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Matthew ChampionView profile

Associate Professor

• Biochemistry
• Physical/Analytical Chemistry
• Microbial Proteomics
• +11 more

Matthew Champion is an Associate Professor in the Department of Chemistry and Biochemistry at the University of Notre Dame, where he leads the Champion Laboratory. His research integrates biochemistry, proteomics, and genetics to investigate microbial pathogenesis, particularly in mycobacteria. Current Position: Associate Professor, University of Notre Dame (2019–present) Previous Academic Roles: Research Associate Professor (2015–2019), Research Assistant Professor (2009–2015), University of Notre Dame Industry Experience: Applied Biosystems (AB Sciex), Mass-Spectrometry-Proteomics Group (2003–2009) Education: Ph.D. in Biochemistry, Texas A&M University (2005); B.S. in Microbiology, University of Iowa (1997) Champion's research focuses on microbial proteomics and metagenomics, with an emphasis on protein secretion systems in pathogenic bacteria like Mycobacterium tuberculosis . His lab develops antibody-free, proteogenetic assays to dissect the ESX-1 secretion system, a key virulence mechanism. He utilizes state-of-the-art quantitative proteomics, capillary electrophoresis, and genetic screening to identify and quantify secreted proteins involved in disease phenotypes. His work has broad applications in understanding bacterial virulence, antigen discovery, and therapeutic targeting. His recent publications span analytical method development, microbial physiology, and systems biology. Trends in his research include innovation in capillary electrophoresis interfaces, streamlined proteomic workflows (e.g., MAP), and deep functional characterization of secretion hierarchies in mycobacteria. His studies frequently appear in high-impact journals such as Cell , PNAS , and Analytical Chemistry . Dr. Champion has mentored numerous graduate students, including Dr. Daniel Hu, Dr. Taylor Lundgren, and Dr. Caitlin Kerr, who have successfully defended their dissertations. His lab actively participates in national conferences such as ASMS, and he contributes to the development of open tools like Skyline for proteomics data analysis. The Champion Lab is part of the analytical and biochemistry divisions within the Department of Chemistry and Biochemistry, fostering interdisciplinary research at the intersection of biology, chemistry, and engineering. The lab maintains a dynamic environment with ongoing projects in microbial secretion, host-pathogen interactions, and analytical instrumentation.

• Biochemistry
• Biophysics
• Protein Folding
• +7 more

Patricia Clark is the Rev. John Cardinal O'Hara, CSC, Professor of Biochemistry and Professor in the Department of Chemistry & Biochemistry at the University of Notre Dame. She also holds a concurrent professorship in Chemical & Biomolecular Engineering and serves as Associate Vice President for Research. She is the Founder & Director of the Biophysics Instrumentation Core Facility and previously founded the Biophysics Graduate Program. Her research focuses on the fundamental mechanisms of protein folding, particularly in the context of cellular environments and β-sheet formation. Key interests include co-translational folding, suppression of misfolding and aggregation, and the biophysics of virulence factor secretion in bacteria. Her work has significant implications for understanding diseases such as Alzheimer’s, cystic fibrosis, and cancer. Her recent publications highlight advances in codon usage effects on protein folding, disordered protein behavior, and computational modeling of protein structure. These works span disciplines in biochemistry, biophysics, bioinformatics, and molecular biology, reflecting a highly interdisciplinary approach. Selected scientific awards include: Dorothy Crowfoot Hodgkin Award, The Protein Society (2023) NIH Director's Pioneer Award (2021) Fellow, American Association for the Advancement of Science (2022) NSF CAREER Award Michael and Kate Barany Award for Young Investigators, Biophysical Society (2013) Prof. Clark has been instrumental in mentoring students and leading large-scale research initiatives. She has directed major core facilities and graduate programs, securing significant grants from NIH, NSF, and the W.M. Keck Foundation. Her leadership extends to national roles, including presidency of the Gibbs Society for Biothermodynamics and chairing subgroups within the Biophysical Society. She leads the Clark Laboratory, which integrates experimental and computational approaches to study protein folding dynamics in vivo and in vitro, and collaborates widely across engineering and life sciences disciplines.

