Find Academic Supervisors

Steven G. ClarkeView profile

Professor

• Biochemistry
• Systems Biology
• Biological Regulation
• +8 more

Dr. Steven G. Clarke is a Distinguished Professor at UCLA Department of Chemistry & Biochemistry and director of research at the Molecular Biology Institute . His work bridges protein chemistry , methylation biology , and aging research through studies of spontaneous protein damage and its repair mechanisms. Education: BA in Chemistry and Zoology, Pomona College (magna cum laude, Phi Beta Kappa) PhD in Biochemistry and Molecular Biology, Harvard University (NSF Fellow) Postdoctoral Fellowship at UC Berkeley (Miller Fellow) Dr. Clarke's research focuses on protein isoaspartyl repair via PCMT1/PIMT enzymes , ribosomal protein methylation in Saccharomyces cerevisiae , and PRMT family characterization including PRMT7 and PRMT9. His lab combines biochemical assays , genetic models , and structural analysis to investigate aging mechanisms and disease implications. Recent publications highlight: COQ5 structure-function analysis in coenzyme Q biosynthesis PCMTD1 ubiquitin ligase interactions PRMT7 substrate specificity in histone H2B Protein isoaspartyl impacts on T cell function in lupus Novel PRMT inhibitors for cancer therapy Methionine addiction in osteosarcoma malignancy Major scientific awards: American Chemical Society Ralph F. Hirschmann Award in Peptide Chemistry NIH MERIT Award Ellison Medical Foundation Senior Scholar Award William C. Rose Award, ASBMB UCLA Distinguished Teaching Award (Eby Award winner) Current lab members include PhD candidates Eric Pang (UCSB) and Sining "Cindy" Wang (UCLA), while undergraduates Celeste Medina-Seymoure , Elizabeth Oroudjeva , Olivia Pacheco , and Jasmine Winter contribute to ongoing proteostasis studies. Collaborations with Profs. Jose Rodriguez and Catherine Clarke demonstrate interdisciplinary research approaches.

Kelly ArnoldView profile

Associate Professor

• Biomedical Computation and Modeling
• Drug Delivery and Therapeutics
• Systems Immunology
• +5 more

Kelly Arnold is an Associate Professor in the Department of Biomedical Engineering at the University of Michigan. Her research integrates systems engineering principles with immunology to investigate variability in immune responses across infection, vaccination, and injury, with a focus on computational modeling and clinical translation. Research Focus Systems-level immune response modeling Vaccination and antibody functionality Vaginal microbiome-host interactions Chronic lung disease progression Computational serology and proteomics Recent Work Her 2025 studies examine SARS-CoV-2 vaccination responses in cancer patients and computational frameworks for vaginal probiotics. Earlier works (2024-2007) span COPD progression, lupus fibrosis, HIV susceptibility, and tissue engineering for fertility preservation. Methodologies include proteomic profiling, network modeling, and microfluidic systems.

