Sunday, 10 March

Evening Workshop: Grant Review Criteria and Procedures

Benjamin Garcia

Washington University School of Medicine in St. Louis

Biography

Benjamin Garcia

Coming Soon!

Successfully Navigating Career Transitions - Panel Discussion presented by Females in Mass Spectrometry (FeMS+)

FEMS+

Biography

FEMS+

Coming Soon!

Opening Plenary Session

Mary-Claire King

Professor of Genome Sciences and of Medicine

University of Washington

United States

Biography

Mary-Claire King

Dr. King grew up in Chicago. She received her BA cum laude in Mathematics from Carleton College in Minnesota, her PhD in Genetics from the University of California at Berkeley, and her postdoctoral training at UC San Francisco. She was professor at UC Berkeley from 1976-1995 and has been American Cancer Society Professor of Medical Genetics and of Genome Sciences at UW since 1995.

Monday, 11 March

Sponsor Breakfast: Comprehensive Proteomics using the SomaScan® 11K Assay: Identification of biomarkers for differential diagnosis of inflammatory bowel disease subtypes and prediction of therapeutic response to biologics

Towia Libermann

Associate Professor of Medicine

Beth Israel Deaconess Medical Center

United States

Biography

Towia Libermann

Dr. Libermann is an internationally recognized translational investigator with a strong track record in precision medicine, biomarker discovery and translational studies of immunological diseases and cancer. Dr. Libermann's lab is focused on applying multi-omics approaches to identify proteins or genes that may be exploited as biomarkers or targets for therapeutic intervention, starting with his seminal discovery of EGF receptor gene amplifications in glioblastomas. Dr. Libermann has been at the forefront of the next generation of proteomics and plays a central role in driving biomarker discovery to the next level. Libermann's group uses the aptamer-based SomaScan proteomics platform, a modified aptamer-based high multiplex immunoassay platform, to discover and validate diagnostic, predictive, and prognostic biomarkers for various diseases using liquid biopsies such as extracellular vesicles and body fluids. Using the latest in machine learning, Libermann's group has developed predictor models for applications in early detection, disease diagnosis, prediction of therapeutic response, monitoring of disease progression, and outcome prediction. Dr. Libermann received his PhD in Immunology in 1986 from the Weizmann Institute of Science and Technology, Rehovot and did a postdoctoral fellowship at the Whitehead Institute, Cambridge.

Donald F. Hunt Distinguished Contribution in Proteomics Award Plenary Session

Neil Kelleher

Walter and Mary Elizabeth Glass Professor of Chemistry, Molecular Biosciences, and Medicine

Northwestern University

United States

Biography

Neil Kelleher

Neil L. Kelleher, PhD is the Walter and Mary Glass Professor of Molecular Biosciences and professor of chemistry in the Weinberg College of Arts and Sciences. He also is director of the 50-person Proteomics Center of Excellence, Director of the Chemistry of Life Processes and a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University. His research is focused in the areas of top-down proteomics, natural products discovery, and cancer biology. With >450 papers, Dr. Kelleher is a cross-disciplinary investigator with international impact in proteomics (the study of proteins).  Together with colleagues in a research consortium (https://www.topdownproteomics.org/), this emerging approach to measure proteins with complete molecular specificity is being advanced to improve the detection and assignment of function to protein modifications and complexes. Now with an H-factor of 89, Kelleher has mentored over 52 Ph.D. students, >200 postdoctoral scholars, and >200 undergraduates. After a breakthrough Nature paper in 2011, Kelleher has continued to push the boundaries of proteomics and is currently advancing a compositional map of proteins in all cell types of the human body.  This "domestication" of the human proteome via precise compositional mapping will improve the efficiency of basic and clinical research and therefore enhance diverse goals for the 21st Century, including designer organs, personalized medicine, and early detection of human disease.

Parallel Session 01: Structural Proteomics in Disease Biology

Fan Liu

Leibniz-Forschungsinstitut für Molekulare Pharmakologie

Germany

Biography

Fan Liu

Fan graduated from Fudan University in Shanghai with a B.Sc. in Biology. Afterwards she joined the lab of Prof. Dr. Mike Goshe at North Carolina State University and obtained her PhD in Biochemistry in 2013. Fan did her postdoc in the lab of Prof. Dr. Albert Heck (Utrecht, The Netherlands). In 2017 Fan joined the Leibniz-Forschungsinstitut for Molecular Pharmacology (FMP) in Berlin as a group leader for Structural Interactomics and head of the proteomics research platform. In addition to her position at the FMP, Fan is jointly appointed as Professor for Structural Interactomics at Charité - Universitätsmedizin Berlin.

Lan Huang

University of California, Irvine

United States

Biography

Lan Huang

Dr. Lan Huang is a Professor of Physiology & Biophysics in the School of Medicine, University of California, Irvine and the Director of UCI High-end Mass Spectrometry Facility. Her research focuses on developing novel, integrated mass spectrometry-based proteomic strategies to characterize macromolecular protein complexes and understand their functions, particularly those in the ubiquitin-proteasome system. During the last two decades, the Huang lab has developed a number of novel methodologies to capture, purify and quantify protein-protein interactions in living cells. She has pioneered the development of sulfoxide-containing MS-cleavable cross-linkers (e.g. DSSO), and thus established a robust cross-linking mass spectrometry (XL-MS) platform that enables the elucidation of interaction networks and structural topologies of native proteomes in vitro and in vivo. The strategies developed by her group have proven highly effective as general proteomic tools for studying protein-protein interactions and protein complexes. She has successfully translated her research findings into practical applications, receiving several patents and commercializing reagents that have made a substantial impact in the scientific community. Her lab has recently applied XL-MS technologies to clinical samples to define protein modules and network topologies of proteomes and understand their associations with human disease.