• Stem Cell Engineering
• Molecular Pathways of Stem Cell Self-Renewal
• Lineage Commitment
• +5 more

Professor Konstantinos Anastassiadis serves as the Chair for Stem Cell Engineering at the Biotechnology Center (BIOTEC), which is part of the Center for Molecular and Cellular Bioengineering (CMCB) at Dresden University of Technology. He has held this professorship since 2016, following his appointment as Research Group Leader for Stem Cell Engineering at BIOTEC from 2004-2016 and Junior Group Leader at the Center for Regenerative Therapies Dresden (CRTD) from 2006-2011. Dr. Anastassiadis earned his Dr. sc. agr. from TU Berlin in 1993, followed by postdoctoral work at TU Munich (1993-1995), EMBL Heidelberg (1996-2001), and BIOTEC, TU Dresden (2002-2003). His academic journey reflects a strong foundation in molecular biology and genetics that has shaped his current research focus. The research interests of Prof. Anastassiadis center on unraveling the molecular pathways that regulate self-renewal and lineage commitment of stem cells, with particular focus on the molecular mechanisms involved in cellular reprogramming. His lab works with various stem cell types including mouse and human embryonic stem cells (mES, hES), neural stem cells (NSCs), mesenchymal stromal cells (MSCs), and induced pluripotent stem cells (iPS). A significant portion of his work involves developing and applying genetic engineering tools to address fundamental questions in stem cell biology. His research has particularly concentrated on the role of histone 3 lysine 27 demethylases UTX (KDM6A) and UTY (KDM6C) in embryonic development and hematopoiesis. Analysis of Prof. Anastassiadis's recent publications reveals a strong focus on stem cell regulation, epigenetic mechanisms, and genetic engineering applications. His work spans multiple model systems including mouse models, human stem cells, and other organisms. A recurring theme is the investigation of chromatin modifiers (particularly histone methylation complexes like MLL/SET proteins) and their roles in development, disease, and stem cell maintenance. His lab has made significant contributions to developing genetic engineering tools including codon-optimized recombinases (Flp, Dre, Vika), transposon-mediated BAC transgenesis, and CRISPR-associated protocols. Prof. Anastassiadis is actively involved in teaching for the international Master's programs in Molecular Bioengineering and Regenerative Biology and Medicine (RegBioMed) at CMCB. He teaches courses including Stem Cell Engineering (every winter semester) and Stem Cells, Development and Regeneration, as well as supervising the Genome and Stem Cell Engineering lab course. The Anastassiadis Group operates within the Biotechnology Center at TU Dresden, where they maintain facilities for stem cell culture, genetic engineering, and molecular analysis. Their research integrates approaches from molecular biology, genetics, epigenetics, and bioengineering to address fundamental questions about stem cell behavior and to develop new tools for stem cell research and potential therapeutic applications.

• Fungal Genomics
• Genomic Evolution
• Fungal Ecology
• +7 more

Marco Alexandre Guerreiro is a fungal genomicist with a focus on evolutionary biology, ecology, and taxonomy. Currently, he works as a PostDoctoral Researcher in Prof. Eva Stukenbrock's lab at the Max-Planck Institute for Evolutionary Biology (Plön, Germany) since 2024, continuing research into the genomic evolution of human fungal pathogens within the Trichosporonales order. His prior positions include PostDoctoral Fellowships at Ruhr-Universität Bochum (2019–2021), where he explored fungal communities in plant leaves, and NOVA University Lisbon (2012–2014) as a Research Associate. Education : PhD in Biology (2014–2019) and MSc in Molecular Genetics and Biomedicine (2010–2012) from Ruhr-Universität Bochum and NOVA University Lisbon respectively; BSc in Biotechnology (2007–2010) from University of Algarve, Portugal. His research spans fungal community ecology, mating-type evolution, and physiological adaptations during lifestyle transitions. Current work employs comparative genomics to unravel genomic signatures of human pathogens and taxonomic diversity within Trichosporonales. Earlier studies addressed biostatistical approaches, denitrification dynamics, and thermophilic fungal isolation. Recent publications highlight his expertise in fungal genomics, including analyses of plant pathogen interactions , effector proteins , thermotolerant species , and meiotic recombination . His work combines multi-meta'omic approaches to link microbial functions to ecosystem processes, such as litter decomposition and niche adaptation on leaves. Scientific Awards : Walter Benjamin Programme Fellowship (2022–2023) from the Deutsche Forschungsgemeinschaft (DFG).