David S. EisenbergView profile

Professor

• Protein Aggregation
• Amyloid Structures
• Prion Diseases
• +5 more

David S. Eisenberg is a Professor of Chemistry and Biochemistry and Biological Chemistry at the University of California, Los Angeles, where he also serves as Director of the UCLA-DOE Institute for Genomics and Proteomics and as an HHMI Investigator. His research focuses on protein interactions, particularly the structural basis for conversion of normal proteins to the amyloid state and conversion of prions to the infectious state. Dr. Eisenberg earned his undergraduate degree in biochemical sciences from Harvard College and his D.Phil. degree in theoretical chemistry from Oxford University on a Rhodes Scholarship. His postdoctoral research was on ice and water with Walter Kauzmann at Princeton and in protein crystallography with Richard Dickerson. He joined the UCLA faculty after his postdoctoral studies. Dr. Eisenberg and his research group focus on protein interactions in amyloid and prion diseases. These diseases involve protein aggregation where normal functional proteins convert to abnormal aggregated forms. Systemic amyloid diseases like dialysis-related amyloidosis result from fiber accumulation until organ failure, while neurodegenerative diseases like Alzheimer's, Parkinson's, ALS, and prion conditions appear to be caused by smaller oligomers. In 2005, his team determined the atomic-level structure for the amyloid fiber spine, revealing a 'steric zipper' of two parallel beta sheets packed across a dry interface. Since then, they've determined approximately 90 amyloid spines from 15 disease-related proteins. In 2010, they identified the structure of a toxic amyloid-related oligomer consisting of six anti-parallel beta strands forming a cylindrical barrel. His recent publications demonstrate continued innovation in amyloid research, with focus areas including structural prediction of amyloid formation, mechanisms of tau fibril disassembly in Alzheimer's disease, cryo-EM analysis of amyloid polymorphism, and structure-based design of inhibitors for amyloid toxicity. His work integrates computational, structural, and biochemical approaches to understand protein aggregation across multiple disease contexts. Dr. Eisenberg has received numerous prestigious awards and honors: National Academy of Sciences Member American Philosophical Society Member Institute of Medicine Member Howard Hughes Medical Institute Investigator Biophysical Society Emily M. Gray Award Harvard Westheimer Medal UCLA Seaborg Medal Technion - Israel Institute of Technology Harvey Prize in Human Health As Director of the UCLA-DOE Institute for Genomics and Proteomics and an HHMI Investigator, Dr. Eisenberg leads significant research initiatives in protein structure and aggregation. His laboratory combines X-ray crystallography, bioinformatics, and biochemical techniques to investigate protein interactions, with particular emphasis on amyloid-forming proteins and their role in disease. The Eisenberg Lab, located in Boyer Hall at UCLA, maintains an active research program investigating the structural basis of protein aggregation. The lab continues to build on its landmark discoveries of amyloid structures while exploring new frontiers in understanding protein misfolding diseases and developing potential therapeutic interventions.

Chang-Jun LiuView profile

Adjunct Professor

• Phenylpropanoid biosynthesis
• Lignin biosynthesis and modification
• Plant cell wall structure
• +7 more

Chang-Jun Liu is a Senior Scientist in the Plant Science Group of the Biology Department at Brookhaven National Laboratory, where he has conducted research on plant phenylpropanoid biosynthesis and lignin metabolism since joining in 2005. He also holds an Adjunct Professor position in the Biochemistry & Cell Biology Department at Stony Brook University and serves as Associate Editor for Plant Cell & Environment (2024-present) and Frontiers in Plant Sciences (2015-present). Dr. Liu's educational background includes: Ph.D. in Plant Biochemistry and Molecular Biology from the Shanghai Institute of Plant Physiology, Chinese Academy of Science (1999) Dr. Liu's research integrates approaches from biochemistry, molecular genetics, biophysics, protein engineering, metabolic engineering, and synthetic biology to investigate phenylpropanoid and lignin biosynthesis in plants. His laboratory addresses fundamental questions about how lignin and related compounds are synthesized and incorporated into cell walls, how regulatory networks govern metabolic activity, and how lignification influences cell wall structure and function. A central aim of his research is optimizing plant feedstocks for efficient lignocellulosic biomass utilization. Analysis of Dr. Liu's publication record reveals a consistent trajectory from fundamental biochemical mechanisms to applied bioenergy solutions. His recent work focuses on cytochrome b5 diversity, electron transfer mechanisms in phenolic biosynthesis, and metabolic engineering approaches to modify lignin composition. This research spans from evolutionary studies of lignin biosynthesis across plant lineages to practical applications in bioenergy crop improvement. Dr. Liu has received recognition for his contributions to science, including: Brookhaven National Laboratory Science and Technology Award (2018) Dr. Liu serves as Editorial Board Member for the Journal of Biological Chemistry (2020-present), PNAS Nexus (2024-present), and Plant Physiology Journal (2025-). He is Scientific Lead at the Joint BioEnergy Institute, Feedstocks Division, Lawrence Berkeley National Laboratory, and Project Lead at the Center for Bioenergy Innovation, Oak Ridge National Laboratory. His research is funded by the U.S. Department of Energy through multiple Bioenergy Research Centers. Dr. Liu leads a research group at Brookhaven National Laboratory focused on elucidating the posttranslational regulation and macromolecular organization of lignin biosynthesis, with applications toward developing designer lignins and reducing biomass recalcitrance for sustainable biofuel production. His work addresses the critical challenge of lignin's dual nature: while it impedes enzymatic access to polysaccharides in biofuel production, it also represents the most abundant renewable source of aromatic carbon for high-value bioproducts.

