & SLC47A9 Genetic Variants with Chronic Kidney Disease

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Online Recorded Courses @ Udemy & Youtube

• Whole Genome Variant Calling @ Linux
• Genomic Selection Signature using Statistics
• Whole Genome Variant Calling @ Galaxy
• Molecular Docking with MOE Software
• Whole Transcriptome Analysis: RNA-Seq @ Linux
• Bioinformatics Assistance in Drug Prescription (In-progress)

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Student Supervised / Co-supervised and Mentoring:

• Three PhD student (Biotechnology, Microbiology) from UVAS & LCWU, Lahore-Pakistan
• Sixteen MS (Biotechnology, Biochemistry, Mathematics) students supervised/co-supervised.
• Twenty BS (Biotechnology/Microbiology/MLT) students co-supervised from

GCU/KCFW/UVAS/GDEC/LGU/UoL-Pakistan)

• Five BS (Hons) Zoology students co-supervised, Govt. Postgraduate College of Science, Wahdat Rd., Lahore
• Ten (M.Phil Biotechnology/Zoology) students co-supervised from GCU/UoS/UoL.
• Three PhD students (Molecular biology and biotechnology/Zoology) mentored as internees from GCU/UVAS/UAF-Pakistan
• Six MS-Mathematics students co-supervised in “Mathematical Genomics & Biological Modeling”.

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Academic Administrative & Managerial Responsibilities:

• Facilitator: Admission campaigns-QU
• HoD-Biotechnology-GDEC, Lahore, Pakistan
• Incharge: Biological sciences degree programs at GDEC, Lahore, Pakistan
• Quality assurance person, course development for VUP-TV network
• Member of “Committee on Unfair Means”-VUP
• Member “quality assurance cell” for BS/MS Bioinformatics degree program at VUP
• Focal person “Biotechnology” for degree accreditation from National Technology Council-HEC
• Student career counselor and motivational speaker.
• Facilitate student to hunt indigenous and foreign scholarships and funding opportunities.
• External examiner for different institutes/universities

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Industrial Oriented Hands–on Local Trainings Attended:

• Training on: Roche: Cobas-AmpliPrep automatic robotics nucleic acid extraction and TaqMan 48 real time PCR System, NeoSense automatic nucleic acid extraction system, Cepheid: SmartCycler Real-time PCR for Quantitative, Qualitative and Genotyping tests.
• Orientation and teachers training workshop, Virtual University of Pakistan.
• Fermenter studies and end-product analysis by HPLC, organized by Institute of Industrial Biotechnology, GCU, Lahore, Pakistan.
• Indigenous On-Campus Training, Virtual University of Pakistan.
• Student Orientation Program, Organized by Institute of Continuing Education and Extension, UVAS, Lahore

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Professional Association/Societies Affiliations:

• Advisory Board Member- Journal of “Futuristic Biotechnology”
• The Society for Research in Medicine-Australia (https://srmed.org/) Member Advisory Board-
• Swiss Association for Animal Sciences (SVT)
• WWF-Pakistan
• MidSouth Computational Biology & Bioinformatics Society
• International Milk Genomics Consortium
• UVAS Alumni Association

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Travel/Supplementary Grants:

• Swiss Government Excellent Scholarship, Switzerland
• The Hans Sigrist Foundation, University of Bern, Switzerland
• International Conference of Natural Science, Engineering and Technology [ICNSET 2019], Sapporo (Jan 19-21, 2019), Japan
• International Forum; Agriculture, Biology and Life Sciences [IFABL] (June 27-29, 2017), Kyoto, Japan
• 22^nd Summer Institute for Statistical Genetics (July 10-28, 2017), Department of Biostatistics, University of Washington- Seattle, USA
• International Agricultural & Biotechnology Conference [IABC] (Nov 2015), Bizerte-Tunisia
• Recent advances & challenges in molecular biology, biochemistry & biotechnology

(August 25-28, 2016), COMSATS University Islamabad, Abbottabad Campus-Pakistan

• CASPAM International Conference on Mathematics and Applications (Nov 6-7, 2017)
• BZU, Multan, Pakistan
• 37^th Congress of Zoology at GCUF (Feb 28 –Mar 02, 2017), Faisalabad, Pakistan

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Oral/Poster Presentations

• Conference Chair/Invited Keynote Speaker: Types of Omics Data and Bridging Approaches in Genetics and Informatics

International Conference of Natural Science, Engineering and Technology (ICNSET 2019), Sapporo, Japan (https://icnset.org/) (Jan 19-21, 2019)

• Guest Speaker: Latest Research Trends in Biosciences: Genetics -to- Bioinformatics -to- Machine Learning

Department of Zoology, Government College of Science, Wahdat Rd., Lahore, Pakistan

(Feb 18, 2023)

• Guest Speaker: Biological Hazards in Aviation

Institute of Aviation Studies, University of Management & Technology (UMT), Lahore, Pakistan (June 22, 2022)

• Oral Presentation: Gene Expression Analysis for Canine Cancer through RT-qPCR

Faculty Development Workshop, “Knowing cancer in small animals to improve their quality of life”, UVAS, Lahore, Pakistan (July 08-10, 2021)

• Oral Presentation: Whole-Genome Variant Calling @ Linux-An Introduction

One day Workshop, UVAS, Lahore, Pakistan (Jan 19, 2022)

• Oral Presentation: Whole-Genome Variant Discovery Pipeline-A Complete Workflow

“1^st International Conference on Genomics of Beneficial Microbes”, NIGAB-NARC, Islamabad, Pakistan (Dec 23, 2021)