• Vascular Biology
• Cancer Biology
• Regenerative Medicine
• +7 more

ZhaoJun Liu is a Professor of Surgery and holds a secondary appointment in Biochemistry and Molecular Biology at the University of Miami Miller School of Medicine . He directs the Vascular Research Laboratory and serves as Associate Director of the Vascular Biology Institute. Education: PhD in Molecular Biology, Osaka University (1996) MD in Medicine, Shanghai Second Military Medical University (1983) Research Interests: Dr. Liu's work bridges vascular biology and cancer biology . In vascular biology, he investigates gene/stem cell therapy for therapeutic angiogenesis, molecular mechanisms of atherosclerosis, and stem cell homing to ischemic/tumor tissues. His cancer research focuses on the Notch signaling pathway 's role in melanoma progression, aiming to develop therapies targeting tumor-stroma interactions. Recent Publications: His research includes nanocarrier-based vascular therapies, Codon-Optimized E-Selectin/AAV2 gene therapy, and Notch pathway modulation in cancer. These span regenerative medicine , vascular biology , and cancer microenvironment disciplines. Scientific Awards: NIH/NHLBI VITA Program Pitch Presentation Trophy Certificate of Recognition for Oral Presentation, Global Congress on Tissue Engineering VITA Program Award, NIH/NHLBI Women’s Cancer Association Award Research Initiatives in Vascular Disease Travel Scholarship, Society for Vascular Surgery JSPS Research Award, Japan Society for Promotion of Science Teaching & Mentorship: Dr. Liu serves as graduate faculty for the Program in Biomedical Sciences (PIBS) at the University of Miami and Florida International University, mentoring MD and PhD students, postdocs, and research associates. His grants include NIH federal funding and Florida state biomedical research programs.

• RNA Biology
• Biochemistry
• Molecular Genetics
• +5 more

Byung Ran Ranny So is an Assistant Professor in the Department of Chemistry and Biochemistry at the University of Texas at Arlington. Her research investigates RNA-binding proteins and their role in non-coding RNA–protein complex biogenesis and gene regulation. She has held positions at the University of Pennsylvania (2010–2020) and LG Chem (2002–2004), following academic training at Sungkyunkwan University (BS/MS) and The Ohio State University (PhD). PhD in Biological Chemistry (2010), The Ohio State University MS in Chemistry (2002) and BS in Chemistry (2000), Sungkyunkwan University Her research focuses on: Biogenesis of snRNP complexes snRNP functions in cancer Small signaling molecules in RNA processing High-throughput small-molecule screening RNA-protein tools for gene therapy Recent publications examine U1 snRNP regulation of transcription, RNA-protein interactions in gene expression, and applications in 3D bioprinting. She has secured federal funding from the NIH and mentors graduate/undergraduate researchers in RNA biology and biochemical techniques. National Institutes of Health grant ($422,522, 2023–2026) NIH scholarship ($56,923, 2024–2025) UTA microplastics exposure assessment grant ($16,000, 2023–2024) Dr. So teaches courses in biochemistry, organic chemistry, and advanced lab techniques while advising doctoral dissertation committees and developing online tools for active learning in biochemical subjects like Structural Biology and Medicinal Chemistry.

