Address

Department of Biochemistry and Biotechnology, KNUST, UPO, PMB, Kumasi, Ghana Tel.: +233 209 583 359, Email: sspandam@knust.edu.gh or pandam@kccr.de

Education

• Bacterial Viral Genomics, Edinburgh Napier University, UK, 2011
• Biomedical Science (Distinction), Edinburgh Napier University, UK, 2006
• Medical Science, Gazi University, Turkey, 2000

Personal Statement

Dr. Salifu is a Biomedical Scientist with interest in application of genomics to clinical practice, precision medicine, profiling species, development of novel tools for diagnostics of bacterial and viral pathogens of human, animal and environmental health.

Dr. Salifu has worked extensively in molecular biology, sequencing genomes, proteomics, bioinformatics, and recombinant protein characterisation.

His current research focuses on:

• Conducting whole genome and targeted sequencing to generate high quality biodata and identify high risk pathogens and therapeutic targets in non- communicable and communicable diseases
• Developing software tools and technologies that makes data visualisation and interpretation accessible to all
• Developing and delivering high quality informatics support, computing infrastructure capable of processing big, complex biomedical data, and storage, and cutting edge tools and resources to enable innovative translational
• Producing a sustainable network of individuals who are well trained in various aspects of data science and bioinformatics ready to assume leadership roles at academic, health care and research

Grants and Awards

• 2017-2022: Co- Principal Investigator, 340,000.00 US Dollars grant from the Fogarty International Center/National Institute of Health for West African Sustainable Leadership and Innovative Training in Bioinformatics Research
• 2017-2022: Co-Principal Investigator, 250,000.00 US Dollars grant from  the National Institute of Health for Informatics solutions for H3Africa consortium
• 2016: Principal Investigator, 15,600.00 Cedis grant from the Millennium Development Villages to assess malaria blood films and also to train laboratory technicians
• 2007: Awarded PhD studentship in bacterial viruses as a source of
•  

2006: Awarded University medal for academic and MSc. research project at Edinburgh Napier University.

Positions

• 2018- to date, Senior Lecturer, Department of Biochemistry and Biotechnology, College of Science, Kwame Nkrumah University of Science and Technology
• 2013 – 2018, Lecturer, Department of Biochemistry and Biotechnology, College of Science, Kwame Nkrumah University of Science and Technology
• 2017 to   Date:    Chairman,   General    laboratory  Committee, Department          of Biochemistry and Biotechnology, KNUST
• 2014 to date, Examiner, BSc, , MPhil. And PhD Theses, KNUST
• 2017 to Date: Co-Chair, Grant and Research Desk, Department of Biochemistry and Biotechnology, KNUST
• 2016 to   Date:    Coordinator,   Postgraduate  Forensic   Science Programmes, Department of Biochemistry and Biotechnology, KNUST
• 2014 – 2015, Coordinator, Postgraduate Biotechnology Programmes, Department of Biochemistry and Biotechnology, KNUST
• 2015 – 2017, Co-Chair, Users-Support Working Group, Pan African Bioinformatics Network
• 2013 to Date: Member, National TB Laboratory Technical Committee
• 09/2012-11/2013 Head of Laboratories, Kumasi Centre for Collaborative Research into Tropical Medicine, Kwame Nkrumah University of Science and
• 01/2012 – 08/2012  Research  Fellow  in  the  Microbiology  and  Biotechnology  group  of Dr. S. Foley, Edinburgh Napier University, UK

Instructor of the following courses

For MSc., MPhil and PhD.

• Genome and Gene Expression
• High throughput Sequencing and GWAS
• Nutrigentics and Nutrigenomics
• Advanced Forensic DNA Technologies
• Molecular Biology Techniques
• Crime Scene Investigation
• Forensic Toxicology

For BSc.

• Integrated Laboratory Methods
• Practical Biomolecular Techniques
• Fundamentals of Bioinformatics

Other Professionally Related Experience

• Professional Member, African Society for Computational Biology (2017 to date)
• Professional Member, Ghana Science Association (2017 to date)
• Professional Member, Ghana Biomedical Convention (2012 to date)
• Professional Member, International Society for Computational Biology (2017 to date)
• Professional Member, American Society for Microbiology (2012 to date)
• Professional Member, African Society for Human Genetics (2012 to date
• Member, University Teachers Association of Ghana (2013 to date)

Active and Ongoing Research

1. Unraveling the genetic signatures of African patients with Burkitt Lymphoma
2. Developing algorithm for denoising the single cell RNA-seq count data for differential gene expression analysis
3. Molecular profiling of breast cancer in diverse ethnic groups
4. The gastric microbiota and its influence on the pathogenesis of gastric cancer patients
5. Comparative complete genome analyses of Helicobacter pylori isolates across  Africa
6. Development of human reference genome for Africa population
7. Novel tool for detection of genetic copy number variation in human genome

