Rafi Ahmad

Førsteamanuensis
Avd./Fakultet:
Enhet:
Institutt for bioteknologi
Besøksadresse:
Rom: 2N1248
Biohuset
Holsetgata 22 N-2317 Hamar
Kart
Postadresse:
Høgskolen i Innlandet
Postboks 400
2418 Elverum

Faglige interesser

Research prize for 2018 to research group 

AMR-Diag project mentioned as a is a defining characteristic of INN University

Link to INN Bioinformatics Strategic Area, lead by Rafi

Talk at Forkningsdagene on Antibiotic Resistance (2017) ;

Talk at Forkningsdagene on Antibiotic Resistance (2018)

News about new project funding from RCN on ABR

Rafi in Media1

Rafi in NRK news from (skip to time 1:20)

Rafi in Media2

Bakgrunn

Rafi is the project leader for two RCN projects ( AMR-Diag and ABR-Diag) on novel diagnostics for antibiotic resistance and is the WP leader for a number of RCN, RFFI and Helse Sør Øst funded projects.

He is affiliated to Nor-OpenScreen (the Norwegian node of the EU-Openscreen infrastructure project) via an MoU with Prof. Kjetil Tasken, Biotechnology Centre, University of Oslo/Oslo University Hospital (OUS).

He is also part of the TTA - Turning the Tide of Antimicrobial resistance consortium ( https://www.ous-research.no/amr/), which is lead by the Oslo University Hospital.

Brief CV

Education Profile

1996 - 2000 Bachelor of Pharmacy, Jamia Hamdard, Delhi, India

2000 - 2001 Master of Science in Bioinformatics, University of Exeter, UK

2004 - 2008 PhD Bioinformatics & Drug Discovery, University of Tromsø, Norway

Work Experience

2018 - Till Date Associate Professor, UiT- The Arctic University of Norway, Tromsø (50% position from Nov-2018)

2016 - Till Date Associate Professor, Inland Norway University of Applied Sciences, Hamar, Norway (70% position from Nov-2018)

2017 -  Expert reviewer for EU H2020 grant applications

2013 - 2015 Leader New Molecule Profiling, Open Innovation, AstraZeneca, Molndal, Sweden

2011 - 2013 Senior Research Scientist, Medivir AB, Stockholm, Sweden

2012 - 2013 Project Leader, Antibiotic Resistance, Medivir AB, Stockholm, Sweden

2008 - 2011 Post Doc Drug Discovery and Design, Norwegian Structural Biology Centre, University of Tromsø, Norway

2002 - 2004 Research Scientist, Team Leader, Accerlys Inc., Banglore, India

Current Students

PostDoc

2017-2020

Abdolrahman

2018-2021

Ekaterina Avershina

2018-2019

Stephan Frye

PhD

2018 - 2021

Yusuf Khan

Master (M. Sc 1 year project) - Current

Roshan Mandal

Sanjeev Shakya

Bijay Thapa

Master (M. Sc 1 year project) - Past (2016 onwards)

Lana Kragulj, Narayan Prasad Koirala, Prabin Bhandari, Elizabeth Wirsiy, Valentina Krivenjeva, Ewelina Rojek, Mithlesh Kumar Ray

Prosjekter (4)

Forskningsområder

Bioteknologi

Ekspertområder

Bioinformatics, Biotechnology, Drug Discovery, Antibiotic Resistance, Big Data Analysis, Next Generation Sequencing, Genomics

Publikasjoner (50)

Utvalgte (50)

