Lysine Post-Translational Modifications Professors and Supervisors | ApplySharif

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Steven G. ClarkeView profile

Professor

University of California, Los AngelesUnited States

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.

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Kathrin LangView profile

Professor

ETH ZurichSwitzerland

Kathrin Lang is a Full Professor at the Department of Chemistry and Applied Biosciences, ETH Zurich, and Head of the Organic Chemistry Laboratory. Her research focuses on chemical biology, particularly the development of tools for genetic code expansion to incorporate non-canonical amino acids into proteins and advance bioorthogonal chemistries for studying biological processes. Keywords: Genetic Code Expansion, Bioorthogonal Chemistry, Protein Engineering, Ubiquitylation Networks, Post-Translational Modifications. Lang’s work emphasizes proximity-triggered crosslinking reactions, bioorthogonal labeling, and in vivo chemistries to address challenges in protein interaction mapping and structural elucidation. Her group’s recent publications highlight methodologies for dual protein labeling, deciphering ubiquitin code, and enhancing cycloaddition reactivity. Current projects include exploring cyclopropene-fused dibenzocyclooctynes for improved labeling and investigating methylated lysine as a conformational regulator in Hsp90. Funding sources include the ERC (Ubl-tool), DFG (SFB1035, SPP1926), and ETH Zurich. She contributes to education through courses like Genetic Code Expansion for Studying Posttranslational Modifications and Chemical Biology and Synthetic Biochemistry . Collaborative efforts span structural biology, microbiology, and synthetic biochemistry, with applications in ubiquitin research and cellular imaging.

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Rafael BrüschweilerView profile

Professor

Ohio State UniversityUnited States

Rafael Brüschweiler is a Professor and Ohio Research Scholar at The Ohio State University, holding joint appointments in the Department of Chemistry and Biochemistry and the Department of Biological Chemistry and Pharmacology. He serves as the NMR Executive Director for the Ohio State Campus Chemical Instrument Center and the NSF-funded National Gateway Ultrahigh Field NMR Center. His research focuses on biophysical chemistry, analytical chemistry, and computational modeling, emphasizing protein dynamics, metabolomics, and NMR method development. He received his Ph.D. from ETH Zurich and completed a postdoc at the Scripps Research Institute. His research integrates experimental NMR, molecular dynamics simulations, and machine learning to study protein structure-function relationships, metabolic pathways, and biomolecular interactions. Key areas include the dynamics of oncogenic K-Ras, glucokinase glucose sensing, and nanoparticle-assisted NMR techniques. His work is funded by the NIH and NSF, with applications in biomedical diagnostics and drug discovery. Dr. Brüschweiler leads a multidisciplinary lab training students and postdocs in NMR spectroscopy, computational methods, and metabolomics. His lab developed tools like DEEP picker and COLMAR for automated NMR data analysis, contributing to the SECIM metabolomics center. He actively recruits students interested in protein dynamics, computational modeling, or metabolomics.

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Scott RothbartView profile

Professor

Van Andel InstituteUnited States

Dr. Scott Rothbart is a Professor in the Department of Epigenetics at Van Andel Institute (VAI), where he leads the Rothbart Laboratory. He earned his B.S. in Food Science and Human Nutrition from the University of Florida and his Ph.D. in Pharmacology and Toxicology from Virginia Commonwealth University. His postdoctoral training was conducted under Dr. Brian Strahl at the University of North Carolina at Chapel Hill. His research focuses on understanding chromatin accessibility, histone post-translational modifications, and DNA methylation's role in disease, particularly cancer. He translates this basic research into epigenetic target identification and drug discovery. Dr. Rothbart has contributed to groundbreaking studies on UHRF1’s role in DNA methylation maintenance and its therapeutic potential in cancer. He co-leads the VAI-SU2C Epigenetics Dream Team and directs the VAI Cancer Epigenetics Training Program. His work has been recognized with awards like the NIH MIRA Award and the American Cancer Society Research Scholar Grant. Research Interests: Chromatin biochemistry, cancer epigenetics, functional proteomics, histone modifications, and epigenetic drug development. His lab develops tools like peptide microarrays and functional proteomics platforms to study histone modifiers and their clinical relevance. Notable Achievements: Published over 122 peer-reviewed papers in 2024, including 63 in high-impact journals. Launched 15 clinical trials through the Epigenetics Dream Team. His lab’s work on viral mimicry therapies and epigenetic drug combinations has advanced cancer treatment strategies. Education: B.S. University of Florida (2004), Ph.D. Virginia Commonwealth University (2009), Postdoctoral Fellowship UNC Chapel Hill (2014).

