About Me

Download Curriculum Vitae

My name is Muhammad Arif and I'm from Indonesia. Currently I'm residing in Rockville, MD, USA, together with my small family (photo above :D).

Current Work
I'm a postdoctoral visiting fellow at The National Institutes of Health (NIH), specifically The National Institute on Alcohol Abuse and Alcoholism (NIAAA). I'm jointly appointed by the Laboratory of Cardiovascular Physiology and Tissue Injury (LCPTI), and the Section on Fibrotic Disorders (SFD).

I'm working with experts in lung-, heart-, and liver-related diseases that develop pre-clinical models to understand disease mechanisms and find new novel therapy targets. I'm bringing new perspectives to both groups with my systems and network biology expertise to improve the quality and accelerate the research. Currently, I'm working on in multiple projects, including development disease models with multi-omics and multi-tissue data. Very very very exciting projects!

Research Interests and Experiences
My interests are in the development and implementation of machine learning and network analysis methods in biological context. I have been involved in multiple projects including multi-omics integration, biological network (co-expression and regulatory network), single-cell transcriptional analysis, metabolic modelling and proteomics analysis. Some of my notable works can be found in the Publication tab, including integration of multi-omics data, multi-tissue analysis on heart attack, biological network database, and my PhD Thesis.

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.

PhD Education
I'm a PhD graduate from 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. I succesfully defended my PhD on 11 June 2021. My PhD project was focusing on the use of systems biology to understand the underlying mechanism of human diseases.

Publications

Last Update: 18 July 2022
Google Scholar: Google Scholar Publons: Publons

Publications By Year [# of Publications]:
2022 [5 Peer-reviewed + 2 Pre-prints]
2021 [21] | 2020 [5] | 2019 [4] | 2018 [4] | 2017 [1] | 2016 [1]
(*: First/Co-First Author)

Key Publications

Multi-omics analysis reveals the impact of microbiota on host metabolism in hepatic steatosis
Advanced Science
M Zeybel*, M Arif*, X Li, O Altay, M Shi, M Akyildiz, B Saglam, MG Gonenli, B Yigit, B Ulukan, D Ural, S Shoaie, H Turkez, J Nielsen, C Zhang, M Uhlén, J Borén, A Mardinoglu
Combined Metabolic Activators accelerates recovery in mild-to-moderate COVID-19
Advanced Science
O Altay*, M Arif*, X Li*, H Yang, M Aydın, G Alkurt, W Kim, D Akyol, C Zhang, G Dinler-Doganay, H Turkez, S Shoaie, J Nielsen, J Borén, O Olmuscelik, L Doganay, M Uhlén, A Mardinoglu
Press Release: Covid-19 patients recover faster with metabolic activator treatment, study shows
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients
Molecular Systems Biology
M Zeybel*, O Altay*, M Arif*, X Li, H Yang, C Fredolini, M Akyildiz, B Saglam, MG Gonenli, D Ural, W Kim, JM Schwenk, C Zhang, S Shoaie, J Nielsen, M Uhlen, J Boren, A Mardinoglu
Systems and Network-based Approaches to Complex Metabolic Diseases
KTH Royal Institute of Technology
M Arif (Doctoral Thesis)
Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction
eLife
M Arif*, M Klevstig*, R Benfeitas, S Doran, H Turkez, M Uhlen, M Clausen, J Wikström, C Zhang, M Levin, A Mardinoglu, J Boren
Press Release: Map of metabolic changes after heart attack holds clues to recovery
Highlights: Heart Attack: Working together (eLife: Insights)
iNetModels 2.0: an interactive visualization and database of multi-omics data
Platform Access: https://inetmodels.com
Nucleic acid Research
M Arif*, C Zhang*, X Li, C Güngör, B Çakmak, M Arslantürk, A Tebani, B Özcan, O Subaş, W Zhou, B Piening, H Turkez, L Fagerberg, N Price, L Hood, M Snyder, J Nielsen, M Uhlen, A Mardinoglu

2022

Peer-Reviewed

Multi-omics analysis reveals the impact of microbiota on host metabolism in hepatic steatosis
Advanced Science
M Zeybel*, M Arif*, X Li*, O Altay, M Shi, M Akyildiz, B Saglam, MG Gonenli, B Yigit, B Ulukan, D Ural, S Shoaie, H Turkez, J Nielsen, C Zhang, M Uhlén, J Borén, A Mardinoglu
Cannabinoid receptor 2 activation alleviates diabetes-induced cardiac dysfunction, inflammation, oxidative stress, and fibrosis
GeroScience
M Rajesh, P Mukhopadhyay, S Bátkai, M Arif*, ZV Varga, C Mátyás, J Paloczi, A Lehocki, G Haskó, P Pacher
Multiomics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity
Cell Systems
AT Ambikan, H Yang, S Krishnan, S Svensson-Akusjärvi, S Gupta, M Lourda, M Sperk, M Arif, C Zhang, H Nordqvist, SM Ponnan, A Sönnerborg, CJ Treutiger, L O’Mahony, A Mardinoglu, R Benfeitas, U Neogi
Machine Learning Analysis Reveals Biomarkers for the Detection of Neurological Diseases
Frontiers in molecular neuroscience
S Lam, M Arif, X Song, M Uhlén, A Mardinoglu
Genome-wide annotation of protein-coding genes in pig
BMC biology
M Karlsson, E Sjöstedt, P Oksvold, Å Sivertsson, J Huang, MB Álvez, M Arif, X Li, L Lin, J Yu, T Ma, F Xu, P Han, H Jiang, A Mardinoglu, C Zhang, K Feilitzen, X Xu, J Wang, H Yang, L Bolund, W Zhong, L Fagerberg, C Lindskog, F Pontén, J Mulder, Y Luo, M Uhlen