Chad Hyer

Brigham Young University

Biography

Chad Hyer

Coming Soon!

Lars Plate

Vanderbilt University

Biography

Lars Plate

Coming Soon!

Parallel Session 02: Innovative Technologies and Methods for Quantitation

Edward Lau

University of Colorado-Anschutz

United States

Biography

Edward Lau

I am an Assistant Professor at the Department of Medicine at the University of Colorado School of Medicine. Prior to starting my lab in Colorado, I completed my PhD at the University of California Los Angeles followed by a postdoctoral fellowship at Stanford University. Research in my group aims to understand how the spatial and temporal dynamics of the proteome are regulated in development, aging, and disease. In prior work, we have developed the protocol and software to apply heavy water and stable isotope labeled amino acids to measure the half-life of thousands of proteins across multiple mouse tissues (Hammond [...] Beynon, Lau; MCP 2022); applied machine learning methods to unravel genewise differences in mRNA-protein correlation and its regulation (Srivastava et al. PLoS Comput Bill 2022); and developed a new method to simultaneously trace the subcellular localization and turnover rates of proteins in cell culture, which is being utilized toward identifying new elements of proteostatic stress response and drug induced cardiotoxicity (Currie et al. bioRxiv 2023). 

Rovshan Sadygov

The University of Texas Medical Branch

United States

Biography

Rovshan Sadygov

Rovshan G. Sadygov, Ph.D., Associate Professor, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX. He is a bioinformatician working on the development and applications of computational tools for the analyses of mass spectral data. His lab has developed d2ome - a tool to quantify label incorporation from LC-MS data of heavy water labeled samples.

Lilian Heil

Thermo Fisher Scientific

Biography

Lilian Heil

Coming Soon!

Michael Hinterberg

SomaLogic, Inc.

Biography

Michael Hinterberg

Coming Soon!

Parallel Session 03: Emerging Machine Learning and AI methods in Proteomics

Bobbie-Jo Webb-Robertson

Pacific Northwest National Laboratory

United States

Biography

Bobbie-Jo Webb-Robertson

Bobbie-Jo Webb-Robertson is the Director of the Biological Sciences Division with the Earth and Biological Sciences Directorate at Pacific Northwest National Laboratory. In addition, she holds joint appointments in the Department of Biomedical Engineering at Oregon Health & Science University, the Department of Pathology, Immunology and Laboratory Medicine at the University of Florida, and the Department of Biostatistics and Informatics at the University of Colorado Anschutz Medical Campus. Dr. Webb-Robertson's research focuses on the development of machine learning (ML) and statistical methods in two primary areas; improving downstream analytics from mass spectrometry derived proteomic, metabolomic and lipidomic data and machine learning driven feature extraction focused on biomarker discovery from complex heterogenous data. Her current research is largely focused on understanding the progression of type 1 diabetes. In that context she is currently leading the development of Artificial Intelligence (AI)/ML-ready data for studies of diabetes mellitus funded through the Human Islet Research Network from the National Institutes of Health, the Data Science lead for the national Pancreatic Organ Donors with diabetes (nPOD) program, and a co-I of the Diabetes Autoimmunity Study in the Young (DAISY). Dr. Webb-Robertson received a BA in mathematics from Eastern Oregon University and a ME in Statistics & Operations Research and PhD in Decision Sciences and Engineering Systems from Rensselaer Polytechnic Institute.

Jesse Meyer

Cedars-Sinai Medical Center

United States

Biography

Jesse Meyer

Jesse G. Meyer is an Assistant Professor at Cedars Sinai Medical Center in Los Angeles, California. He received his Bachelor of Science degree in Biochemistry in his home state at the University of Minnesota. He then moved to the University of California San Diego to get his PhD in the Chemistry Department. He was a postdoctoral fellow at the Buck Institute for Research on Aging and then the University of Wisconsin Madison. He was named among the Rising Stars in Proteomics and Metabolomics by the Journal of Proteome Research in 2021 and received the ASMS Research Award in 2023. His group does research on human disease by developing and applying techniques at the interface of omics and data science.

Vartika Tewari

Northeastern University

Biography

Vartika Tewari

Coming Soon!

Fengchao Yu

University of Michigan

Biography

Fengchao Yu

Coming Soon!

Parallel Session 04: The Omics of Aging and Age Related Diseases

Judit Villen

University of Washington

United States

Biography

Judit Villen

Judit Villen is a Professor in the Department of Genome Sciences at the University of Washington in Seattle. She earned her PhD in Chemistry from the University of Barcelona developing peptide vaccines. She was a postdoctoral fellow at Harvard Medical School developing phosphoproteomic methods and applications. She has a track record of creative, interdisciplinary, technology-driven, and collaborative biomedical research. Research in her laboratory focuses on the organization and function of the proteome. They develop mass spectrometry-based proteomics technologies and apply these technologies to study cellular signaling in cancer, metabolic diseases, and aging. Beyond signaling studies, her lab has invented a high throughput, non-genetic, mutagenesis technology to study the impact of amino acid substitutions on protein function on a proteome-wide scale using mass spectrometry, with the goal of accelerating variant interpretation. Prof. Villen has been a recipient of an NIH K99/R00 Pathway to Independence award, an Ellison Foundation New Scholar award, the ASMS Research award, and the US HUPO Robert Cotter award. She has been named a "Highly cited researcher" by Thomson Reuters/Clarivate.