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Huazhong ShiView profile

Professor

Texas Tech UniversityUnited States

Dr. Huazhong Shi is a Professor in the Department of Chemistry and Biochemistry at Texas Tech University. His research focuses on molecular biology, biochemistry, and plant stress response mechanisms, with a particular emphasis on gene editing for crop improvement, herbicide resistance development, and computational simulations of protein-small molecule interactions. Ph.D., Wuhan University, China, 1995 Research Associate, University of Arizona, 1999-2001 Research Associate, University of California, 2001-2003 Research Associate, Purdue University, 2003-2004 Dr. Shi’s research explores gene editing strategies to enhance crop traits such as clonal seed production, haploid induction, and herbicide resistance. His lab also investigates molecular dynamics simulations to understand enzyme-herbicide interactions and stress-inducible gene regulation. Key projects include engineering salt-tolerant crops via Na+/H+ antiporter optimization and elucidating the roles of SHI genes in stress response pathways. The 15 most recent publications highlight advancements in gene editing for hybrid vigor preservation, directed evolution of herbicide-resistant enzymes, and computational modeling of stress tolerance mechanisms. These works span disciplines including plant biotechnology, environmental toxicology, and agricultural sustainability, with subfields such as RNA splicing, redox biology, and nutrient-stress interactions. Dr. Shi’s lab includes graduate students Yihui Yuan, Hongjia Qian, Amna Aqdas, Karthik Kalvakuntla, and Shoumik Kundu, alongside research associate Dr. Jianfei Guo. His work contributes to global food security through biotechnological innovations in crop resilience to environmental stresses.

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Dukka KCView profile

Adjunct Professor

Michigan Technological UniversityUnited States

Dukka KC is an Adjunct Professor in the Department of Computer Science at Michigan Technological University and a member of the Institute of Computing and Cybersystems (ICC). His research focuses on computational data science with applications in bioinformatics, computational biology, and health informatics, particularly leveraging machine learning and high-performance computing to develop predictive tools for protein and nucleic acid modifications. Ph.D., Informatics, Kyoto University, 2006 M.Inf., Informatics, Kyoto University, 2003 B.Eng., Computer Science, Kyoto University, 2001 Research interests include: Developing GPU-accelerated bioinformatics tools (e.g., GPU-I-TASSER) Predicting post-translational modification sites using deep learning (e.g., DeepNGlyPred, DeepRMethylSite) Machine learning approaches for malonylation, succinylation, and sulfenylation site prediction High-throughput analysis of next-generation sequencing data Interdisciplinary projects in biometrics, cybersecurity, and disaster prediction Recent publications highlight a strong trend in applying deep learning to protein structure and function prediction, GPU-parallelization for computational efficiency, and machine learning for both biological and cybersecurity applications. The lab also emphasizes cross-domain collaborations and the development of scalable bioinformatics workflows. Grants and funding include projects like the President's Convergence Science Initiative (PI, $300K), NSF III grants for protein function prediction ($111K), and multi-institutional collaborations on biometric test-beds and synthetic biology research. The KC Lab at Michigan Tech specializes in integrating computational data science with molecular biology, focusing on protein/RNA/DNA modification site prediction and contributing to large-scale proteome analysis through machine learning-driven pipelines.

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Jeffrey W. BodeView profile

Professor

University of ZurichSwitzerland

Professor Jeffrey W. Bode serves as Full Professor at the Department of Chemistry and Applied Biosciences at ETH Zurich, Switzerland, and maintains a secondary affiliation with the Institute of Transformative Biomolecules at Nagoya University, Japan. His internationally recognized research laboratory develops novel chemical reactions that operate under physiological conditions, bridging synthetic organic chemistry with biological applications. The Bode Research Group specializes in creating chemical methodologies that function in water and biological environments, including proteins, cells, and tissues. Their major research thrusts include acylboronate chemistry (particularly potassium acyltrifluoroborates or KATs), protein synthesis through ketoacid-hydroxylamine (KAHA) ligation, synthetic fermentation for drug discovery, and SnAP chemistry for N-heterocycle synthesis. These innovations enable applications in wound healing, drug delivery, cellular encapsulation, and artificial tissue development. The group's work on chemoselective ligation reactions has fundamentally advanced amide bond formation without traditional coupling reagents. Recent publications demonstrate a strong trajectory toward automated synthesis platforms, protein engineering, advanced bioconjugation techniques, and applications in chemical biology. The group has successfully commercialized SnAP chemistry through Sigma Aldrich and developed KAHA ligation into a robust method for synthesizing large proteins. Their research consistently focuses on creating molecules inaccessible through existing technologies, with particular emphasis on physiological compatibility and biological relevance. Professor Bode leads an international research team of approximately thirty PhD students and postdoctoral researchers from twenty different countries. The Bode Research Group maintains extensive collaborations across disciplines, contributing significantly to chemical biology, medicinal chemistry, and materials science. Their laboratory is equipped with advanced automation platforms for organic synthesis and maintains strong connections with pharmaceutical and biotechnology industries for translational applications of their chemical methodologies.

