About Me

Download Curriculum Vitae

My name is Muhammad Arif and I'm from Indonesia. Currently I'm residing in a nice suburb area of Stockholm, Sweden, together with my small family.

Current Work and Education
I'm a PhD student at KTH Royal Institute of Technology and also Science for Life Laboratory (SciLifeLab) under the supervision of Professor Adil Mardinoglu and Professor Mathias Uhlén. I'm part of Systems Medicine group at SciLifeLab.

PhD and Collaborative Projects
My PhD project is focusing on the use of systems biology to understand the underlying mechanism of cardiovascular disease (CVD). As part of my education and works, I'm involved in multiple projects including single-cell transcriptional analysis, biological network (co-expression and regulatory network), multi-omics integration, metabolic modelling and proteomics analysis.

Interests in Research and Education
My interests are in the development and implementation of machine learning and network analysis methods in biological context. On top of research activity, I'm very interested as well in teaching (both introductory and advanced level) and doing outreach programs.
If you have any collaboration for research or teaching, or even side projects, please drop me a message.

Publications

(*: First/Co-First Author)

Key Publications

The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non‐alcoholic fatty liver disease
Molecular Systems Biology
C Zhang*, E Bjornson*, M Arif*, A Tebani, A Lovric, R Benfeitas, M Ozcan, K Juszczak, W Kim, JT Kim, G Bidkhori, M Ståhlman, PO Bergh, M Adiels, H Turkez, MR Taskinen, J Bosley, HU Marschall, J Nielsen, M Uhlén, J Borén, A Mardinoglu
MOBN: an interactive database of multi-omics biological networks
BioRxiv
C Zhang*, M Arif*, X Li, S Lee, A Tebani, W Zhou, BD Piening, L Fagerberg, N Price, L Hood, MP Snyder, J Nielsen, M Uhlen, A Mardinoglu
TCSBN: a database of tissue and cancer specific biological networks
Nucleic acids research
S Lee*, C Zhang*, M Arif*, Z Liu, R Benfeitas, G Bidkhori, S Deshmukh, MA Shobky, A Lovric, J Boren, J Nielsen, M Uhlen, A Mardinoglu
A pathology atlas of the human cancer transcriptome
Science
M Uhlen, C Zhang, S Lee, E Sjöstedt, L Fagerberg, G Bidkhori, R Benfeitas, M Arif, Z Liu, F Edfors, K Sanli, K Feilitzen, P Oksvold, E Lundberg, S Hober, P Nilsson, J Mattsson, JM Schwenk, H Brunnström, B Glimelius, T Sjöblom, PH Edqvist, D Djureinovic, P Micke, C Lindskog, A Mardinoglu, F Ponten
Scalable 5-Tuple Packet Classification in Overlay Network-Based SDN
KTH Master Thesis Project
M Arif (Supervisors: Dr. Viktoria Fodor (KTH) and Dr. Albert Cabellos(UPC))

2020

Integration of molecular profiles in a longitudinal wellness profiling cohort
Nature Communications
A Tebani, A Gummesson, W Zhong, IS Koistinen, T Lakshmikanth, LM Olsson, F Boulund, M Neiman, H Stenlund, C Hellström, MJ Karlsson, M Arif, T Dodig-Crnković, A Mardinoglu, S Lee, C Zhang, Y Chen, A Olin, J Mikes, H Danielsson, K Feilitzen, PA Jansson, O Angerås, M Huss, S Kjellqvist, J Odeberg, F Edfors, V Tremaroli, B Forsström, JM Schwenk, P Nilsson, T Moritz, F Bäckhed, L Engstrand, P Brodin, G Bergström, M Uhlen, L Fagerberg
Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women
Cell Reports
M Chapman, M Arif, E B Emanuelsson, S M Reitzner, M E Lindholm, A Mardinoglu, C J Sundberg
The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non‐alcoholic fatty liver disease
Molecular Systems Biology
C Zhang*, E Bjornson*, M Arif*, A Tebani, A Lovric, R Benfeitas, M Ozcan, K Juszczak, W Kim, JT Kim, G Bidkhori, M Ståhlman, PO Bergh, M Adiels, H Turkez, MR Taskinen, J Bosley, HU Marschall, J Nielsen, M Uhlén, J Borén, A Mardinoglu
Classification of clear cell renal cell carcinoma based on PKM alternative splicing
Heliyon
X Li, B Turanli, K Juszczak, W Kim, M Arif, Y Sato, S Ogawa, H Turkez, J Nielsen, J Boren, M Uhlen, C Zhang, A Mardinoglu
Boosting Natural Killer Cell-Mediated Targeting of Sarcoma Through DNAM-1 and NKG2D
Frontiers in Immunology
EC Sayitoglu, AM Georgoudaki, M Chrobok, D Ozkazanc, BJ Josey, M Arif, K Kusser, M Hartman, TM Chinn, R Potens, C Pamukcu, R Krueger, C Zhang, A Mardinoglu, E Alici, HT Temple, T Sutlu, AD Duru