  • Ahmad, Rafi (). AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance.
  • Ray, Mithlesh Kumar; Kommisrud, Elisabeth; Ahmad, Rafi (). Bioinformatics analysis of epigenetic data from bull and boar semen samples. Høgskolen i Hedmark. 76 s.
  • Wirsiy, Elizabeth Musah; Larsen, Frank; Ahmad, Rafi (). Feasibility of using a sequence-based method (AMR-Diag) for detection of antibiotic resistance in Humans. Høgskolen i Hedmark. 52 s.
  • Harstad, Håvard; Bredberg, Anders; Ahmad, Rafi (). Nanopore-based DNA sequencing in clinical microbiology: preliminary assessment of basic requirements.
  • Ahmad, Rafi; Rojek, Ewelina; Naseer, Mohammed Umaer (). Molecular typing, antimicrobial resistance profiling and phylogeny of Campylobacter based on whole genome sequencing. Høgskolen i Hedmark. 71 s.
  • Ahmad, Rafi (). AMR-Diag: A Novel Diagnostic Tool for Sequence-Based Prediction of Antimicrobial Resistance.
  • Ahmad, Rafi (). AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance..
  • Ahmad, Rafi (). AMR-Diag - et sanntids- og kostnadseffektivt diagnostisk verktøy for påvisning av antibakteriell resistens.
  • Yang, Yu; Stathis, Dimitrios; Sharma, Prashant; Paul, Kolin; Hemani, Ahmed; Grabherr, Manfred G.; Ahmad, Rafi (). RiBoSOM: Rapid Bacterial Genome Identification Using Self-Organizing Map implemented on the Synchoros SiLago Platform.
  • Yang, Yu; Stathis, Dimitrios; Sharma, Prashant; Paul, Kolin; Hemani, Ahmed; Grabherr, Manfred G.; Ahmad, Rafi (). RiBoSOM: Rapid Bacterial Genome Identification Using Self-Organizing Map implemented on the Synchoros SiLago Platform. Association for Computing Machinery (ACM). ISBN 978-1-4503-6494-2. 10 s.
  • Thode, Sunniva Katharina; Rojek, Ewelina; Kozlowski, Mikolaj; Ahmad, Rafi; Haugen, Peik (). Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives.
  • Krivenjeva, Valentina; Wilson, Robert Charles; Ahmad, Rafi (). Bioinformatic Analysis of RNA-seq Data from Cultivated Strawberry (Fragaria x ananassa) and Experimental Validation of New Transcripts Related to Cold Tolerance. Høgskolen i Hedmark. 98 s.
  • Kragulj, Lana; Solberg, Trygve Roger; Ahmad, Rafi (). Investigating Cattle as a Potential Model to Study Human Diseases - Including Genome-Wide Association Studies and Comparative Genomics Between the Species. Høgskolen i Hedmark. 91 s.
  • Koirala, Narayan Prasad; Naseer, Mohammed Umaer; Ahmad, Rafi (). Comparing different whole genome sequence based phylogenetic approaches for the description of enterohemorrhagic Escherichia coli O103 in Norway from 2006-2016. Høgskolen i Hedmark. 73 s.
  • Dukic, Aleksandra; Guillaume, Pidoux; Ahmad, Rafi; Tasken, Kjetil (). Targeting the Connexin43-Ezrin interaction.
  • Dukic, Aleksandra; Ahmad, Rafi; Tasken, Kjetil (). Targeting the Connexin43-Ezrin interaction.
  • Ahmad, Rafi (). AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance.
  • Ahmad, Rafi (). Utvikling av nye antibiotika og diagnostikk.
  • Ahmad, Rafi; Borowiec, Paulina; Falck-Ytter, Anne Bergljot; Strætkvern, Knut Olav (). Extraction, Solubility and Antimicrobial Activity of (-) Usnic Acid in Ethanol, a Pharmaceutically Relevant Solvent.
  • Slettli, Victoria Konovalenko; Svarva, Frøydis; Danielsen, Anette; Ahmad, Rafi (). The use of Liberating structures in the teaching practice of the lecturers at Inland Norway University of Applied Sciences.
  • Ahmad, Rafi (). Bioinformatics: application and potential.
  • Ahmad, Rafi (). Human Genetics and Next Generation Sequencing.
  • Ahmad, Rafi (). Bioinformatics projects at Hedmark University of Applied Sciences.
  • Ahmad, Rafi (). Bioinformatics projects at Hedmark University of Applied Sciences.
  • Ahmad, Rafi (). Bioinformatics: Application and Potential.
  • Bhandari, Prabin; Wilson, Robert Charles; Ahmad, Rafi (). Bioinformatic Analysis of RNA-Seq Data from Cultivated Strawberry (Fragaria x ananassa) and Identification of Transcripts Related to Cold Tolerance. Høgskolen i Hedmark. 85 s.