• Computational Biology
• Bioinformatics
• Phylogenetics
• +5 more

Maria Anisimova is Professor and Director of the Bioinformatics Center at the Institute of Computational Life Sciences (ICLS) within ZHAW Zurich University of Applied Sciences, Wädenswil, Switzerland. Her research spans evolutionary biology, computational genomics, and bioinformatics tool development, focusing on tandem repeats, codon usage, and indel evolution. Her publications address: Computational challenges in codon optimization (2025) Indel-aware phylogenetic methods (2024-2025) Tandem repeat dynamics in cancer and evolution (2022-2025) Ontology-driven biomedical data querying (2022) She has received multiple research grants from: Swiss National Science Foundation (grants 193832, 182330, 176316, 157064, 127325) European Commission (grant 823886) European Cooperation in Science and Technology (grant C16.0072) Maria leads collaborative projects in: Trans-omic cancer research Repeat protein classification Indel evolutionary modeling Biomedical data integration Her lab develops bioinformatics tools like TRAL, ProPIP, and ARPIP for tandem repeat analysis and sequence alignment.

Ivo HofackerView profile

Professor

• Computational Biology
• RNA Bioinformatics
• RNA Secondary Structures
• +2 more

Ivo Hofacker is a Professor at the University of Vienna, holding a double appointment in the Faculty of Chemistry and Faculty of Computer Science. He leads the Research Group Bioinformatics and Computational Biology at the Institute for Theoretical Chemistry. His research focuses on computational biology , with emphasis on RNA bioinformatics (including the Vienna RNA Package for RNA structure prediction) and systems chemistry problems like combinatorial reaction networks. His work spans RNA structure prediction, RNA-RNA interactions, and development of bioinformatics tools. Recent publications (2021-2024) explore RNA 3D modeling, evolutionary constraints, viral RNA structures, membrane protein optimization, and limitations of deep learning in RNA folding. His group actively develops methods integrating phylogenetic data, chemical probing, and biophysical analyses. He collaborates extensively across disciplines, contributing to virology, microbiology, and biophysics. No awards or student advisees are explicitly mentioned in the source material.

• Bioinformatics
• Data Analytics
• Machine Learning
• +3 more

Pengyao Ping is an NHMRC grant-funded researcher and bioinformatician at the Adelaide Medical School, University of Adelaide. His research integrates clinical, genetic, and proteomic datasets using machine learning to investigate complex diseases. Current projects leverage UK Biobank and All of Us Research Program data to study pharmacological treatment responses. Education: Background in bioinformatics, data analytics, and computer science. Research Focus: Develops statistical frameworks for large-scale biomedical datasets. Recent publications show strong emphasis on genomic data processing, viral host interactions, and computational vaccine design. Collaborations: Works extensively with epidemiologists and psychiatrists. Utilizes high-performance computing for genomic analyses. Future Work: Expanding research on AI-driven drug response prediction and multi-omics integration.

• Systems Biology
• Biochemistry
• Molecular Biology
• +4 more

Prof. JL Snoep holds dual academic appointments as Full Professor of Systems Biology at the Faculty of Science, Vrije Universiteit Amsterdam and as Hoogleraar (Full Professor) at Stellenbosch University, South Africa , since 2000. His research focuses on systems-level understanding of metabolic pathways, enzyme kinetics, and cellular dynamics with applications to medicine and biotechnology. Research Interests include: Metabolic pathway modeling and regulation Enzyme structure-function relationships Systems biology approaches to disease mechanisms Pharmacological implications of steroid metabolism Microbial metabolic engineering Recent work addresses glycolytic oscillations, enzymatic synthesis of metabolites like cyclic-2,3-diphosphoglycerate, and the role of hydroxysteroid dehydrogenases in hormone regulation. His contributions span 126+ publications and 4 datasets on malaria pathogenesis modeling. Prof. Snoep has supervised 5 PhD theses and collaborates internationally on projects involving metabolic modeling and enzyme characterization. His research aligns with UN SDGs related to health and sustainable development through studies on kidney disease mechanisms and drug discovery.