Michele KlingbeilView profile

Professor

• Parasitology
• Molecular Biology
• Microbiology
• +4 more

Michele Klingbeil is a Professor in the Department of Microbiology at the University of Massachusetts Amherst, where she leads the Klingbeil DNA Replication Laboratory. She received her PhD in Cell and Molecular Biology from the University of Toledo in 1996 and previously worked at Johns Hopkins School of Medicine before moving to UMass in July 2007. Her educational background includes: PhD in Cell and Molecular Biology, University of Toledo, 1996 Dr. Klingbeil's research focuses on the unique biology of trypanosomatid parasites, particularly Trypanosoma brucei , the causative agent of African sleeping sickness. Her laboratory investigates two main areas: (1) replication of the unusual mitochondrial DNA network called kinetoplast DNA (kDNA), and (2) nuclear DNA replication initiation. Her work on kDNA is particularly significant as this structure is essential for parasite survival but has no counterpart in mammalian hosts, making it an attractive drug target. She employs a combination of reverse genetics (RNAi), cell biology, and biochemistry to understand the replication and repair mechanisms of kDNA, with a special focus on a family of four DNA polymerases related to bacterial Pol I. Dr. Klingbeil's recent publications reveal her laboratory's deep investigation into mitochondrial DNA polymerases in trypanosomatids, with discoveries showing multiple polymerases having specialized functions in kDNA replication and repair. Her research has established that several of these polymerases are essential for parasite viability, opening new avenues for drug development. She has also made significant contributions to understanding the simplified Origin Recognition Complex in trypanosomatids compared to other eukaryotes. Dr. Klingbeil has received the Thomas G. Lessie Distinguished Lectureship Award for her impact on teaching at the graduate level. Her research is funded by the National Institutes of Health, U.S. Department of Agriculture, the Joeph P. Healey Endowment, and the University of Massachusetts Amherst. She has mentored numerous graduate and undergraduate students, including current PhD candidates Dave Bruhn, Jeniffer Concepción, and Juemin Luo, as well as visiting scholar Eva Vidal Rico. Her former students have gone on to positions at institutions including Dana Farber/Broad Institute, Regis College, and Flagship Ventures. The laboratory regularly participates in scientific conferences including the Molecular Parasitology Meeting at Woods Hole and the Kinetoplastid Molecular Cell Biology conference. Dr. Klingbeil teaches several courses including Parasitology (MICRO 590S), Parasitology Lab (MICRO 590L), Molecular Mechanisms of Pathogenesis (MICRO 797P), Advanced Cell Biology (MCB 641), and Writing in Microbiology (MICRO 360). Her laboratory organizes regular social events including pumpkin carving parties and outings to Six Flags New England and Mt. Sugarloaf.

David VocadloView profile

Professor

• Bioorganic Chemistry
• Chemical Biology
• Glycobiology
• +3 more

David Vocadlo is a Distinguished Professor of Chemistry and Molecular Biology & Biochemistry at Simon Fraser University (SFU), holding the Canada Research Chair in Chemical Biology. His research focuses on Chemical Glycobiology, investigating carbohydrate-processing enzymes and developing chemical tools to study glycan roles in health and disease. His lab explores O-GlcNAc signaling, neurodegenerative disorders (e.g., Alzheimer’s, Parkinson’s), and enzyme inhibitors for therapeutic applications. Education: PhD from University of British Columbia (UBC), followed by a CIHR postdoctoral fellowship at UC Berkeley. Key roles include E.W.R. Steacie Memorial Fellow and Royal Society Fellow. Research highlights include O-GlcNAcase inhibitors for neuroprotection, glycan structure-function relationships, and enzyme activity imaging tools. Collaborates globally with experts in glycobiology and employs cutting-edge techniques like chemical synthesis, mass spectrometry, and live-cell imaging. Awards: Distinguished Professor title, Canada Research Chair, Royal Society Fellowship. Active in training researchers through SFU’s graduate programs, emphasizing interdisciplinary approaches. Lab members work on topics ranging from enzyme mechanisms to disease modeling.