Pre-Print (Not Peer Reviewed Yet)

Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning
BioRxiv
C Zhang, M Shi, W Kim, M Arif, M Klevstig, X Li, H Yang, C Bayram, I Bolar, Ö Tozlu, A Hacimuftuoglu, S Yildirim, Y Wei, X Shi, J Nielsen, H Turkez, M Uhlen, J Boren, A Mardinoglu
Hexokinase 1b is a novel target for Non–small-cell lung cancer
BioRxiv
Y Yozgat, E Karakoc, O Sahin, S Cimen, WM Rabeh, MS Aydin, A Mardinoglu, I Gursel, A Cakir, O Sensoy, EM Ozdemir, Y Bayrak, MZ Gunluoglu, O Saatci, J Jabbar, JC Ferreira, MD Aslan, M Yildirim, S Mansoor, BE Kerman, Z Aladag, W Kim, M Arif, E Vatandaslar, OE Tok, Z Dogru, AGO Demir, TC Yildirim, I Yozgat, S Senturk, G Ozturk, MA Cevher

2021

Peer-Reviewed

Revealing the Molecular Mechanisms of Alzheimer’s Disease Based on Network Analysis
International journal of molecular sciences
A Bayraktar, S Lam, O Altay, X Li, M Yuan, C Zhang, M Arif, H Turkez, M Uhlén, S Shoaie, A Mardinoglu
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients
Molecular Systems Biology
M Zeybel*, O Altay*, M Arif*, X Li, H Yang, C Fredolini, M Akyildiz, B Saglam, MG Gonenli, D Ural, W Kim, JM Schwenk, C Zhang, S Shoaie, J Nielsen, M Uhlen, J Boren, A Mardinoglu
Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms
EBioMedicine
W Zhong, O Altay, M Arif, F Edfors, L Doganay, A Mardinoglu, M Uhlen, L Fagerberg
Systems analysis reveals ageing-related perturbations in retinoids and sex hormones in Alzheimer's and Parkinson's diseases
Biomedicines
S Lam, N Hartmann, R Benfeitas, C Zhang, M Arif, H Turkez, M Uhlen, C Englert, RD Knight, A Mardinoglu
A network-based approach reveals the dysregulated transcriptional regulation in non-alcohol fatty liver disease
iScience
H Yang, M Arif, Y Meng, X Li, KE Shong, H Turkez, J Nielsen, M Uhlén, J Borén, C Zhang, A Mardinoglu
Glucosylceramide synthase deficiency in the heart compromises β1-adrenergic receptor trafficking
European Heart Journal
L Andersson, M Cinato, I Mardani, A Miljanovic, M Arif, A Koh, M Lindbom, M Laudette, E Bollano, E Omerovic, M Klevstig, M Henricsson, P Fogelstrand, K Swärd, M Ekstrand, M Levin, J Wikström, S Doran, T Hyötyläinen, L Sinisalu, M Orešič, Å Tivesten, M Adiels, MO Bergo, R Proia, A Mardinoglu, A Jeppsson, J Borén, MC Levin
A single–cell type transcriptomics map of human tissues
Science Advances
M Karlsson, C Zhang, L Méar, W Zhong, A Digre, B Katona, E Sjöstedt, L Butler, J Odeberg, P Dusart, F Edfors, P Oksvold, K Feilitzen, M Zwahlen, M Arif, O Altay, X Li, M Ozcan, A Mardonoglu, L Fagerberg, J Mulder, Y Luo, F Ponten, M Uhlén, C Lindskog
Combined Metabolic Activators accelerates recovery in mild-to-moderate COVID-19
Advanced Science
O Altay*, M Arif*, X Li*, H Yang, M Aydın, G Alkurt, W Kim, D Akyol, C Zhang, G Dinler-Doganay, H Turkez, S Shoaie, J Nielsen, J Borén, O Olmuscelik, L Doganay, M Uhlén, A Mardinoglu
Press Release: Covid-19 patients recover faster with metabolic activator treatment, study shows
Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning
iScience
X Li, W Kim, K Juszczak, M Arif, Y Sato, H Kume, S Ogawa, H Turkez, J Boren, J Nielsen, M Uhlen, C Zhang, A Mardinoglu
Systems and Network-based Approaches to Complex Metabolic Diseases
KTH Royal Institute of Technology
M Arif (Doctoral Thesis)
Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction
eLife
M Arif*, M Klevstig*, R Benfeitas, S Doran, H Turkez, M Uhlen, M Clausen, J Wikström, C Zhang, M Levin, A Mardinoglu, J Boren
Press Release: Map of metabolic changes after heart attack holds clues to recovery
Highlighted in: Heart Attack: Working together (eLife: Insights)