Brian MortonView profile

Professor

• Molecular evolution
• Evolutionary genomics
• Genome evolution
• +5 more

Brian R. Morton is a Professor of Biological Sciences at Barnard College, Columbia University, where he has been a faculty member since 1995. His research focuses on genome evolution, particularly in plant plastid genomes, and chemosensory receptor systems in insects like Manduca sexta. He holds a BS from the University of Toronto and a PhD from the University of California, Riverside. Research Interests: Professor Morton’s work explores selective constraints on codon usage, nucleotide substitution dynamics, and structural evolution of plastid genomes. His lab also investigates chemosensory receptors in insects, using CRISPR-Cas9 to study gene function. These studies bridge molecular evolution, bioinformatics, and experimental genetics. Publications Trends: His recent work emphasizes Gymnosperm chloroplast DNA asymmetry and mutation processes in angiosperms, reflecting a continued focus on evolutionary genomics. Earlier studies on Manduca sexta receptors highlight his interdisciplinary approach to understanding sensory systems. Awards: No specific awards listed, though his contributions to plant and insect genomics are widely recognized. Advising & Teaching: Advised students including Theyjasvi Ashok, Nina Kalkus, and Joy Barrett. Teaches courses in genetics, bioinformatics, and science policy. Active in mentoring through Barnard’s Project Lab in Molecular Genetics. Labs/Teams: Leads a research group at Barnard, collaborating with institutions like the University of California and international partners on CRISPR applications and comparative genomics.

Martin CarrView profile

Senior Lecturer

• Protist evolution
• Origin of animals
• Genome evolution
• +5 more

Martin Carr is a Senior Lecturer in the Department of Physical and Life Sciences within the School of Applied Sciences at the University of Huddersfield. He is also a Member of the Evolutionary Genomics Research Centre and holds an Associate Membership with the Cellular and Molecular Models of Disease Centre. Dr. Carr is actively accepting PhD students and has a research profile that spans evolutionary biology, genomics, and protistology. His educational background includes Biochemistry and Genetics studies followed by a PhD in population genetics from the University of Nottingham. His postdoctoral career took him to the Natural History Museum in London, UCL, and the Universities of York and Leeds, where he developed expertise in bioinformatics, phylogenetics, and population genetics. Dr. Carr's research focuses on the eukaryotic supergroup Opisthokonta, particularly on choanoflagellates as the sister-group to animals. His work explores how animals evolved from unicellular ancestors through genomic and molecular analyses. Additional research interests include transposable elements, genome evolution, and the population genetics of these genetic parasites. His fingerprint analysis shows strong emphasis on Choanoflagellata (100%), DNA Transposable Elements (38%), Phylogeny (31%), Genome (25%), and Retroelements (23%). His publication record shows consistent output since 2001, with recent publications in 2025, 2023, and 2022 spanning topics from choanoflagellate phylogeny to protistan origins of animals and fungi. His work demonstrates a clear focus on molecular evolution and the genomic basis of evolutionary transitions, particularly the animal-fungal-protist relationships within Opisthokonta. Dr. Carr is an active member of the scientific community, serving as Treasurer of the British Society of Protist Biology (BSPB) since 2009 and as a committee member since that time. He is also a member of the Genetics Society. His professional activities include numerous peer reviews for journals like Nature Communications and Open Biology, as well as oral presentations at conferences. His research contributes to UN Sustainable Development Goals related to understanding biodiversity and evolutionary processes. With a Google Scholar h-index of 18 from 2,268 citations, his work has gained significant recognition in the field of evolutionary biology and protistology.