Christopher M. OverallView profile

Professor

• Protease Proteomics
• Systems Biology
• Degradomics
• +6 more

Christopher M. Overall is a Full Professor at the University of British Columbia in the Faculty of Dentistry, Department of Oral Biological and Medical Sciences . He is also a Principal Scientist at the Centre for Blood Research and holds associate memberships in UBC's Biochemistry & Molecular Biology , Obstetrics and Gynecology , and Bioinformatics Graduate Program departments. As a Canada Research Chair Laureate , he pioneered the field of degradomics to study proteases in vivo. B.D.S., University of Adelaide Ph.D., University of Toronto Postdoctoral Fellowship, UBC (with Nobel Laureate Michael Smith) Dr. Overall’s research focuses on protease proteomics and systems biology , particularly degradomics to analyze protease substrates in diseases like COVID-19 and immunodeficiency . His work on matrix metalloproteinases has revealed new therapeutic strategies for inflammatory diseases and cancer . His 15 most recent articles (2015–2008) demonstrate expertise in TAILS proteomics , protein terminomics , and protease network analysis with applications in arthritis , antiviral immunity , and precision medicine . Scientific Awards 2022 Helmut Holzer Award 2018 Royal Society of Canada Fellow 2014 Tony Pawson Canadian Proteomics Award 2013 IADR Distinguished Scientist Award Dr. Overall has mentored 61 trainees , including 9 full professors with department chairs, and received the UBC John McNeill Mentorship Award (2023). He leads the HUPO Chromosome-centric Human Proteome Project and consults for Genentech and Novartis .

Ralph H. ColbyView profile

Professor

• Polymer Physics
• Rheology
• Ionomers
• +5 more

Ralph H. Colby serves as Professor of Materials Science and Engineering and Chemical Engineering at Pennsylvania State University's College of Earth and Mineral Sciences, holding the Corning Faculty Fellowship. His research focuses on molecular-level dynamics in complex fluids, particularly polymers, ionomers, and liquid crystalline systems. With over 130 publications and authorship of the textbook Polymer Physics (2003), he directs an active research program examining structure-property relationships in soft matter. B.S. in Materials Science and Engineering, Cornell University (1979) M.S. in Chemical Engineering, Northwestern University (1983) Ph.D. in Chemical Engineering, Northwestern University (1985) Professor Colby's research spans polymer physics, rheology, and materials for energy applications. His group employs mechanical rheology, dielectric spectroscopy, and scattering techniques to investigate ion transport in single-ion conductors for batteries, dynamics of glass-forming liquids, and self-assembly in polyelectrolyte systems. Current work emphasizes structure-property relationships in ionomers, liquid crystalline polymers, and branched architectures. Analysis of recent publications reveals consistent focus on ionomer membranes for energy applications, processing-structure relationships in advanced polymers, and fundamental dynamics of complex fluids. Key trends include increasing integration of computational modeling with experimental characterization, expansion into sustainable materials processing, and growing emphasis on applications in battery technology and biomedical materials. Penn State Faculty Scholar Medal for Outstanding Achievement (2022) Bingham Medal, Society of Rheology (2012) American Chemical Society Fellowship Corning Faculty Fellowship in Materials Science and Engineering Professor Colby leads multiple federally funded projects including NSF's 'Fundamental Studies of Flow-Induced Polymer Crystallization' and DOE's 'Conduction mechanisms and structure of ionomeric single-ion conductors'. His group maintains strong industry partnerships with Corning Incorporated and participates in interdisciplinary initiatives like the Penn State Intercollege Graduate Degree Program in Materials Science and Engineering. Current research includes collaborations on breast cancer adherence interventions in Rwanda and conjugated polymer development for flexible electronics. The Colby Research Group operates specialized facilities for rheological characterization, dielectric spectroscopy, and X-ray scattering at Penn State's Materials Research Institute. The team maintains active collaborations with national laboratories and international research groups, focusing on translating fundamental polymer physics discoveries into practical applications for energy storage and advanced manufacturing.

