About Me
Download Curriculum Vitae
My name is Muhammad Arif and I'm from Indonesia. Currently I'm residing in Bethesda, MD, USA, together with my small family (photo above :D).
Personal Statement (Excerpt from Biosketch)
As a systems biology expert working among experimental biologists, chemists, and clinicians, my key role is to navigate the research with data-driven approaches. This perfectly aligns with my main interest in developing systems biology approaches and algorithms, especially machine learning and biological networks, as hypothesis-free tools to facilitate basic, translational, and clinical research for human diseases. Specifically, I am interested in the integration of multi-omics data and studying crosstalk between different organs in responding to complex diseases. Since 2021, I joined the National Institutes of Health (NIH), USA, as a postdoctoral fellow, jointly appointed by the the Section on Fibrotic Disorders (SFD) and the Laboratory of Cardiovascular Physiology and Tissue Injury (LCPTI). My research focus is to utilize big multi-omics data, from tissue and single-cell levels, for the discovery of biomarkers and therapeutic targets in progressive diseases and conditions, including aging and pulmonary fibrosis (PF), and facilitate pre- to clinical translational process. By analyzing multi-omics data with network and machine learning analyses, I have recently identified candidate treatment targets to attenuate the effect of aging on the heart and liver. In my other project, I have also identified progression signatures of PF and synergistic drug targets to be combined with a known PF treatment target, Cannabinoid Receptor 1. Both projects were recently published in two leading journals in the area, Advanced Science and GeroScience. Currently, we are working on several other data-driven projects, including multi-organ interactions in aging processes and the development of new multi-omics diagnostic tools in PF, specifically in Hermansky-Pudlak Syndrome patients.
My academic experiences have exposed me to the full pre- and clinical experiments cycle. After finishing my doctoral study in a fully computational lab, I decided to join fully experimental labs for my postdoctoral research. Here, I am also learning the processes in experimental pre-clinical research, from sample preparation, in-vivo and in-vitro experiments, to data acquisition. This experience has been insightful and allowed me to fully understand the entire data life cycle, together with its associated difficulties, from its very first experimental setup to downstream analysis.
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.