• Muscle Development
• Zebrafish Genetics
• Membrane Biology
• +5 more

Dr. Tom Hall is a Researcher at the Institute for Molecular Bioscience , University of Queensland. His work focuses on muscle development , caveolae regulation , and genetic modeling in zebrafish . Doctor of Philosophy, University of St Andrews Research interests include: Muscle Biology: Mechanisms of muscle homeostasis, transverse tubule development, and muscular dystrophy models. Caveolae Dynamics: Role in mechanoprotection, oxidative stress response, and lipid regulation. Genomic Tools: Cre-Lox systems, proximity labeling, and large genomic deletions in zebrafish. Recent work trends emphasize: Targeting the minor spliceosome for broad cancer therapy Mechanisms of pro-ferroptotic lipid signaling in membrane stability Advancements in zebrafish transgenics for disease modeling Structural characterization of Cavin1 complexes using nanobodies Current funding includes: NHMRC IDEAS Grant (2025-2028): Scalable methodology for evaluating genetic variants of uncertain significance Australian Functional Genomics Network Grant (2022-2026): CAV3 variant analysis Grants and projects: ARC Discovery Project (2020-2023): Molecular dissection of membrane domain formation NHMRC Project Grant (2016-2019): Transverse tubule development in skeletal muscle Dr. Hall supervises PhD students as an Associate Advisor in collaboration with Professor Robert Parton and Dr. Harriet Lo. His lab specializes in: Membrane Biology: Caveolae structure, Cavin protein interactions Genetic Modeling: Zebrafish systems for muscular disorders and drug delivery

• Gene Therapy
• Molecular Biology
• Genetics
• +7 more

Alisha M Gruntman, DVM, PhD, is an Assistant Professor at UMass Chan Medical School’s T.H. Chan School of Medicine. She holds multiple affiliations across the Gene Therapy Center, Genetic and Cellular Medicine, NeuroNexus Institute, Pediatrics, and graduate programs including the Interdisciplinary Graduate Program, Millennium MD/PhD Program, Neuroscience, and Translational Science. Education: DVM in Veterinary Medicine from Purdue University, PhD in Gene Therapy from University of Massachusetts Medical School Her research focuses on gene therapy, molecular biology, and translational science, with an emphasis on adeno-associated virus (AAV) vector engineering, immune response modulation, and protein replacement therapies for genetic disorders like alpha-1 antitrypsin deficiency and maple syrup urine disease. She specializes in cross-species models (mice, primates, alpacas) to address both human and veterinary medical needs. Recent publications highlight her work on AAV capsid modifications for liver detargeting, therapeutic gene editing in metabolic disorders, and immune tolerance induction for gene therapy. Her studies span molecular biology, genetics, and biochemical approaches to improve vector safety and efficacy in preclinical models.

• Protein Structure Prediction
• Protein Evolution
• Computational Biology
• +5 more

Ingemar André is a Professor at Lund University in the Department of Biochemistry and Structural Biology, affiliated with the eSSENCE: The e-Science Collaboration. His research integrates computational and experimental methods to study protein structure, evolution, and self-assembly. Key areas include AI-driven protein structure prediction, high-throughput protein stability analysis, and synthetic biology applications. Education: No specific academic degrees listed in the provided text. Research Interests: Dr. André’s work focuses on understanding protein interactions, evolution, and self-assembly pathways through computational modeling and experimental techniques. He develops AI-based tools for protein design and simulates evolutionary processes to predict structural changes. His experimental work includes high-throughput methods for characterizing protein biophysical properties in vivo. Recent Projects: Optimizing codon sequences for recombinant protein production (2023–2026, Novo Nordisk Foundation). Massively parallel protein stability measurements for evolutionary studies (2023–2027, Swedish Research Council). Awards: Sven and Ebba-Christina Hagberg Prize (2015). The Svedberg Prize (2015). Advising & Grants: Leads multiple research initiatives, including Synbio@Lund, a synthetic biology theme at the Pufendorf Institute for Advanced Studies. His grants focus on protein engineering and computational methods. Labs/Teams: Collaborates with interdisciplinary groups in synthetic biology and e-Science, emphasizing sustainable applications of bioengineering.