• Biosensors
• Functional Nucleic Acids
• Sol-Gel Materials
• +3 more

John D Brennan is a Professor in the Department of Chemistry & Chemical Biology at McMaster University. He is affiliated with the Biointerfaces Institute and focuses on developing innovative biosensing technologies and functional nucleic acid-based assays. His research integrates materials science, biochemistry, and analytical chemistry to create practical diagnostic tools for healthcare applications. Key research areas include the design of DNA aptamers and DNAzymes for detecting biomarkers (e.g., eosinophil peroxidase, SARS-CoV-2 spike proteins), development of paper-based diagnostic platforms, and optimization of sol-gel materials for enzyme entrapment. His work emphasizes high-throughput screening, point-of-care testing, and CRISPR-based biosensing systems. Notable contributions include a rapid sputum-based assay for asthma biomarkers and a universal DNA aptamer for SARS-CoV-2 variants. His lab also explores functional nucleic acid circuits and their integration into scalable diagnostic devices. Brennan’s teaching includes advanced courses in analytical chemistry and biochemical assay development. His work has been featured in journals like *Angewandte Chemie*, *Analytical Chemistry*, and *ChemBioChem*, with a focus on translating fundamental research into practical clinical applications.

Zhe JiView profile

Assistant Professor

• Data Science
• Computational Biology
• Functional Genomics
• +4 more

Zhe Ji is an Assistant Professor in the Department of Biomedical Engineering at McCormick School of Engineering and the Department of Pharmacology at Feinberg School of Medicine, Northwestern University. His research integrates computational and experimental genomics to study gene transcription and RNA translation in cell fate commitment and oncogenic processes, aiming to develop precision medicine strategies. **Education**: Postdoctoral Fellow in Cancer Systems Biology, Harvard Medical School Postdoctoral Fellow in Computational Biology, Broad Institute of MIT and Harvard Ph.D. in Computational Genomics, Rutgers University B.S. in Biotechnology, Nanjing University, China **Research Focus**: Keywords include Data Science, Computational Biology, Functional Genomics, RNA, Cancer, Inflammation, and Machine Learning. The lab explores regulatory mechanisms underlying disease, with a focus on translational control, cancer metastasis, and inflammatory networks. **Grants & Advising**: No specific grants or student advisees listed. The lab emphasizes collaborative projects and computational-experimental approaches. **Lab Affiliations**: Zhe Ji’s lab is part of Northwestern’s interdisciplinary environment, bridging engineering and medicine to advance genomic technologies and therapeutic strategies.

Sachdev SidhuView profile

Research Professor

• Synthetic Antibodies
• Protein Engineering
• Biotechnology
• +5 more

Sachdev Sidhu is a Research Professor and Entrepreneur in Residence at the University of Waterloo. His research focuses on synthetic antibodies, protein engineering, and biotechnological applications. He leads efforts in developing novel therapeutic antibodies, engineered protein systems, and molecular tools for biomedical research. His work spans cancer therapy, viral infection countermeasures, and regenerative medicine. Sidhu is also involved in translational research, bridging academic discoveries with commercial applications through entrepreneurial ventures. Key research interests include synthetic antibody libraries, CAR T-cell engineering, ubiquitin-based therapeutics, and phage display technologies. He has contributed to advancements in targeted therapies for glioblastoma, leukemia, and ocular diseases. His team develops innovative methods for protein design, such as engineered ubiquitin variants and modular antibody architectures. Publications highlight breakthroughs in antibody-based treatments, including synNotch CAR T cells for glioblastoma and neutralizing antibodies against SARS-CoV-2. His work integrates structural biology, molecular biology, and computational approaches to address complex biomedical challenges. Sidhu collaborates with industry partners to advance technologies into clinical and commercial settings.

David GraingerView profile

Professor

• Bacterial Chromosome Biology
• Pathogenicity
• Antibiotic Resistance Mechanisms
• +3 more