Toshiko Tanaka

NIH

United States

Biography

Toshiko Tanaka

Dr. Tanaka is a Staff Scientist at the Translational Gerontology Branch, Longitudinal Study Section of the National Institute on Aging. Her research focuses on the identification of aging biomarkers using -omics data including genetics, proteomics and metabolomics. Using omics data, Dr. Tanaka has developed measures of biological age, including proteomic clocks. One of the aims of her research is to finetune these -omics based clocks to better predict health trajectories. A secondary aim is to understand what factors that influence the pace of aging measured by epigenetic and proteomic clocks.

Hanno Steen

Boston Children's Hospital and Harvard Medical School

Biography

Hanno Steen

Coming Soon!

Haley Tarbox

Johns Hopkins University

Biography

Haley Tarbox

Coming Soon!

Parallel Session 05: Serendipity in Proteomics (ECR Session)

Lisa Jones

UCSD

United States

Biography

Lisa Jones

Lisa M. Jones is the Chancellor's Associate Endowed Chair of Chemistry and Biochemistry at the University of California San Diego. She received her PhD in Chemistry from Georgia State University. She received postdoctoral training in structural virology at the University of Alabama-Birmingham and in MS-based protein footprinting at Washington University in St. Louis. Her research is focused on extending the protein footprinting method fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry into complex model systems. Her lab has extended the method for in-cell analysis to provide structural information across the proteome. She has further developed the method for in vivo analysis in C. elegans, an animal model for human disease. Her lab aims to understand the biological causes of health disparities in cancer and other diseases. She also has a passion for increasing diversity in STEM and participates in several outreach initiatives to achieve this.

John Price

BYU

United States

Biography

John Price

John Price grew up farming and ranching in rural Idaho. He was always inspired by how the world restarted every spring by producing new life. He studied Chemistry and Biochemistry at Utah State University in order to understand the mechanisms that produced these amazing results. Starting as an undergraduate he worked with Dr. Lisa Berreau to create synthetic models of enzyme active sites using novel small molecule chelators of metal atoms. His graduate work at Pennsylvania State University used entire enzymes. Here he studied the steps of oxygen activation on iron atoms in dioxygenase enzymes with Drs. J. Martin Bollinger and Carsten Krebs. His success there led to an ambitious project applying kinetic approaches to the study of prion protein aggregates in the brain with Stanley Prusiner at the University of California San Francisco. At UCSF, he published the first proteome scale measurement of in vivo protein turnover. This showed that regulation of protein turnover occurred at the level of the tissue, multiprotein complex, and individual sequence. He was recruited away from UCSF to develop some intellectual property and start a research and development division at a small biotech company. After finishing the commercial development, he decided to continue research into the regulation of protein homeostasis as a faculty member in the Chemistry and Biochemistry Department at Brigham Young University.

Reema Banarjee

National Institute on Aging, NIH

Biography

Reema Banarjee

Coming Soon!

Jolene Duda

University of Minnesota

United States

Biography

Jolene Duda

Coming Soon!

Parallel Session 06: Advances in Single-Cell MS

Jason Derks

Biography

Jason Derks

Jason Derks received his undergraduate education from UC Santa Barbara and his PhD from Northeastern University. His doctoral work, completed in the laboratory of Prof. Nikolai Slavov, focused on increasing the throughput of bulk and single cell proteomics. As a postdoc in the Slavov laboratory, Jason is interested in applying these developments to associate functional and proteomic variability at high throughput to gain mechanistic insights which can be experimentally tested. Specifically, his postdoctoral work has applied single nucleus proteomics to identify proteins which regulate nucleocytoplasmic transport in LPS-stimulated macrophages.

Sarah Parker

Cedars-Sinai Medical Center

United States

Biography

Sarah Parker

Sarah Parker is an Associate Professor in the Department of Cardiology at Cedars-Sinai Medical Center, where she is also the co-director of the proteomics and metabolomics core facility in the Board of Governors Innovation Center. Her research utilizes proteomic techniques, including emerging single-cell and spatial proteomics, to elucidate mechanisms and biomarkers of aortic aneurysm, atherosclerosis, cardiovascular and other diseases.

Ryan Kelly

Brigham Young University

Biography

Ryan Kelly

Coming Soon!

Stanislau Stanisheuski

Oregon State University

United States

Biography

Stanislau Stanisheuski

Coming Soon!

Evening Workshop: CPTAC

Bing Zhang

Biography

Bing Zhang

Dr. Bing Zhang is a Cancer Prevention and Research Institute of Texas (CPRIT) Scholar, McNair Medical Institute Scholar, and Professor of Molecular and Human Genetics in Baylor College of Medicine. He is an internationally recognized leader in computational cancer proteogenomics, with a focus on developing informatics solutions that help translate cancer genomic and proteomic data into biological and clinical insights.