Highlights of Five Selected Peer-review Publications

1. Globally, about 1.24 million cases of hematologic malignancies are recorded, of which 58% die. Early detection remains a challenge and prognostic markers are unreliable. In this study, we mined public databases for RNA-seq data on four common HMs to identify novel biomarkers that could serve as HM management and treatment targets. Applying special bioinformatics analysis, we showed that high expression of the following genes: SRSF1 (Serine/Arginine Splicing Factor 1), SRSF6 (Serine/Arginine Splicing Factor 6), UBE2Z (Ubiquitin Conjugating Enzyme 2Z) and PCF11 (Cleavage and Polyadenylation Factor Subunit 11), and low expression of HECW2 (E3 Ubiquitin-Protein Ligase) were correlated with poor prognosis in hematologic malignancies. Publication: Salifu, S. P. and Doughan, (2022). New clues to prognostic biomarkers of four hematological malignancies. J Cancer; 13(8):2490-2503. doi:10.7150/jca.69274.
2. Burkitt lymphoma (BL) is one of the most aggressive forms of non-Hodgkin’s lymphomas that affect children and young The expression of genes and other molecular markers during carcinogenesis can be the basis for diagnosis, prognosis and the design of new and effective drugs for the management of  cancers. The aim of this study was to identify genes that can serve as prognostic  and therapeutic targets for BL. We analysed RNA-seq data of BL transcriptome sequencing projects in Africa using standard RNA-seq analyses pipeline. We  showed that six genes (ADAMTSL4, SEMA5B, ADAMTS15, THBS2, SPON1 and THBS1) were associated to survival of Burkitt lymphoma patients and that can serve as biomarkers for prognosis for Burkitt Lymphoma management. Publication: Doughan A, Salifu SP. (2022) Genes associated with diagnosis and prognosis of Burkitt lymphoma. IET Syst Biol. 2022 Nov 10. doi: 10.1049/syb2.12054.  Epub ahead of print. PMID: 36354023.

3. Meningitis remains significant burden in Ghana health care with frequent lost of lives during outbreaks of the disease. The transmission dynamics of the disease keep changing as a result of movement and interaction of individuals from low-risk to high-risk meningitis affected areas during outbreak season. In this study, we explored the mechanisms to manage and prevent the disease at minimal We developed a mathematical model that ascertains the dynamics involved in meningitis transmissions and showed that the best and most cost effective strategy to control meningitis is to combine vaccination with treatment vis-à-vis Ghana’s current approach, largely treatment of affected cases. Publication: Opoku, NKO, Borkor, RN, Adu, AF, Nyarko, HN, Doughan, A, Appiah, EM, Yakubu, B, Mensah, I, Salifu, SP (2022) Modelling the Transmission Dynamics of Meningitis among High and Low-Risk People in Ghana with Cost-Effectiveness Analysis”, Abstract and Applied Analysis, vol.  2022,  Article  ID  9084283,  24  pages, 2022.https://doi.org/10.1155/2022/9084283

4. Currently, free and public available bioinformatics supports to African researchers are limited. As a Co-Chair of bioinformatics users support, we developed and implemented user support platform. We evaluated the framework using automatically generated logs, user feedback and qualitative tickets, which revealed that communication methods, ticketing strategies and technical platforms are key to effectiveness of help desk platform for bioinformatics community and the resources should be regularly monitored and Publication: Kumuthini, J., Zass, L., Panji, S., Salifu, S. P., Kayondo, J. K., Nembaware,V., Mbiyavanga, M., Olabode,A., Kishk, A., Wells, G., Mulder, N. J. and as members of the Sustainability and Outreach Work Package of the H3ABioNet Consortium (2019). The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa’s capacity for genomics research. BMC bioinformatics, 20(1), 741. doi:10.1186/s12859-019- 3322-3
5. Africa is not unique in its need for basic bioinformatics training for individuals from diverse range of academic backgrounds. However, logistical challenges in Africa, most notably access to bioinformatics expertise and Internet stability must be addressed in order to meet this need on the continent. We developed innovative, free-of-charge introduction to bioinformatics course, taking these challenges into account to provide on-site training and develop local expertise in   We  enrolled 364 participants in 20 institutions across African countries with trainers pre-recorded their lectures, uploaded on a learning Moodle. The classrooms downloaded and watched the recordings locally during contact sessions. The  trainers were available via video conferencing to take questions during contact sessions, as well as via online questions and discussion forum outside the contact session time. Publication: Gurwitz, K. T., Aron, S., Panji, S., Maslamoney, S., Fernandes, P. L., Judge, D. P., Ghouila, A., Entfellner, J. B. D., Guerfali, F. Z., Saunders, C., Alzohairy, A. M., Salifu, S. P., Ahmed, R., Cloete, R., Kayondo, J., Ssemwanga, D. and Mulder, N. (2017). Designing a course model for distance- based online bioinformatics training in Africa: The H3ABioNet experience. PLoS Computational Biology, 13(10): e1005715