  • Liang, Zhe; Demko, Viktor; Wilson, Robert Charles; Johnson, Kenneth; Ahmad, Rafi; Perroud, Pierre-Francois; Quatrano, Ralph; Zhao, Sen; Shalchian-Tabrizi, Kamran; Otegui, Marisa; Olsen, Odd-Arne; Johansen, Wenche (). The catalytic domain CysPc of the DEK1 calpain is functionally conserved in land plants.
  • Ahmad, Rafi; Hansen, Geir Åsmund; Hansen, Hilde; Hjerde, Erik; Pedersen, hege lynum; Paulsen, steinar; Nyrud, May Liss Julianne; Strauss, Anja; Willassen, Nils Peder; Haugen, Peik (). Prediction, microarray and northern blot analyses identify new intergenic small RNAs in aliivibrio salmonicida.
  • Hansen, Geir Åsmund; Ahmad, Rafi; Hjerde, erik; Fenton, Christopher Graham; Willassen, Nils Peder; Haugen, Peik (). Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida. 12 s.
  • Ahmad, Rafi (). Computer-aided discovery of Endonuclease I inhibitors and their potential commercial applications..
  • Ahmad, Rafi (). Insight into Computer-aided drug design: A Kinase Case Study.
  • Oliveira, Taiana Maia De; Ahmad, Rafi; Engh, Richard Alan (). VX680 Binding in Aurora A: pi-pi Interactions Involving the Conserved Aromatic Amino Acid of the Flexible Glycine-Rich Loop.
  • Saradhi, Pardha; Leiros, Hanna-Kirsti S.; Ahmad, Rafi; Spencer, James; Leiros, Ingar; Walsh, Timothy R.; Sundsfjord, Arnfinn; Samuelsen, Ørjan (). Structural and Computational Investigations of VIM-7: Insights into the Substrate Specificity of VIM Metallo-beta-Lactamases.
  • Ahmad, Rafi (). VX680 Binding Interactions with the Glycine Rich Loop Aromat of Aurora A..
  • Drabløs, Finn; Petersen, Kjell; Johansen, Jostein; Nygård, Ståle; Ahmad, Rafi; Smalås, Arne; Hovig, Eivind; Jonassen, Inge (). The FUGE Bioinformatics platform: a central platform in the FUGE2 period.
  • Drabløs, Finn; Petersen, Kjell; Johansen, Jostein; Nygård, Ståle; Ahmad, Rafi; Smalås, Arne; Hovig, Eivind; Jonassen, Inge (). The FUGE Bioinformatics platform: a central platform in the FUGE2 period.
  • Pedersen, hege lynum; Ahmad, Rafi; Riise, EK; Leiros, Hanna-Kirsti S.; Hauglid, Stefan; Espelid, S; Brandsdal, Bjørn Olav; Leiros, Ingar; Willassen, Nils P; Haugen, Peik (). Experimental and computational characterization of the ferric uptake regulator from Aliivibrio salmonicida (Vibrio salmonicida).
  • Ahmad, Rafi (). Fur protein: Binding free energy calculations and per-residue free energy decomposition..
  • Ahmad, Rafi; Brandsdal, Bjørn Olav; Michaud-Soret, Isabelle; Willassen, Nils Peder (). Ferric uptake regulator protein: Binding free energy calculations and per-residue free energy decomposition.
  • Ahmad, Rafi; Hjerde, erik; Hansen, Geir Åsmund; Haugen, Peik; Willassen, Nils Peder (). Prediction and Experimental Testing of Ferric Uptake Regulator Regulons in Vibrios.
  • Ahmad, Rafi (). A Computational Study of the Ferric Uptake Regulator from Vibrios: Structure, Function & Biological Role. ISBN 978-82-7589-213-1. 110 s.
  • Ahmad, Rafi; Brandsdal, Bjørn Olav; Michaud-Soret, Isabelle; Willassen, Nils Peder (). Ferric uptake regulator protein: Binding free energy calculations and per-residue free energy decomposition.
  • Ahmad, Rafi; Hjerde, erik; Hansen, Geir Åsmund; Haugen, Peik; Willassen, Nils Peder (). Prediction and Experimental Testing of Ferric Uptake Regulator Regulons in Vibrios. 10 s.
  • Ahmad, Rafi (). Discovery by chance: The sRNA2 story.
  • Ahmad, Rafi (). Fur: Modeling and Simulation studies.
  • Ahmad, Rafi (). Prediction and experimental testing of Fur regulons in vibrios.
  • Ahmad, Rafi (). Prediction and experimental testing of Fur regulons in vibrios.
  • Fenton, christopher graham; Ahmad, Rafi; Sælensminde, Gisle; Willassen, Nils Peder (). Envision Software Package for the Concerted Study of Biological Data.
  • Hansen, Geir Å; Krentz, Corinne; Ahmad, Rafi; Haugen, Peik; Paulsen, steinar; Willassen, Nils Peder (). Identification of small RNAs involved in iron homeostasis and quorum sensing in Vibrio salmonicida and V. fischeri.
  • Ahmad, Rafi (). DiaBase: An information resource for molecular target-based drug discovery for diabetes.