David Fenyo

NYU School of Medicine

Biography

David Fenyo

Dr. David Fenyö received a PhD in Physics from Uppsala University in Sweden and after switching to computational biology, he did a postdoc at the Rockefeller University, co-founded a bioinformatics company and worked at GE Healthcare. He has over 35 years of experience with all aspects of biomedical data analysis in both academia and industry and his work has resulted in over 250 scientific publications. In 2010 he joined NYU School of Medicine where he is currently Professor of Biochemistry and Molecular Pharmacology, Director for the Ph.D. program in Systems and Computational Biomedicine and the Master's program in Biomedical Informatics. His research focuses on applying data science methods to analyze quantitative data, model biological systems, and predict patient outcome and select treatments. His efforts to integrate data from multiple technologies-including mass spectrometry, sequencing, microscopy, and electronic health records-have provided a wide array of powerful tools to discover and verify biomarkers and therapeutic targets in cancer.

D. R. Mani

Broad Institute / MIT and Harvard

Biography

D. R. Mani

D. R. Mani is Director of Computational Proteomics in the Proteomics Platform at the Broad Institute of MIT and Harvard. For over two decades, he has been applying computational pattern recognition, machine learning, signal processing, and statistical data analysis to the analysis of omics data generated from a wide range of bio-assays, including mass spectrometry-based proteomics and gene expression profiling. His research has focused on the design and implementation of innovative algorithms to enable proteogenomic analysis, immunopeptidomics, pattern-based discovery of proteomic biomarker candidates, evaluation of data quality, assessment of variability and reproducibility in mass spectrometry-based assays, and data visualization. Mani is a principal investigator for the National Cancer Institute Clinical Proteomics Tumor Analysis Consortium (NCI-CPTAC) Proteogenomic Data Analysis Center (PGDAC) at the Broad, he has been leading multi-omic data analysis for almost all projects in the Broad Proteomics Platform. He has a Ph.D. in computer science from the University of Pennsylvania and a M.S. in biostatistics from the Harvard School of Public Health.

Xu Zhang

NCI Office of Cancer Clinical Proteomics Research (OCCPR) within the Division of Cancer Treatment & Diagnosis (DCTD)

Biography

Xu Zhang

Dr. Xu Zhang is a Program Manager in the Office of Cancer Clinical Proteomics Research (OCCPR) at the National Cancer Institute (NCI), National Institutes of Health (NIH). She provides scientific expertise in Proteomics Data Science/Data Management, manages and oversees the grants and contracts that support proteomics data analysis, informatics and software tools, and data management activities for NCI's Clinical Proteomic Tumor Analysis Consortium (CPTAC), International Cancer Proteogenome Consortium (ICPC), and the Applied Proteogenomics Organizational Learning and Outcomes (APOLLO) network. Dr. Zhang has extensive experience in the proteogenomic field, especially in proteomics data management.

Tuesday, 12 March

Sponsor Breakfast: Robust Preparation is the Key - Why Should YOUR Protein Samples be Any Different?

Debadeep BHATTACHARYYA

Covaris Inc

Biography

Debadeep BHATTACHARYYA

Deb Bhattacharyya received his Masters of Science in Chemistry from Indian Institute of Technology (Mumbai, India) and his PhD in Chemistry and Biochemistry from Emory University (Atlanta, GA, USA). From his doctoral studies to his stint as a Research Associate at the University of North Carolina - Chapel Hill, Deb's research work in Oncology focused on high-definition structural elucidation of Protein-DNA and Protein-Protein complexes in cancer research. In his professional career spanning more than 17 years in biotechnology, Deb has worked for several Mass Spectrometry manufacturing organizations focused on designing, developing, and optimizing workflows on proteomics, biomarker, and biotherapeutic characterization and quantitation. Deb has also been instrumental in launching several MS instruments and LC-MS based workflows that has helped many organizations achieve success in their protein analysis workflows. At Covaris, Deb is the Vice President of Business Development and Emerging Markets and capitalizes his expertise and experience in expanding Adaptive Focused Acoustic® (AFA®) Technology's capabilities in multi-omics comprising Genomics, Epigenomics, Proteomics, and Metabolomics. Deb has authored/co-authored more than 50 articles on varied topics and applications ranging from cancer research to forensic toxicology, clinical research to biopharma.

Robert J. Cotter New Investigator Award Plenary Session

Ying Zhu

Genentech

Biography

Ying Zhu

Dr. Ying Zhu is a Senior Principal Scientist and Group Lead in the Department of Microchemistry, Proteomics, and Lipidomics at Genentech Inc. Dr. Zhu obtained his Ph.D. degree in Analytical Chemistry in 2010 from Zhejiang University with the guidance of Prof. Qun Fang. Afterward, he underwent two rounds of postdoctoral training at the Engineering School of Zhejiang University under the advisory of Prof. Ying Mu in 2013, and at Pacific Northwest National Laboratory (PNNL) under the guidance of Dr. Ryan Kelly in 2018. He then became a Staff Scientist and Principal Investigator in PNNL in the summer of 2018, where he focused on improving the sensitivity and throughput of mass spectrometry-based bioanalysis by interfacing advanced microfluidics, robotics, chemistry, optics, and related engineering technologies. Dr. Zhu is the key developer of the nanoPOTS platform, which has become one of the driving technologies for single-cell proteomics. His group also introduced and developed a couple of sample isolation technologies for single-cell and spatial proteomics, including imaging-based single-cell sorting and laser-ablation-based tissue microsampling. Since joining Genentech in 2022, he has been leading a team focusing on the development and implementation of single-cell and spatial proteomics technologies for early-stage drug discovery and biomarker identification. Throughout his career, Dr. Zhu has received numerous awards, such as the 2023 Rising Star in Measurement Science, Top 40 Most Influential People in Analytical Science under 40 years of age, Pathway to Excellence award for technology commercialization, and M. T. Thomas Award for Outstanding Postdoctoral Achievement.

