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2024 Central region candidatesCandidates are listed alphabetically by surname. |
Ben CollinsReader (Associate Professor) in Biochemistry/Proteomics, Queen's University Belfast, United Kingdom
1) Improve the education of life scientists with respect to how proteomic technologies can be brought to bear on their research and add substantial value to frontier questions. I am an active member of the HUPO Education and training committee (ETC) organizer webinars and precongress sessions. I have significant experience teaching on, and organizing, courses focused on targeted proteomics and DIA/SWATH at ETH Zurich and worldwide. The video lectures from our courses have attracted 145,000+ views and 1700+ subscribers on YouTube (https://goo.gl/wN6Gzj). 2) Increase the visibility and utility of proteomics in the field of drug discovery. My research group (collinslab.net) has recently turned towards the interface of proteomics and drug discovery. At the 2024 HUPO World Congress I will chair a precongress session on 'Chemoproteomics and Drug Discovery' where we intend to propose a HUPO initiative on this key topic. We aim to increase interactions with pharma/biotech companies and to educate the next generation of scientists by organizing a summer school series on this topic beginning in 2025. Vadim DemichevMSTARS Group Leader, Charite University Medicine Berlin, Germany
In recent years, proteomics has seen remarkable successes and is playing an increasingly important role in biomedical science. We also have exciting prospects, from proteomics becoming an indispensable tool in many areas of fundamental research, to enhancing the future personalised medicine approaches. Here, I believe, it is essential to make proteomics as open and accessible as possible for scientists working in diverse fields. I am keen to actively contribute to the work of HUPO towards this, and ask you to consider my application to join the HUPO Council 2025-2027. I would particularly like to join the Education and Training Committee and/or the Marketing and Outreach Committee. In the past, I have co-organised the "Proteomics: from fundamentals to application" training course by the British Biochemical Society (online, 2021) and the "St Nicholas Mass Spectrometry Symposium" (Berlin, 2022), as well as gave guest workshops/lectures at the "Workshop on Single Cell Proteomics" by the Institute of Biotechnology CAS (Prague, 2022) and twice at the "EMBO Practical Course in Targeted Proteomics" (Barcelona, 2022 and 2023). Although so far my experience as an event organiser is limited, I am enthusiastic to continue such work as a member of HUPO Committees, and I believe the scope of my research can be of great help here, in particular when it comes to mass spectrometry-based proteomics data analysis. I ultimately wish to help create resources, organise events and establish training and scientific exchange platforms that will make working with proteomics data an effortless routine task for any biology laboratory. This is also a key part in proteomics outreach, and I am particularly keen to work on engaging scientists from different fields and introducing them to the powerful capabilities of proteomics. Klaus LindpaintnerVP Glycobiology Solutions, Bruker, Germany  My career has taken me from clinical medicine, treating patients at the bedside, to the pharmaceutical industry and more recently, to enabling technologies, with a common denominator being biomarker-informed, targeted personalized approaches to health care. My interest has always been the translational interface between basic science and clinical applications and actionability. I began this journey as a geneticist, witnessed the rise (and, to some extent, the fall) of this discipline, becoming, every step along the way of the biological cascade ever more cognizant of the of the overarching importance of the far more complex and dynamic -- but inherently information-richer -- domains of proteomics and, of late, posttranslational protein modifications. I would see my role on the Council as a promoter of the study this next frontier, proteoforms and their differentiated functions in the context of multiomics ecosystems. I believe that with my background in clinical medicine, academic and industry-based basic research, drug and diagnostic development, and enabling technologies I could bring an potentially valuable spectrum of insights, particularly also with respect to translational science, to the organization. While I realize that that I have not been a longstanding member of the organization, I believe I might be able to bring some new viewpoints into the deliberations and discussions. It would be a great privilege to serve.