Professor David Grainger is a faculty member at the University of Birmingham's School of Biosciences, specializing in Molecular Microbiology. He leads the Grainger Lab, focusing on bacterial chromosome biology, pathogenicity, and antibiotic resistance. His research integrates high-throughput techniques and single-molecule analysis to study gene regulation and bacterial pathogenesis. Education: PhD (2004), PGCE (2000), BSc (1999) in Biochemistry from the University of Birmingham. Affiliations: Part of the Institute of Microbiology and Infection (IMI), collaborating with experts in genomics, proteomics, and structural biology. Research Interests: Deciphering chromosome biology of pathogenic bacteria, including transcriptional regulation, toxin production control, and antibiotic resistance pathways. Utilizes cutting-edge methods like Hi-C for 3D chromatin analysis and single-molecule microscopy. Recent Articles: Focused on transposon capture mechanisms, bacterial promoter diversity, and quorum sensing signaling. Highlights include studies on Salmonella regulons and Vibrio cholerae biofilm suppression. Awards: Wellcome Trust Career Development Fellowship (2008), Runner-up in 'Science Snaps' competition for scientific communication. Grants: Career Development Fellowship-funded establishment of his research group at the University of Warwick (2008). Labs/Teams: Grainger Lab at the University of Birmingham, part of the IMI network. Engages in public science outreach via Twitter and lab website.

Benjamin MachtaView profile

Assistant Professor

• Biophysics
• Condensed Matter Physics
• Statistical Physics
• +3 more

Benjamin Machta is an Assistant Professor of Physics at Yale University, affiliated with the Department of Physics and the QBio Institute. He holds a BS from Brown University and a PhD from Cornell University, followed by a postdoctoral fellowship at Princeton University. His research focuses on applying theoretical physics to understand biological systems, particularly leveraging statistical physics and information theory to study biological membranes near critical points and the energetic constraints of biological signaling. Education: BS in Physics (Brown University), PhD in Physics (Cornell University), Postdoc at Princeton University (Lewis-Sigler Theory Fellow). Research Interests include: membrane criticality, phase transitions in biological systems, information-theoretic limits in organism function, and energy dissipation in biological processes. His work often bridges theoretical models with experimental data, such as collaborations with Sarah Veatch’s lab on membrane phase behavior. Publications highlight themes like membrane criticality, protein phase separation, and energy constraints in signaling. His group’s current projects explore cochlear mechanics, thermodynamic control in biological systems, and the role of criticality in sensory systems. Awards: 2019 Simons Investigator Award. Lab Affiliations: QBio Institute and Department of Physics at Yale, located in YSB-C164. Group members include postdocs Isabella Graf and Michael Abbott, and graduate students Asheesh Momi, Mason Rouches, and others.

• Virology
• Molecular Biology
• Genomics
• +6 more

James Van Etten is the William Allington Distinguished Professor of Plant Pathology at the University of Nebraska-Lincoln, affiliated with the School of Biological Sciences and Nebraska Center for Virology. His research focuses on chloroviruses—large dsDNA viruses infecting Chlorella-like algae—with emphasis on DNA replication, restriction systems, and membrane transport proteins. Key research themes include: Viral DNA modification systems Host-virus interactions Structural virology Evolution of organellar genomes Recent work analyzed: SMRT sequencing of viral methylation patterns Chlorovirus cryopreservation methods Potassium channel biophysics Host chemical signaling mechanisms Lab webpage: vanettenlab.unl.edu

Waldemar KolanusView profile

Professor

• Molecular Immunology
• Cell Signaling
• Signal Transduction Pathways
• +4 more

Prof. Waldemar Kolanus leads the Molecular Immunology and Cell Biology department at the University of Bonn's Life & Medical Sciences Institute (LIMES) . His research bridges immunoregulation , stem cell dynamics , and metabolic stress responses in immune cells. Unit 2 member at LIMES Principal investigator in SFB 704 and ImmunoSensation Cluster Leads a multidisciplinary lab with postdocs, PhD students, and technical staff His work focuses on intracellular signaling pathways connecting immune activation to tissue homeostasis, particularly through: Cytohesin proteins in integrin-mediated adhesion and migration TRIM71 in stem cell regulation and congenital hydrocephalus High-salt environments affecting macrophage function Publication trends show expertise in immune cell migration , genetic models , and chemical inhibition , with frequent use of mice and zebrafish for in vivo studies. Key articles explore: TRIM71's dual role in auditory development and germ cell maintenance Cytohesin family's Golgi regulation and insulin signaling Ruxolitinib's off-target migration inhibition of dendritic cells Contact details: Address: LIMES Institute, Carl-Troll-Straße 31, Bonn Email: kolanus.sekretariat@uni-bonn.de Phone: +49 228 73-62788