Parallel Session 07: Post-Translational Modifications to Proteoforms

Luca Fornelli

University of Oklahoma

United States

Biography

Luca Fornelli

Dr. Luca Fornelli earned both his B.Sc. and M.Sc. in Biotechnology from the University of Padova, Italy. He received his PhD under the supervision of Dr. Yury Tsybin at the École Polytechnique Fédérale de Lausanne, Switzerland, with a thesis focused on the characterization of antibodies by middle-down and top-down mass spectrometry. He later obtained a postdoctoral fellowship from the Swiss National Science Foundation and joined the research group of Dr. Neil Kelleher at Northwestern University. Since 2019 Dr. Fornelli works as an Assistant Professor at the University of Oklahoma, where he develops new methods for top-down proteomics. He has been nominated "Emerging Investigator" by the Journal of the American Society for Mass Spectrometry in 2021, and received the ASMS Research Award in the same year. He is also the recipient of the 2022 BBA Rising Star Award.

Ryan Julian

UC Riverside

United States

Biography

Ryan Julian

Ryan Julian is a professor of Chemistry at the University of California, Riverside, where he leads a mass spectrometry research group. Dr. Julian obtained his PhD in 2003 at Caltech under the guidance of Jack Beauchamp, focusing on a variety of molecular recognition and ion chemistry projects. He pursued postdoctoral training for two years focused on instrumentation and ion mobility with David Clemmer and Martin Jarrold at Indiana University. Since 2005 in his own lab at UCR, research interests have spanned a broad range of subjects including gas-phase ion chemistry, radical-directed dissociation, antioxidant capacity, and the development of a variety of MS-based structural tools. Most recently, a particular interest in the study of isomerization in long-lived proteins and how these modifications relate to age-related diseases has become a major focus.

Justyna Fert-Bober

PhD, Assistant Professor

Department of Cardiology, Smidt Heart Institute, Cedars Sinai

Biography

Justyna Fert-Bober

Coming Soon!

Trishika Chowdhury

University of Alabama

Biography

Trishika Chowdhury

Coming Soon!

Parallel Session 08: Cascadia Proteomics: Research from the Pacific Northwest

Alexis Chang

University of Washington Department of Genome Sciences

Biography

Alexis Chang

Coming Soon!

Jacob Porter

Oregon Health and Science University - Knight Cancer Research Building

Biography

Jacob Porter

Coming Soon!

Mereena George Ushakumary

Pacific Northwest National Laboratory

Biography

Mereena George Ushakumary

Coming Soon!

Nicholas Day

Pacific Northwest National Laboratory

Biography

Nicholas Day

Coming Soon!

Gennifer Merrihew

University of Washington

Biography

Gennifer Merrihew

Coming Soon!

Sponsor Lunch: Automating proteomics for scale

Danielle Swaney

Biography

Danielle Swaney

Danielle Swaney develops mass spectrometry strategies to dissect the complex signaling interplay of PTMs and protein-protein interactions in cellular processes and their relation to complex diseases. Her lab has a particular interest in proteome perturbations associated with neurodegenerative and infectious diseases to identify new signaling pathways and therapeutic targets, together advancing personalized medicine.

Lindsay Pino

Co-Founder and CTO

Talus

United States

Biography

Lindsay Pino

Lindsay is the co-founder and chief technology officer at Talus Bio. With over a decade's experience in analytical chemistry and computational biology, she develops technologies for quantitative proteomics. In particular, at Talus, she's working on the challenges associated with scaling up quantitative proteomics experiments. She is directly involved in a large variety of research projects spanning cancer drug discovery, chemoproteomics, epigenetics, and spatiotemporal proteomics.

Sponsor Lunch: A high-throughput journey through modified proteins and proteomes

Benjamin Garcia

Washington University School of Medicine in St. Louis

Biography

Benjamin Garcia

Coming Soon!

Parallel Session 09: Biomarkers and Precision Medicine

Mark Flory

Oregon Health and Science University

United States

Biography

Mark Flory

Mark Flory is a Senior Research Scientist at Oregon Health and Science University (OHSU) in Portland and is specifically positioned in the Cancer Early Detection Advanced Research Center (CEDAR) of OHSU's Knight Cancer Institute. Mark received his Ph.D. in Molecular and Cellular Biology at the University of Washington working in Trisha Davis' group, and subsequently trained on proteomic mass spectrometry in Ruedi Aebersold's group at the Seattle Institute for Systems Biology. Mark has since enjoyed professional positions spanning the academic and biotech sectors including work with Parag Mallick in the Canary Center at Stanford for Early Cancer Detection. At OHSU Mark now focuses on implementing powerful proteomic technologies, including Seer Proteograph and Bruker timsTOF mass spectrometry, to facilitate biomarker discovery aimed at uncovering clinically actionable signatures for early cancer detection and to gain new insights into mechanisms underlying disease progression.

Amit Dey

National Institute on Aging-NIH

Biography

Amit Dey

Coming Soon!

Elizabeth Dhummakupt

US Army DEVCOM Chemical Biological Center

Biography

Elizabeth Dhummakupt

Coming Soon!

Jeff Whittaker

Fred Hutchinson Cancer Research Center

Biography

Jeff Whittaker

Coming Soon!