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Lesley StarkView profile

Senior Lecturer

University of EdinburghUnited Kingdom

Lesley Stark is a Senior Lecturer and Principal Investigator at the Edinburgh Cancer Research Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh. Her research focuses on the interplay between nucleolar stress, NF-κB signaling, and cancer prevention, particularly investigating aspirin’s anti-tumour mechanisms. Education: B.Sc. Cell Biology and Immunology (1st Class), University of Aberdeen (1990) PhD, University of Edinburgh (1995), supervised by Professor C Bird Caledonian Research Foundation Fellowship (2002) Research Interests: Her group studies NF-κB nucleolar stress response pathways, precision cancer prevention, and biomarkers of aspirin response in colorectal cancer. Recent work connects nucleolar dysfunction to aging and senescence. She uses proteomics, organoid cultures, and animal models to validate therapeutic targets. Scientific Awards: Caledonian Research Foundation Fellowship (2002) Fellow of the Royal Society of Biology (2014) Post Graduate Certificate in Academic Practice (2020) Fellow of the Higher Education Authority (2020) Teaching Roles: Course coordinator for Cancer Cell Biology (MScR) and teaches Cancer Biology and Medicine (undergraduate). She served as IGMM Director of Masters Teaching (2019-present) and on the Biomedical Sciences Board of Studies (2018-present).

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Gary E. GibsonView profile

Professor

Cornell UniversityUnited States

Gary E. Gibson is a tenured Professor of Neuroscience at Weill Cornell Medicine , where he serves as Lab Director at the Laboratory for Mitochondrial Biology and Metabolic Dysfunction in Neurodegeneration . He also holds the position of Associate Director at the Dementia Research Service within the Burke Neurological Institute . His academic career spans institutions including UCLA (where he completed postdoctoral work and faculty appointments) and Cornell University , where he earned his Ph.D. Education: B.S. in Zoology and Chemistry, University of Wyoming Ph.D. in Physiology (Biochemistry/Neuroscience), Cornell University Research Focus: Dr. Gibson's work centers on mitochondrial dysfunction and oxidative stress in neurodegenerative diseases (Alzheimer's, Huntington's, Parkinson's). His lab investigates: Mechanisms of α-ketoglutarate dehydrogenase complex (KGDHC) deficiency Metabolism-calcium signaling interactions Protein post-translational modifications (succinylation, acetylation) Thiamine-dependent metabolic pathways Translational studies using induced pluripotent stem cells Clinical trials testing metabolic interventions (e.g., benfotiamine) Publications reveal expertise in: TCA cycle enzyme abnormalities Neurodegenerative biomarker discovery Calcium dyshomeostasis Metabolic-epigenetic crosstalk Neuroprotective strategies Animal models of oxidative stress Honors: ASN Award for Outstanding Young Investigator Three U.S. patents NIH Director’s Talk and other honorary lectureships Grants: Continuously funded by NIH/NIA grants (P01AG014930) for mitochondrial dysfunction research since 1999. Serves on Alzheimer’s Association and American Federation for Aging Research review panels.

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Sarah FranklinView profile

Associate Professor

University of UtahUnited States

Sarah Franklin is an Associate Professor of Cardiovascular Medicine at the University of Utah School of Medicine, where she leads research on epigenetic regulation of heart disease. She also serves as Assistant Director for the Rural & Underserved Utah Training Experience (RUUTE) program, mentoring students through summer research initiatives. Education: B.S. and Ph.D. in Molecular Biology from Brigham Young University Her research focuses on chromatin remodeling and histone modifications in cardiac hypertrophy and failure, utilizing proteomics, animal models, and biochemical approaches. Recent work explores SMYD1a's role in mitochondrial protection and translational applications for ischemic injury. The 15 most recent publications highlight her contributions to proteomic analysis of cardioprotective therapies (2025), genetic cardiomyopathy mechanisms (2023-2024), and foundational studies on chromatin structure in cardiac physiology (2011-2016). Key subfields include histone methylation, mitochondrial dynamics, and rural medical education.