Integrative study of diet-induced mouse models of NAFLD identifies PPARα as a sexually dimorphic drug target
Gut
S Smati, A Polizzi, A Fougerat, S Ellero-Simatos, Y Blum, Y Lippi, M Régnier, A Laroyenne, M Huillet, M Arif, C Zhang, F Lasserre, A Marrot, TA Saati, JH Wan, C Sommer, C Naylies, A Batut, C Lukowicz, T Fougeray, B Tramunt, P Dubot, L Smith, J Bertrand-Michel, N Hennuyer, JP Pradere, B Staels, R Burcelin, F Lenfant, JF Arnal, T Levade, L Gamet-Payrastre, S Lagarrigue, N Loiseau, S Lotersztajn, C Postic, W Wahli, C Bureau, M Guillaume, A Mardinoglu, A Montagner, P Gourdy, H Guillou
iNetModels 2.0: an interactive visualization and database of multi-omics data
Nucleic acid Research
Platform Access: https://inetmodels.com
M Arif*, C Zhang*, X Li, C Güngör, B Çakmak, M Arslantürk, A Tebani, B Özcan, O Subaş, W Zhou, B Piening, H Turkez, L Fagerberg, N Price, L Hood, M Snyder, J Nielsen, M Uhlen, A Mardinoglu
Molecular pathways behind acquired obesity: adipose tissue and skeletal muscle multiomics in monozygotic twin pairs discordant for BMI
Cell Reports Medicine
BW Kolk, S Saari, A Lovric, M Arif, M Alvarez, A Ko, Z Miao, N Sahebekhtiari, M Muniandy, S Heinonen, A Oghabian, R Jokinen, S Jukarainen, A Hakkarainen, J Lundbom, J Kuula, PH Groop, T Tukiainen, N Lundbom, A Rissanen, J Kaprio, EG Williams, N Zamboni, A Mardinoglu, P Pajukanta, KH Pietiläinen
Multi-omics approaches for revealing the complexity of cardiovascular disease
Briefings in Bioinformatics
S Doran, M Arif, S Lam, A Bayraktar, H Turkez, M Uhlen, J Boren, A Mardinoglu
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
Nature
D Mahdessian, AJ Cesnik, C Gnann, F Danielsson, L Stenström, M Arif, C Zhang, R Shutten, A Bäckström, P Thul, NH Cho, O Carja, M Uhlén, A Mardinoglu, C Stadler, C Lindskog, B Ayoglu, MD Leonetti, F Pontén, D Sullivan, E Lundberg
Discovery of functional alternatively spliced PKM transcripts in human cancers
Cancers
X Li, W Kim, M Arif, C Gao, A Hober, D Kotol, L Strandberg, B Forsström, Å Sivertsson, P Oksvold, H Turkez, M Grøtli, Y Sato, H Kume, S Ogawa, J Boren, J Nielsen, M Uhlen, C Zhang, A Mardinoglu

Pre-Print (Not Peer Reviewed Yet)

GutMicroNet: an interactive platform for gut microbiome interaction exploration
Platform Access: https://gutmicro.net
bioRxiv
M Arif*, T Portlock*, C Güngör, E Koç, B Özcan, O Subaş, B Çakmak, H Turkez, M Uhlén, A Mardinoglu, S Shoaie
Combined Metabolic Activators Improves Cognitive Functions in Alzheimer's Disease
medRxiv
B Yulug, O Altay, X Li, L Hanoglu, S Cankaya, S Lam, H Yang, E Coskun, E İdil, R Nogaylar, C Bayram, I Bolat, S ONER, O TOZLU, ME Arslan, A HACIMUFTUOGLU, S YILDIRIM, M Arif, C ZHANG, J NIELSEN, H TURKEZ, J BOREN, M UHLEN, A MARDINOGLU
Combined Metabolic Activators Improve Cognitive Functions without Altering Motor Scores in Parkinson's Disease
medRxiv
B Yulug, O Altay, X Li, L Hanoglu, S Cankaya, S Lam, H Yang, E Coskun, E İdil, R Nogaylar, A HACIMUFTUOGLU, M Arif, S Shoaie, C Zhang, J Nielsen, H Turkez, J Borén, M Uhlen, A Mardinoglu
Network Analyses Links Epicardial Fat Metabolism to Human Coronary Heart Disease
SneakPeek CellPress
S Doran, M Arif, M Clausen, J Wikström, M Bohlooly-Y, A Jeppsson, M Levin, A Mardinoglu, J Boren

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
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

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
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

2017

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, teaching request, or anything, feel free to reach me through my social media or drop me an email (like the good ol' days)