Parallel Session 10: Chemical Proteomics and Drug Discovery

Keriann Backus

UCLA

United States

Biography

Keriann Backus

Keriann Backus is an Assistant Professor of Biological Chemistry and Chemistry and Biochemistry at the University of California, Los Angeles. Her research interests include the developing of new chemical probes, chemoproteomic and proteogenomic methods to study and rewire protein function in health and disease. Dr. Backus received a BS in Chemistry and BA in Latin American Studies in 2007 from Brown University. Her doctoral research was conducted in the laboratories of Benjamin Davis (Oxford) and Clifton Barry (NIH, NIAID) as a 2007 Rhodes Scholar and an NIH Oxford Cambridge Scholar. Her PhD work focused on the development of chemical probes to label and image Mycobacterium tuberculosis. In 2012, Backus completed her doctorate and began an NIH postdoctoral fellowship at The Scripps Research Institute in the laboratory of Benjamin Cravatt. Her postdoctoral research developed chemoproteomic methods for the proteome-wide identification of ligandable cysteine and lysine residues. At UCLA, Dr. Backus's research has been recognized by numerous awards, including a Beckman Young Investigator, DARPA Young Faculty Award, a V Scholar Research Award, Packard Fellowship, NIH New Innovator Award, and Ono Breakthrough Science Initiative Award.

Christopher Parker

Associate Professor

The Scripps Research Institute

United States

Biography

Christopher Parker

Chris is an Associate Professor in the Department of Chemistry at Scripps Research. His lab's research focuses on employing chemoproteomic platforms to develop useful small molecules to modulate complex biological processes and illuminate mechanisms of disease, such as cancer and immune conditions. Chris obtained his B.S. in Chemistry at Case Western University in 2007 and his Ph.D. in Chemistry at Yale University in 2013 under the guidance of Professor David Spiegel. He performed postdoctoral work as an American Cancer Society fellow at Scripps Research with Professor Ben Cravatt, and in 2018 he joined the faculty.

Dingyin Tao

National Center for Advancing Translational Sciences, National Institutes of Health

Biography

Dingyin Tao

Coming Soon!

Nathan Basisty

National Institute on Aging, NIH

Biography

Nathan Basisty

Coming Soon!

Parallel Session 11: Multiplexed and Spatial Imaging Omics

Summer Gibbs

Oregon Health and Science University

United States

Biography

Summer Gibbs

Dr. Summer Gibbs has 20 years of experience in the field of molecular imaging with expertise in fluorescent contrast agent development and its clinical translation as well as single cell fluorescence imaging technologies. She completed her Ph.D. in Biomedical Engineering under the direction of Brian Pogue, Ph.D. at the Thayer School of Engineering at Dartmouth College in 2008. She joined Dr. John Frangioni's Laboratory for her postdoctoral training where she completed three years of postdoctoral training and was promoted to Instructor in Medicine. She joined the faculty in the Biomedical Engineering Department at Oregon Health and Science University (OHSU) as an Assistant Professor in June 2012 and was promoted to Professor in July 2022. The current focus of her laboratory is on the development of novel fluorescent probes and fluorescence imaging technologies to improved macroscopic and microscopic patient-specific imaging.

Kristin Burnum-Johnson

Science Group Leader for Functional and Systems Biology

Pacific Northwest National Laboratory

United States

Biography

Kristin Burnum-Johnson

Dr. Kristin Burnum-Johnson is the Group Leader of Functional and Systems Biology at the Environmental Molecular Sciences Laboratory located at Pacific Northwest National Laboratory (PNNL). Kristin earned her Ph.D. in Biochemistry from Vanderbilt University with Prof. Richard M. Caprioli, and then completed a postdoctoral fellowship at PNNL with Dr. Richard D. Smith. She was selected to receive a 2019 Early Career Research Program award from the U.S. Department of Energy Office of Science. Her research program is dedicated to characterizing the molecular landscape of heterogeneous samples using novel mass spectrometry approaches to address specific biological, medical, and environmental research questions.

Julia Ekiert

UIC

Biography

Julia Ekiert

Coming Soon!

Andrew Emili

Oregon Health and Science University

Biography

Andrew Emili

Coming Soon!

Parallel Session 12: Functional Characterization of the Proteome

Tianhao Yu

The University of Illinois at Urbana-Champaign

United States

Biography

Tianhao Yu

Tianhao Yu is currently a Ph.D. candidate in the Chemical and Biomolecular Engineering department at University of Illinois at Urbana Champaign under the supervision of Dr. Huimin Zhao. Tianhao received his B.S. in Chemical engineering from University of Rochester in 2019. His research focuses on applying machine Learning to address various topics in the field of synthetic biology. During his Ph.D. training, he has published several peer-reviewed research articles and reviews in top-tier journals such as Science and Nature Catalysis. He is the recipient of Mavis future faculty fellowship and Glenn E. and Barbara R. Ullyot Graduate Fellowship.

Nick Riley

University of Washington

United States

Biography

Nick Riley

Nicholas M. Riley is an Assistant Professor of Chemistry at the University of Washington. He completed his ACS Certified B.S. degree in Chemistry from the University of South Carolina in 2012 with Honors from the South Carolina Honors College, and he earned his Ph.D. in chemistry in 2018 while working on electron-transfer dissociation-centric methodology in the research group of Prof. Joshua J. Coon at the University of Wisconsin-Madison. He then was an NIH K00 and K99 postdoctoral fellow with 2022 Nobel Laureate in Chemistry Prof. Carolyn R. Bertozzi at Stanford University, where he focused on MS-based glycoproteomics and chemical glycobiology. His research program at UW is focused on innovative bioanalytical and chemical biology technologies to investigate essential principles of glycocode regulation and dysregulation.