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Brad FergusonView profile

Associate Professor

University of Nevada, RenoUnited States

Brad Ferguson is an Associate Professor in the Department of Environmental Sciences & Health at the University of Nevada, Reno. His research investigates the epigenetic mechanisms linking metabolic diseases like obesity and diabetes to cardiac remodeling, with a focus on histone deacetylases (HDACs), acetyltransferases (HATs), and dietary bioactives. Key techniques: bioinformatics, cell culture, animal models. Primary research themes: chromatin regulation, metabolic-cardiovascular crosstalk, microbiome-epigenome interactions. The lab emphasizes dietary epigenetic modifiers and translational approaches to develop therapies for cardio-metabolic disorders. Recent publications highlight intersections between: Epigenetic aging and caloric restriction HDAC inhibition in cardiac/hypertension models Muscle physiology and post-translational modifications Nutritional programming in livestock and human systems No scientific awards were explicitly documented in the provided materials.

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Binhua ZhouView profile

Professor

University of KentuckyUnited States

Binhua Zhou, Ph.D., holds the Madeline F. James and Edith D. Gardner Chair in Cancer Research at the Markey Cancer Center, University of Kentucky. He serves as Professor in the Department of Molecular and Cellular Biochemistry, Director of the Breast Cancer Research Program, and Program Leader for the Molecular and Cellular Oncology Research Program. His academic qualifications include a Doctor of Medicine from Guangzhou Medical College (1986), a Ph.D. from the University of Texas at Austin (1996), and postdoctoral training at the University of Texas Health Science Center (2001). Dr. Zhou's research focuses on molecular mechanisms of cancer metastasis, particularly epithelial-mesenchymal transition (EMT) regulation by Snail/Slug transcription factors in breast and pancreatic cancers. Key areas include metabolic reprogramming in metastasis, signaling pathway alterations, and therapeutic targeting of NNMT in triple-negative breast cancer. His work employs biochemical, molecular, and cellular approaches to identify targets for metastasis prevention. Analysis of recent publications (2020-2025) reveals dominant themes: EMT-linked metabolic adaptation, ferroptosis suppression, STAT3/SNAIL synergy in metastasis, and myeloid cell regulation in breast cancer. His group consistently explores intersections between transcriptional control, tumor metabolism, and microenvironment remodeling. Awards & Honors Young Investigator Award for Breast Cancer Research (1998) Alexander Wang Memorial Award, 3rd Prize (2000) Career Development Award, Ovarian Cancer Spore Program (1999) Wethington Excellence in Research Award (2009) Award for Cancer Research (2009) Dr. Zhou leads multiple NIH-funded projects as Principal Investigator, including NCI grants targeting NNMT in breast cancer progression and DoD-funded obesity-cancer initiatives. He directs the Breast Cancer Research Program, coordinating interdisciplinary teams investigating metastasis mechanisms and therapeutic innovation.

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Christine BeuckView profile

Assistant Professor

University of Duisburg-EssenGermany

Dr. Christine Beuck is an Assistant Professor at the University of Duisburg-Essen, affiliated with the Faculty of Biology and the Centre for Medical Biotechnology (ZMB). Her research focuses on structural and medicinal biochemistry, particularly using Nuclear Magnetic Resonance (NMR) spectroscopy to study protein interactions and supramolecular ligand binding. She is a key member of the Collaborative Research Center (CRC) 1093, investigating protein interactions with synthetic ligands and their biological implications. Education: She earned a Diploma in Chemistry from TU Dortmund (2001) and a Ph.D. in Chemistry from RWTH Aachen University (2005) under Prof. E. Weinhold. Postdoctoral training included work at The Scripps Research Institute (2005–2014) under Prof. J. R. Williamson, followed by a Japan exchange program at Tokyo University (2005) and a Lithuania exchange at the Institute of Biotechnology (2003). Research Interests: Her work combines NMR spectroscopy with biochemical techniques (e.g., fluorescence, ITC, BLI) to analyze protein-ligand interactions, protein structures, and dynamics. She pioneered side-chain-specific NMR experiments for lysine/arginine residues and employs advanced NMR methods like BEST-TROSY for large proteins. Applications span drug design, understanding disease-linked protein dysfunctions, and nanotechnology (e.g., gold nanoparticle characterization). Advising & Grants: While specific grants are not detailed, her CRC 1093 affiliation indicates collaborative funding. Her research contributes to developing supramolecular ligands to modulate biological interactions, with potential medical and biotechnological applications. Labs/Teams: She leads projects in the ZMB and collaborates with institutions worldwide, including The Scripps Research Institute and Tokyo University. Her lab integrates structural biology, medicinal chemistry, and nanotechnology to address complex biological questions.