Selected Peer-reviewed Publications

6. Salifu, S. P. and Doughan, A. (2022). New clues to prognostic biomarkers of four hematological J Cancer; 13(8):2490-2503. doi:10.7150/jca.69274.
7. Doughan A, and Salifu SP. (2022) Genes associated with diagnosis and prognosis of Burkitt lymphoma. IET Syst Biol. 2022 Nov 10. doi: 10.1049/syb2.12054. Epub ahead of print. PMID:
8. Opoku, NKO, Borkor, RN, Adu, AF, Nyarko, HN, Doughan, A, Appiah, EM, Yakubu, B, Mensah, I, Salifu, SP (2022) Modelling the Transmission Dynamics of Meningitis among High and Low-Risk People in Ghana with Cost-Effectiveness Analysis”, Abstract and Applied Analysis, vol. 2022, Article ID 9084283, 24 pages, 2022.https://doi.org/10.1155/2022/9084283
9. Schwartz, R., Brooksbank, C., Gaeta, B., Mulder, N., Morgan, S., Satagopam, V., Ras, V., Salifu, P., Tyagi, S., Mazandu, G. K., Aron, S., Lloret-Llinares, M., Kumuthini, J., Brazas, M., Gall, A., Moore, B., & Holinski. A., (2021). Guidelines for developing and updating short courses and course programs using the ISCB  competency framework (0.1). Zenodo. https://doi.org/10.5281/zenodo.541810
10. Ghazal H, Adam Y, Idrissi Azami A, Sehli S, Nyarko HN, Chaouni B, Olasehinde G, Isewon I, Adebiyi M, Ajani O, Matovu E, Obembe O, Ajamma Y, Kuzamunu G, Pandam Salifu S, Kayondo J, Benkahla A, Adebiyi (2021). Plant genomics in Africa: present and prospects. Plant J. 2021 Jul;107(1):21-36. doi: 10.1111/tpj.15272. Epub 2021 Jul 2. Review. PubMed PMID: 33837593.

Conference Papers

1. Salifu, S. P. (2022). Collection in Africa: An Overview of What Exists and Possibility

of Microbiota Collection, 2^nd Global Microbiome Network Symposium, 13-14th June 2022

2. Appiah, E. and Salifu, S. P. (2022). Gastric Microbiome and Gastric Carcinogenesis: Bacterial Diversity, Co-occurrence Patterns and Predictive Models, Microbiome in Health and Diseases, Welcome Connecting Science, UK (Virtual), 24-26th October 2022
3. Appiah, E. and Salifu, S. P. (2022). Gastric Microbiome and Gastric Carcinogenesis: Bacterial Diversity, Co-occurrence Patterns and Predictive Models., African Microbiome Day, September, 2022
4. Appiah,    M.   and   Salifu,   S. P.  (2022).      Gastric Microbiome and Gastric

Carcinogenesis: Bacterial Diversity, Co-occurrence Patterns and Predictive Models. Intelligent Systems in Molecular Biology, Madison, USA (virtual), 10-14th July 2022

5. Appiah,  M.      and Salifu, S. P. (2022). Gastric Microbiome and Gastric

Carcinogenesis: Bacterial Diversity, Co-occurrence Patterns, 3rd Annual Global Health in Bioinformatics Symposium, Mali (Virtual), 6th June 2022

6. Appiah, E. and Salifu, S. P. (2022). Gastric Microbiome Predictive Models for Gastric Carcinogenesis, H3Africa 19th Consortium Meeting, Abuja , Nigeria, 30th May – 2nd June 2022
7. Adu, A. F. and Salifu, S. P. (2022). Benchmarking of ten assembly methods for assembling African genomes using PacBio HiFi sequencing data, International Genome Graph Symposium 2022, Monte Verita, Switzerland, 3^rd-7^th July 2022
8. Adu, A. F. and Salifu, S. P. (2022). Benchmarking of long-read Assembly Tools for Analysing African Genomes, H3Africa 19th Consortium Meeting, Abuja , Nigeria,  30^th May – 2^nd June 2022
9. Opoku, N. and Salifu, S. P. (2022). Comprehensive Benchmarking of Detecting Copy Number Variants Tools Using Whole-Exome Sequencing, H3Africa 19th Consortium Meeting, Abuja , Nigeria, 30^th May – 2^nd June 2022

Reference

• Available on request