Clara (Mengzhou) Hu

University of California, San Diego

Biography

Clara (Mengzhou) Hu

Coming Soon!

Ashley Frankenfield

George Washington University

United States

Biography

Ashley Frankenfield

Coming Soon!

Evening Workshop: Human Microbiome and Clinical Metaproteomics

Pratik Jagtap

University of Minnesota

Biography

Pratik Jagtap

His current research interests include developing analytical workflows for the analysis of complex data, with particular emphasis on MS-based proteomics applications in metaproteomics, proteogenomics, and data-independent acquisition (DIA) data analysis.

Timothy Griffin

University of Minnesota

Biography

Timothy Griffin

Research interests in developing and applying MS-based proteomics and metaproteomics to questions in human biology; co-leader in Galaxy for proteomics (Galaxy-P) project for developing bioinformatics tools for multi-omic data analysis including metaproteomics.

Wednesday, 13 March

Sponsor Breakfast: Joining Forces: Next-Generation Protein Sequencing and Mass Spectrometry to Power PTM Analysis

Justyna Fert-Bober

PhD, Assistant Professor

Department of Cardiology, Smidt Heart Institute, Cedars Sinai

Biography

Justyna Fert-Bober

Fert-Bober, is an Assistant Professor at Cedars-Sinai Heart Institute, with a broad background of biochemistry, molecular biology, immunology, and proteomics. She received her master from Faculty of Biotechnology, the University of Wroclaw , and her PhD from Wroclaw Medical University in Poland. Fert-Bober received grants from NIH and national foundation. Her research involves interinstitutional collaborations focused on identifying novel and/or largely understudied protein posttranslational modifications (PTMs) called citrullination. Citrulline posttranslational modification of proteins is mediated by protein arginine deiminase (PADI) family members. It plays both a physiological role, for instance, during apoptosis and epigenetics, and a pathological role in the development of inflammatory diseases and cancer. Fert-Bober expertise and strengths in biochemistry and proteomics have allowed her to develop a mass spectrometry (MS) method to identify citrullination at the peptide level, improving the spectrum of citrullinated proteins and allowing for the etiological importance of these citrullinated proteins as a source of neoantigens. In addition to expertise in LC‒MS/MS method development as well as high-throughput sample analysis in plasma and tissue matrices, her research pioneer on the role of PAD and citrullinated proteins in heart disease.

Kenneth Skinner

PhD, Staff Scientist

Scientific Partnering, Quantum-Si

Biography

Kenneth Skinner

Kenneth Skinner is a staff scientist spearheading scientific partnerships at Quantum-Si, which has commercialized a protein sequencer with single-molecule resolution. Skinner graduated from Morehouse College and earned his doctorate in chemical biology at Harvard University. His thesis work revealed druggable sites in therapeutic proteins with chemical probes and mass spectrometry. His research as lead author has resulted in peer-reviewed publications in biophysics and medicinal chemistry. He is also a co-inventor on patent applications describing methods for polypeptide analysis. Skinner's industrial experience includes pharmaceuticals and startups developing benchtop platforms for diagnostics and drug discovery. Beyond the bench, Skinner is interested in science policy and mentoring the next generation of biotech talent.

Sponsor Breakfast: Enhancing biological discovery through integrated multi-omics with Seer and Next-Generation Metabolomics

Ethan Stancliffe

Panome Bio

Biography

Ethan Stancliffe

Ethan Stancliffe, PhD, is the Director of Metabolomics at Panome Bio. Dr. Stancliffe completed his PhD work in Computational and Systems Biology at Washington University in St. Louis with research focused on computational methods for the analysis and processing of untargeted metabolomics data. Dr. Stancliffe also holds a BS in Biomedical Engineering and Applied Mathematics from the University of Iowa.

Gilbert S. Omenn Computational Proteomics Award Lecture

Parag Mallick

Nautilus Biotechnology, Stanford University

Biography

Parag Mallick

Dr. Parag Mallick is an Associate Professor at Stanford University. Originally trained as an engineer and biochemist, his research spans proteomics, computational and experimental systems biology, cancer biology and nanotechnology. Dr. Mallick received his B.S. in Computer Science from Washington University in St. Louis. He then obtained his Ph.D. from UCLA in Chemistry & Biochemistry, where he worked with Dr. David Eisenberg. He completed his post-doctoral studies at The Institute for Systems Biology with Dr. Ruedi Aebersold. In addition to developing computational proteomics methods the Mallick lab has been pioneering systems-biology approaches towards understanding disease mechanisms, discovering biomarkers and enabling personalized medicine. In addition, his group has been developing model-based and physics-based approaches to machine learning. Beyond Stanford, Parag is co-founder of Nautilus Biotechnology, a company developing a next generation, single-molecule, protein analysis platform.