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Blagoy BlagoevView profile

Professor

University of Southern DenmarkDenmark

Blagoy Blagoev is a Professor at the University of Southern Denmark , Department of Biochemistry and Molecular Biology, and a leading researcher in Biomedical Mass Spectrometry and Systems Biology . He serves as Principal Investigator (PI) in the ATLAS Center for Functional Genomics and Tissue Plasticity , focusing on metabolic disorders and ubiquitin signaling. Department of Biochemistry and Molecular Biology ATLAS Center Research Interests : His work spans Proteomics , Ubiquitination , Metallic Dysfunction-Associated Steatotic Liver Disease , and Stem Cell Differentiation . Recent projects include investigating hepatic stellate cell metabolism and non-canonical ubiquitin signaling mechanisms . Scientific Trends : Recent publications highlight multi-omics approaches to liver disease, pharmacological targeting of CK2 in obesity, and fetal metabolic adaptation during maternal inflammation. The work integrates mass spectrometry , single-cell analysis , and signaling pathway mapping . Grants & Collaborations : Active in international collaborations, he participates in projects funded by the U.S. Department of Defense , Novo Nordisk Foundation , and Danish Research Council . Current grants explore PD-1 signaling , mesenchymal stem cell transcription complexes , and adipose-liver crosstalk . PhD Supervision : Mentors students including Christoffer Wernberg , Francesca Boel , and Ditte Hansen in proteomics and metabolic research.

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Joanna McgouranView profile

Associate Professor

Trinity College DublinIreland

Dr. Joanna Mcgouran is an Associate Professor in the Department of Chemistry at Trinity College Dublin, where she leads research in translational organic chemistry and chemical biology. She holds a 1st class MChem and D.Phil. from the University of Oxford and completed postdoctoral training in both the Department of Medicine and the Chemistry Department at Oxford, working with Professors Benedikt Kessler and Tom Brown, respectively. In 2016, she joined Trinity College Dublin as the Schuler Assistant Professor in Translational Organic Chemistry, advancing to Associate Professor. 1st class MChem, University of Oxford D.Phil., University of Oxford (Supervisor: Prof. Ben Davis) Postdoctoral Researcher, Department of Medicine, University of Oxford (Prof. Benedikt Kessler) Postdoctoral Researcher, Chemistry Department, University of Oxford (Prof. Tom Brown) Her research focuses on the development of activity-based probes and inhibitors targeting enzymes involved in DNA repair and ubiquitin signaling pathways. She investigates the mechanisms of nucleases like SNM1A and deubiquitinating enzymes using synthetic chemistry, biochemical assays, and proteomics. Her work aims to understand enzyme function in DNA damage response and develop novel therapeutic strategies for diseases including cancer. Her recent publications reveal a strong trend in designing chemical tools for probing enzyme activity, particularly through modified nucleosides, covalent labeling, and photocatalytic methods. She frequently publishes in high-impact journals such as Nature , ACS Chemical Biology , and Organic and Biomolecular Chemistry , emphasizing interdisciplinary approaches that bridge organic synthesis and biological application. MA, University of Oxford, 2009 Scholarship, University of Oxford, 2002–2005 Dr. Mcgouran has secured significant research funding from Science Foundation Ireland, the Irish Research Council, the Wellcome Trust, and Trinity College Dublin. Her funded projects support the development of probes for DNA processing enzymes, cyclic peptide inhibitors of nucleotide excision repair, and tools for studying p53 deubiquitination. While student names are not listed in the provided text, her active research group and grant leadership imply she mentors PhD and Master’s students. She leads multiple projects on disulfide modification, oligonucleotide probes, and activity-based profiling, often collaborating across disciplines. Her laboratory is involved in creating innovative chemical tools that enable precise interrogation of enzyme activity in live cells and disease models.

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