Vitenskapelige artikler og bokkapitler (13)

  • Yang, Yu; Stathis, Dimitrios; Sharma, Prashant; Paul, Kolin; Hemani, Ahmed; Grabherr, Manfred G.; Ahmad, Rafi (). RiBoSOM: Rapid Bacterial Genome Identification Using Self-Organizing Map implemented on the Synchoros SiLago Platform.
  • Thode, Sunniva Katharina; Rojek, Ewelina; Kozlowski, Mikolaj; Ahmad, Rafi; Haugen, Peik (). Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives.
  • Ahmad, Rafi; Borowiec, Paulina; Falck-Ytter, Anne Bergljot; Strætkvern, Knut Olav (). Extraction, Solubility and Antimicrobial Activity of (-) Usnic Acid in Ethanol, a Pharmaceutically Relevant Solvent.
  • Liang, Zhe; Demko, Viktor; Wilson, Robert Charles; Johnson, Kenneth; Ahmad, Rafi; Perroud, Pierre-Francois; Quatrano, Ralph; Zhao, Sen; Shalchian-Tabrizi, Kamran; Otegui, Marisa; Olsen, Odd-Arne; Johansen, Wenche (). The catalytic domain CysPc of the DEK1 calpain is functionally conserved in land plants.
  • Ahmad, Rafi; Hansen, Geir Åsmund; Hansen, Hilde; Hjerde, Erik; Pedersen, hege lynum; Paulsen, steinar; Nyrud, May Liss Julianne; Strauss, Anja; Willassen, Nils Peder; Haugen, Peik (). Prediction, microarray and northern blot analyses identify new intergenic small RNAs in aliivibrio salmonicida.
  • Hansen, Geir Åsmund; Ahmad, Rafi; Hjerde, erik; Fenton, Christopher Graham; Willassen, Nils Peder; Haugen, Peik (). Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida. 12 s.
  • Oliveira, Taiana Maia De; Ahmad, Rafi; Engh, Richard Alan (). VX680 Binding in Aurora A: pi-pi Interactions Involving the Conserved Aromatic Amino Acid of the Flexible Glycine-Rich Loop.
  • Saradhi, Pardha; Leiros, Hanna-Kirsti S.; Ahmad, Rafi; Spencer, James; Leiros, Ingar; Walsh, Timothy R.; Sundsfjord, Arnfinn; Samuelsen, Ørjan (). Structural and Computational Investigations of VIM-7: Insights into the Substrate Specificity of VIM Metallo-beta-Lactamases.
  • Pedersen, hege lynum; Ahmad, Rafi; Riise, EK; Leiros, Hanna-Kirsti S.; Hauglid, Stefan; Espelid, S; Brandsdal, Bjørn Olav; Leiros, Ingar; Willassen, Nils P; Haugen, Peik (). Experimental and computational characterization of the ferric uptake regulator from Aliivibrio salmonicida (Vibrio salmonicida).
  • Ahmad, Rafi; Brandsdal, Bjørn Olav; Michaud-Soret, Isabelle; Willassen, Nils Peder (). Ferric uptake regulator protein: Binding free energy calculations and per-residue free energy decomposition.
  • Ahmad, Rafi; Hjerde, erik; Hansen, Geir Åsmund; Haugen, Peik; Willassen, Nils Peder (). Prediction and Experimental Testing of Ferric Uptake Regulator Regulons in Vibrios.
  • Ahmad, Rafi; Brandsdal, Bjørn Olav; Michaud-Soret, Isabelle; Willassen, Nils Peder (). Ferric uptake regulator protein: Binding free energy calculations and per-residue free energy decomposition.
  • Ahmad, Rafi; Hjerde, erik; Hansen, Geir Åsmund; Haugen, Peik; Willassen, Nils Peder (). Prediction and Experimental Testing of Ferric Uptake Regulator Regulons in Vibrios. 10 s.