Parallel Session 13: Translational Approaches: Nontraditional Models, Infectious and Rare Diseases

Ileana Cristea

Princeton University

United States

Biography

Ileana Cristea

Ileana Cristea is the Henry L. Hillman Professor in Molecular Biology at Princeton University. Her laboratory investigates host-pathogen interactions and mechanisms of cellular defense during infection with human viruses. Towards this goal, she has been at the forefront of promoting the integration of the fields of virology and proteomics. She has developed methods for studying spatial and temporal virus-host protein interactions, bridging developments in mass spectrometry to important findings in virology. For example, her laboratory has contributed to the emergence of the research field of nuclear viral DNA sensing in immune response, to uncovering mechanisms driving organelle remodeling and a mitochondria-ER encapsulation structure during infection, and to the discovery of sirtuins as antiviral factors for therapeutic intervention. Dr. Cristea is the Past-President of the American Human Proteome Organization (US HUPO), the past-chair of the Biology/Disease-driven Human Proteome Project (B/D-HPP) of HUPO, and the Chair of the Infectious Disease team of HUPO B/D-HPP. She has taught the summer Proteomics Course at Cold Spring Harbor Laboratory for over ten years, and is Senior Editor for mSystems and Associate Editor for the Journal of Proteome Research. She was recognized with the Bordoli Prize from the British Mass Spectrometry Society (2001), NIDA Avant-Garde Award for HIV/AIDS Research (2008), Human Frontiers Science Program Young Investigator Award (2009), Early Career Award in Mass Spectrometry from ACS (2011), ASMS Research Award (2012), Molecular Cellular Proteomics Lectureship (2013), Mallinckrodt Scholar Award (2015), Discovery Award in Proteomic Sciences at HUPO (2017), and the Princeton University Graduate Mentoring Award (2020).

Edward Marcotte

University of Texas

United States

Biography

Edward Marcotte

Edward Marcotte obtained his bachelor's degree and Ph.D. from the University of Texas at Austin and performed a postdoc at UCLA. He is an evolutionary biochemist whose research broadly uses tools of proteomics, bioinformatics, and systems and synthetic biology, with current work focused on the interactions, dynamics, and evolution of proteins across the tree of life. Marcotte has authored 240 journal publications and 23 issued/in process patents, received a National Institutes of Health Director's Pioneer Award, was elected a Fellow of the Royal Society of Chemistry, the American Academy of Microbiology, and the American Association for the Advancement of Science, and co-founded the single molecule protein sequencing company Erisyon, Inc. He is a Professor in the Department of Molecular Biosciences at the University of Texas, where he holds the Mr. and Mrs. Corbin J. Robertson, Sr. Regents Chair in Molecular Biology.

Michael Gilbert

University of Pennsylvania

Biography

Michael Gilbert

Coming Soon!

Joseph Dybas

Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia

Biography

Joseph Dybas

Coming Soon!

Parallel Session 14: Transcription Factors

Lindsay Pino

Co-Founder and CTO

Talus

United States

Biography

Lindsay Pino

Lindsay is the co-founder and chief technology officer at Talus Bio. With over a decade's experience in analytical chemistry and computational biology, she develops technologies for quantitative proteomics. In particular, at Talus, she's working on the challenges associated with scaling-up quantitative proteomics experiments. She is directly involved in a large variety of research projects spanning cancer drug discovery, chemoproteomics, epigenetics, and spatiotemporal proteomics.

Thomas Vondriska

UCLA

United States

Biography

Thomas Vondriska

Thomas Vondriska, PhD is a Professor in the Departments of Anesthesiology, Physiology and Medicine (Cardiology) in the David Geffen School of Medicine at UCLA. He is also Vice Chair for Research in the Department of Anesthesiology and Director of the Division of Molecular Medicine. Prior to UCLA, he trained at the University of Louisville in myocardial ischemia, molecular signaling, and proteomics. Dr. Vondriska is an editorial board member at Circulation, American Journal of Physiology and Journal of Molecular & Cellular Cardiology and his lab has been consistently funded by the NIH since its inception. He also co-directs the UCLA Physiology Outreach Program (www.uclapop.org). The Vondriska lab investigates epigenomic processes in the cardiovascular system. Ongoing research examines the molecular basis for remodeling of chromatin architecture in animal models and humans towards the goals of: (1) building basic structure-function models of chromatin in multicellular organisms; (2) understanding epigenomic processes that drive cardiovascular disease; and (3) developing novel therapeutic agents for heart failure that work by remodeling chromatin. The Vondriska lab has trained >50 students, fellows and clinician-scientists (www.vondriskalab.org; Twitter: @VondriskaLab).

Xingyu Liu

Washington University School of Medicine in St. Louis

Biography

Xingyu Liu

Coming Soon!

Yuling Dai

UW-Madison

Biography

Yuling Dai

Coming Soon!

Catherine E. Costello Award for Exemplary Achievements in Proteomics Plenary Session, US HUPO Business Meeting and Closing Remarks

Jennifer Van Eyk

Cedars-Sinai Medical Center

Biography

Jennifer Van Eyk

Dr. Van Eyk is a Professor of Medicine at Cedars-Sinai Medical Center, Director of the Basic Science Research in the Barbra Streisand Woman's Hearth Center and Director of the new Advance Clinical Biosystems Institute where she recently moved from Johns Hopkins University. Most recently she has become the co-director of the Cedars Sinai Precision Health, focused on in-hospital and population individualization of health care. Dr. Van Eyk is an international leader in the area of clinical proteomics and her lab has focused the developing technical pipelines for de novo discovery and larger scale quantitative mass spectrometry methods. This includes multiple reaction monitoring (MRM, also known as SRM) and most recently data independent acquisition. Her laboratory is well known for the extreme technical quality of the data generated, rigorous quality control with tight %CV while applying these to key clinical questions. The aim is to maximize throughput and reproducibility in order to move targeted and robust discovery methods into large population healthy continuous assessment and clinical grade assays focusing on brain and cardiovascular diseases.