• Oral Presentation: The LCORL Locus is under Selection in Large-Sized Pakistani Goat Breeds

National Conference on Entrepreneurship Avenues in Biological Sciences, Lahore Garrison University, Lahore, Pakistan (Jan 8-9, 2020)

• Oral Presentation: Livestock Biodiversity of Pakistan

Institute of Genetics, University of Bern-Switzerland (Sep 24, 2018)

• Oral Presentation: Selection Signature Correlating with Body Size in Pakistani Goats and Genomic Architecture Specific to Kamori & Nachi Breeds

Institute of Genetics, University of Bern-Switzerland (May 06, 2019)

• Oral Presentation: Expression Profiling of Hspb1 and Tp53 Genes through RT-qPCR in Different Cancer Types of Canis familiaris

International Forum; Agriculture, Biology and Life Sciences, Kyoto, Japan (June 27-29, 2017)

• Oral Presentation: Proteomic Data Mining through k-Mean Clustering Method using Mathematica Software

CASPAM International Conference on Mathematics and Applications, BZU, Multan, Pakistan

(Nov 6-7, 2017)

• Oral Presentation: Genome-Wide Association Study of Cat Mammary Tumor using 63,000 SNP Chip through PLINK Data Analysis Tool Set.

37^th congress of zoology at GCU-Faisalabad, Pakistan (Feb 28 –Mar 02, 2017)

• Oral Presentation: Mammary Tumor Associated Hspb1 Mutations and Screening of Eight Cat Populations of the World

Recent advances & challenges in molecular biology, biochemistry & biotechnology, Organized by COMSATS University Islamabad, Abbottabad Campus-Pakistan (August 25-28, 2016)

• Oral Presentation: Genetic Testing for Cancer

Symposium on “Potential Impact of genetic testing and counseling” Held on August 4^th, 2016, organized by the department of molecular biology, Virtual University of Pakistan, Lahore, Pakistan

• Oral Presentation: Gene Expression Profiling through RT-qPCR using Comparative Ct Method

Conference on “Insight of molecular biology research tools used in applied biological research” Held on August 6^th, 2015, organized by the department of molecular biology, Virtual University of Pakistan, Lahore, Pakistan

• Oral Presentation: Constructing data matrix and statistical testing of sequence and gene expression data using “R”

Bioinformatics workshop; Hands-on training on analysis of biological data using R” Held on January 5^th, 2016, organized by the department of bioinformatics and computational biology, Virtual University of Pakistan, Lahore, Pakistan

• Oral Presentation: Differential Expression and Data Analysis Methods

“Hands-on training on Real-Time PCR” Held on Sep 17^th – 18^th, 2014, organized by Quality operations Laboratory (QOL), UVAS, Lahore, Pakistan

• Oral Presentation: “Short training on basic molecular biology techniques” Held on July 8^th – 10^th, 2014, organized by institute of biochemistry and biotechnology, UVAS, Lahore, Pakistan
• Oral Presentation: Gene Expression Profiling & Mutation Analysis in P53 & HSPB1 Genes as Cancer Diagnostic Markers

College of Veterinary Sciences, University of Missouri-Columbia, MO, USA

• Poster Presentation: Selection Signature Correlating with Body Size in Pakistani Goats

Swiss Association for Animal Sciences, AgroVet Strickhof – Lindau, Switzerland, April 16, 2019

• Poster Presentation: Heterogeneity in curly coated dogs: a second KRT71 allele

10^th International Conference on Canine and Feline Genetics and Genomics (ICCFGG), May 26-29, 2019, Bern, Switzerland

• Poster Presentation: “International Conference on Emerging trends in Life Sciences”, Held on July 04, 2014, FCCU, Lahore, Pakistan
• Poster Presentation: Genetic Analysis of Coat Color Phenotypes in Genetically Diverse Goat Breeds

Graduate School for Cellular and Biomedical Sciences (GCB) Symposium, Jan 31, 2019. Bern, Switzerland.

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National /International Liaison/Collaborations:

• BGI Genomics Co., Ltd., Tai Po, Hong Kong
• University of Bern, Switzerland
• Washington State University, Pullman, Washington, USA
• Animal Genomics and Improvement Laboratory, ARS-USDA, USA
• University of Missouri Columbia, Missouri, USA
• National Institute of Genetics, Mishima, Japan
• Simmons University, Boston, Massachusetts, USA
• The University of Queensland, Brisbane, Australia
• Tabuk University, Tabuk, Kingdom of Saudi Arabia
• Kinnaird College for Women, Lahore, Pakistan
• University of Veterinary and Animal Sciences (UVAS), Lahore, Pakistan
• Government College University, Faisalabad, Pakistan
• Forman Christian College University (FCCU), Lahore, Pakistan
• Government Postgraduate College of Science, Wahdat Rd., Lahore, Pakistan
• University of Lahore, Lahore, Pakistan
• Lahore Garrison University, Lahore, Pakistan

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National/International Electronic/Print Media Projections:

• Koh-e-Noor Channel: COVID-19/SARS-CoV2 research projection

• Real Face Media: COVID-19/SARS-CoV2 research projection

• Awaz Radio FM 107: COVID-19/SARS-CoV2 research projection

• Activity Report-2018 Hans Sigrist Foundation

https://www.sigrist.unibe.ch/e190362/e190370/e255692/files806716/Hans_Sigrist_Stiftung_Annual_Report_2018_eng.pdf

• ICNSET-2019

https://icnset.org/2019/

• Feline Genetics and Comparative Genomics Lab, University of Missouri-Columbia, USA

http://felinegenetics.missouri.edu/lab-personnel/952-2