Bøker (9)

  • Ray, Mithlesh Kumar; Kommisrud, Elisabeth; Ahmad, Rafi (). Bioinformatics analysis of epigenetic data from bull and boar semen samples. Høgskolen i Hedmark. 76 s.
  • Wirsiy, Elizabeth Musah; Larsen, Frank; Ahmad, Rafi (). Feasibility of using a sequence-based method (AMR-Diag) for detection of antibiotic resistance in Humans. Høgskolen i Hedmark. 52 s.
  • Ahmad, Rafi; Rojek, Ewelina; Naseer, Mohammed Umaer (). Molecular typing, antimicrobial resistance profiling and phylogeny of Campylobacter based on whole genome sequencing. Høgskolen i Hedmark. 71 s.
  • Yang, Yu; Stathis, Dimitrios; Sharma, Prashant; Paul, Kolin; Hemani, Ahmed; Grabherr, Manfred G.; Ahmad, Rafi (). RiBoSOM: Rapid Bacterial Genome Identification Using Self-Organizing Map implemented on the Synchoros SiLago Platform. Association for Computing Machinery (ACM). ISBN 978-1-4503-6494-2. 10 s.
  • Krivenjeva, Valentina; Wilson, Robert Charles; Ahmad, Rafi (). Bioinformatic Analysis of RNA-seq Data from Cultivated Strawberry (Fragaria x ananassa) and Experimental Validation of New Transcripts Related to Cold Tolerance. Høgskolen i Hedmark. 98 s.
  • Kragulj, Lana; Solberg, Trygve Roger; Ahmad, Rafi (). Investigating Cattle as a Potential Model to Study Human Diseases - Including Genome-Wide Association Studies and Comparative Genomics Between the Species. Høgskolen i Hedmark. 91 s.
  • Koirala, Narayan Prasad; Naseer, Mohammed Umaer; Ahmad, Rafi (). Comparing different whole genome sequence based phylogenetic approaches for the description of enterohemorrhagic Escherichia coli O103 in Norway from 2006-2016. Høgskolen i Hedmark. 73 s.
  • Bhandari, Prabin; Wilson, Robert Charles; Ahmad, Rafi (). Bioinformatic Analysis of RNA-Seq Data from Cultivated Strawberry (Fragaria x ananassa) and Identification of Transcripts Related to Cold Tolerance. Høgskolen i Hedmark. 85 s.
  • Ahmad, Rafi (). A Computational Study of the Ferric Uptake Regulator from Vibrios: Structure, Function & Biological Role. ISBN 978-82-7589-213-1. 110 s.