2019

Cardiac expression of the microsomal triglyceride transport protein protects the heart function during ischemia
Journal of molecular and cellular cardiology
M Klevstig, M Arif, M Mannila, S Svedlund, I Mardani, M Ståhlman, L Andersson, M Lindbom, A Miljanovic, A Franco-Cereceda, P Eriksson, A Jeppsson, LM Gan, M Levin, A Mardinoglu, E Ehrenborg, J Borén
Pyruvate kinase L/R is a regulator of lipid metabolism and mitochondrial function
Metabolic engineering
Z Liu, C Zhang, S Lee, W Kim, M Klevstig, AM Harzandi, N Sikanic, M Arif, M Ståhlman, J Nielsen, M Uhlen, J Boren, A Mardinoglu
Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis
EBioMedicine
R Benfeitas, G Bidkhori, B Mukhopadhyay, M Klevstig, M Arif, C Zhang, S Lee, R Cinar, J Nielsen, M Uhlen, J Boren, G Kunos, A Mardinoglu
Discovery of functional alternatively spliced PKM transcripts in human cancers
BioRxiv
X Li, C Zhang, W Kim, M Arif, C Gao, A Hober, D Kotol, L Strandberg, B Forsström, Å Sivertsson, P Oksvold, M Grøtli, Y Sato, H Kume, S Ogawa, J Boren, J Nielsen, M Uhlen, A Mardinoglu
Elucidating the reprograming of colorectal cancer metabolism using genome-scale metabolic modeling
Frontiers in oncology
C Zhang, M Aldrees, M Arif, X Li, A Mardinoglu, M Aziz
MOBN: an interactive database of multi-omics biological networks
BioRxiv
C Zhang*, M Arif*, X Li, S Lee, A Tebani, W Zhou, BD Piening, L Fagerberg, N Price, L Hood, MP Snyder, J Nielsen, M Uhlen, A Mardinoglu
Spatiotemporal dissection of the cell cycle regulated human proteome
BioRxiv
D Mahdessian, D Sullivan, F Danielsson, M Arif, C Zhang, L Akesson, C Gnann, R Schutten, P Thul, O Carja, B Ayoglu, A Mardinoglu, F Ponten, M Uhen, C Lindskog, E Lundberg

2018

Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome
Scientific reports
A Lovric, M Granér, E Bjornson, M Arif, R Benfeitas, K Nyman, M Ståhlman, MO Pentikäinen, J Lundbom, A Hakkarainen, R Sirén, MS Nieminen, N Lundbom, K Lauerma, MR Taskinen, A Mardinoglu, J Boren
ESS: a tool for genome-scale quantification of essentiality score for reaction/genes in constraint-based modeling
Frontiers in physiology
C Zhang, S Lee, R Benfeitas, G Bidkhori, M Arif, A Mardinoglu
Metabolic network-based identification and prioritization of anti-cancer targets based on expression data in hepatocellular carcinoma
Frontiers in physiology
G Bidkhori, R Benfeitas, E Elmas, MN Kararoudi, M Arif, M Uhlen, J Nielsen, A Mardinoglu

2017

TCSBN: a database of tissue and cancer specific biological networks
Nucleic acids research
S Lee*, C Zhang*, M Arif*, Z Liu, R Benfeitas, G Bidkhori, S Deshmukh, MA Shobky, A Lovric, J Boren, J Nielsen, M Uhlen, A Mardinoglu
A pathology atlas of the human cancer transcriptome
Science
M Uhlen, C Zhang, S Lee, E Sjöstedt, L Fagerberg, G Bidkhori, R Benfeitas, M Arif, Z Liu, F Edfors, K Sanli, K Feilitzen, P Oksvold, E Lundberg, S Hober, P Nilsson, J Mattsson, JM Schwenk, H Brunnström, B Glimelius, T Sjöblom, PH Edqvist, D Djureinovic, P Micke, C Lindskog, A Mardinoglu, F Ponten

2016

Scalable 5-Tuple Packet Classification in Overlay Network-Based SDN
KTH Master Thesis Project
M Arif (Supervisors: Dr. Viktoria Fodor (KTH) and Dr. Albert Cabellos(UPC))

Contact

Thank you for visiting my website!

If you have any questions, suggestions, proposal for collaboration or anything, feel free to reach me through my social media or drop me an email (like the good old times).