Vitenskapelige konferansebidrag (12)

  • Ahmad, Rafi (). AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance.
  • Ahmad, Rafi (). AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance..
  • Dukic, Aleksandra; Guillaume, Pidoux; Ahmad, Rafi; Tasken, Kjetil (). Targeting the Connexin43-Ezrin interaction.
  • Dukic, Aleksandra; Ahmad, Rafi; Tasken, Kjetil (). Targeting the Connexin43-Ezrin interaction.
  • Ahmad, Rafi (). AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance.
  • Ahmad, Rafi (). VX680 Binding Interactions with the Glycine Rich Loop Aromat of Aurora A..
  • Drabløs, Finn; Petersen, Kjell; Johansen, Jostein; Nygård, Ståle; Ahmad, Rafi; Smalås, Arne; Hovig, Eivind; Jonassen, Inge (). The FUGE Bioinformatics platform: a central platform in the FUGE2 period.
  • Ahmad, Rafi (). Prediction and experimental testing of Fur regulons in vibrios.
  • Ahmad, Rafi (). Prediction and experimental testing of Fur regulons in vibrios.
  • Fenton, christopher graham; Ahmad, Rafi; Sælensminde, Gisle; Willassen, Nils Peder (). Envision Software Package for the Concerted Study of Biological Data.
  • Hansen, Geir Å; Krentz, Corinne; Ahmad, Rafi; Haugen, Peik; Paulsen, steinar; Willassen, Nils Peder (). Identification of small RNAs involved in iron homeostasis and quorum sensing in Vibrio salmonicida and V. fischeri.
  • Ahmad, Rafi (). DiaBase: An information resource for molecular target-based drug discovery for diabetes.

Annet (16)

  • Harstad, Håvard; Bredberg, Anders; Ahmad, Rafi (). Nanopore-based DNA sequencing in clinical microbiology: preliminary assessment of basic requirements.
  • Ahmad, Rafi (). AMR-Diag: A Novel Diagnostic Tool for Sequence-Based Prediction of Antimicrobial Resistance.
  • Ahmad, Rafi (). AMR-Diag - et sanntids- og kostnadseffektivt diagnostisk verktøy for påvisning av antibakteriell resistens.
  • Ahmad, Rafi (). Utvikling av nye antibiotika og diagnostikk.
  • Slettli, Victoria Konovalenko; Svarva, Frøydis; Danielsen, Anette; Ahmad, Rafi (). The use of Liberating structures in the teaching practice of the lecturers at Inland Norway University of Applied Sciences.
  • Ahmad, Rafi (). Bioinformatics: application and potential.
  • Ahmad, Rafi (). Human Genetics and Next Generation Sequencing.
  • Ahmad, Rafi (). Bioinformatics projects at Hedmark University of Applied Sciences.
  • Ahmad, Rafi (). Bioinformatics projects at Hedmark University of Applied Sciences.
  • Ahmad, Rafi (). Bioinformatics: Application and Potential.
  • Ahmad, Rafi (). Computer-aided discovery of Endonuclease I inhibitors and their potential commercial applications..
  • Ahmad, Rafi (). Insight into Computer-aided drug design: A Kinase Case Study.
  • Drabløs, Finn; Petersen, Kjell; Johansen, Jostein; Nygård, Ståle; Ahmad, Rafi; Smalås, Arne; Hovig, Eivind; Jonassen, Inge (). The FUGE Bioinformatics platform: a central platform in the FUGE2 period.
  • Ahmad, Rafi (). Fur protein: Binding free energy calculations and per-residue free energy decomposition..
  • Ahmad, Rafi (). Discovery by chance: The sRNA2 story.
  • Ahmad, Rafi (). Fur: Modeling and Simulation studies.