Boris MacekProfessor, University of Tuebingen, Germany  My whole career is devoted to proteome research for and I see HUPO as the leading organization for advancement and promotion of research in our field. It would be an honor to serve on the HUPO Council and contribute to its activities. Here I will briefly summarize my experience in the field. In 1999 I graduated from the University of Zagreb, Croatia (Major in Molecular Biology), and joined the group of Prof. Dr. Jasna Peter-Katalinic at the Institute for Medical Physics and Biophysics at the University of Muenster, Germany (Institute director Franz Hillenkamp). With Prof. Katalinic I worked on development and application of MS methods to study unstable posttranslational modifications, especially O-glysosylation. In 2003 I obtained PhD in Biology at the University of Muenster. From mid-2003 to mid-2004 I performed a year of compulsory Civil Service in Croatia and in 2004 joined the group of Matthias Mann at the University of Southern Denmark, Odense. In 2005 I moved with the Mann lab from Odense to the Max Planck Institute for Biochemistry in Martinsried, Germany, where I pursued research on Ser/Thr/Tyr phosphoproteomes of model bacteria and helped in organization of HUPO Conference in Munich. I stayed in Matthias Mann's laboratory until the end of 2008, when I was appointed Junior Professor (W1, tenure-track) at the University of Tuebingen, Germany, and Director of the Proteome Center Tuebingen (PCT). I obtained tenure and was promoted to a full professor in 2014. My scientific interests include proteogenomics, quantitative phosphoproteomics and metaproteomics. In my career I co-authored 192 peer-reviewed publications (51 as senior author), attracted 5,975 Million Euro of external funding, supervised 15 PhD theses (of which four are in progress) and oversaw more than 1000 core facility projects. Since 2015 I serve in the Editorial Board of the journal Molecular and Cellular Proteomics. Jonathan MudgeTeam Leader, EMBL-EBI, United Kingdom  Most of my career has been spent working on human gene annotation as part of the GENCODE / Ensembl project, especially on the discovery and validation of protein-coding genes. My original background is in molecular evolution, and in recent years this has proved a highly useful method by which to identify missing microproteins that are conserved in vertebrate genomes. More recently, it has became clear to me that Ribo-seq has enormous potential to provide a high-resolution map of human translation, although the fact that this technique routinely finds thousands of new, non-canonical ORFs is as bewildering as it is fascinating, Thus, working in collaboration with many great people across the globe, I am helping to lead efforts to understand and annotate these translations as functional sequence elements. A major question is which ones encode bona fide missing human proteins? Proteomics data can naturally help answer this, although immunopeptidomics datasets may yet prove more useful... once we agree on a standardised approach for their integration. Ultimately, it is only when we bring these different approaches together that we begin to understand the nature of the 'dark proteome'. Nonetheless, numerous outstanding questions remain. For example, how do we demonstrate the true functionality of proteins that are not deeply conserved? How do we annotate proteins that are specific to cancer cells, and possibly aberrant? Where do we start - or restart - with transposon annotation? Traditionally, HUPO efforts have been based around protein annotation as opposed to protein-coding gene annotation. The difference is subtle, but important; the latter, for example, also considers gene structure and transcription. In fact I have worked closely with UniProt for many years on the EMBL-EBI campus; our annotations exist as part of a shared ecosystem. In this way I have already contributed to HUPO efforts for many years by proxy. Now I am looking for more direct involvement, especially in HUPO-HPP. Not just in the identification of missing proteins, but also in the potential reclassification of existing annotations (there is much work to do here). I think it would be great if HUPO and GENCODE / Ensembl gene annotation efforts became more closely aligned, and that is ultimately what I am looking to achieve with my candidacy. Paola RoncadaFull Professor, Microbiology and Animal Infectious Disease, University Magna Graecia of Catanzaro, Italy
As a Principal Investigator in many national and international projects, I have successfully managed multidisciplinary research that integrate human, animal, and environmental health. My research has been published in high-impact journals and presented at international conferences, reflecting my commitment to advancing scientific knowledge and fostering academic discourse. My involvement with One Health initiatives has provided me with a comprehensive perspective on how proteomics can address complex health issues that cross species and ecosystem boundaries. I have actively contributed to advisory boards and committees, advocating for integrated health approaches and promoting interdisciplinary collaborations. If elected again to the HUPO Council, I will leverage my expertise to promote interdisciplinary research and foster global collaborations. with a special focus in Early career Reseracher, sharing my long experience in Italian proteomics association. I am committed to advancing open science and data sharing, ensuring that proteomics research addresses pressing global health challenges. My vision is to cultivate innovation and inclusivity within the proteomics community, driving scientific progress for the betterment of public health. Thank you for considering my candidacy. Amirata SaeiAssistant Professor, Karolinska Institutet, Sweden 
I am writing to apply for membership in the prestigious HUPO council. I am an Assistant Professor at Karolinska Institute, and my lab is interested in applying unique multidimensional proteomics tools to study "metabolite-protein" and "host-pathogen" interactions. We aim to identify metabolic vulnerabilities for developing therapeutic strategies against cancer. I received a Ph.D. working with Prof. Roman Zubarev at Karolinska Institute, focusing on the development of mass spectrometry-based proteomics tools for anticancer drug target deconvolution. As a Swedish Research Council postdoctoral fellow, I worked with Prof. Steven Gygi's lab at Harvard Medical School on applying stability proteomics for studying metabolite-protein interactions. I then joined Prof. Michael Hall at the Biozentrum, Switzerland, as an independent Ambizione Fellow funded by the Swiss National Science Foundation. My main objective was to learn from colleagues in metabolism and establish a unique direction in bridging proteomics and cancer metabolism. I have pioneered the development of several proteomics tools for elucidation of drug target and disease mechanisms, with a special focus on cancer. These tools include but are not limited to ProTargetMiner (Nat Comm 2019), Proteome Integral Solubility Alteration assay (PISA; JPR 2019), System-wide Identification of Enzyme Substrates by Thermal Analysis (Nat Comm 2021), PISA-Express (Nat Comm 2021), and PISA-REX (BioRxiv 2023). I have received numerous grants including the Thermo Scientific Tandem Mass Tag Gold Award in 2019. It would be a privilege to serve as a member of the HUPO council, as it would help me build strong connections and professional profile throughout the proteomics community. I am particularly interested in expanding the application of proteomics in personalized medicine, biomarker discovery and meta-proteomics. I am enthusiastic about contributing to the HUPO Council. My extensive academic and research experience, coupled with a strong publication record, demonstrates my commitment to advancing the field of proteomics and my capability of bringing innovative perspectives to the council within its strategic plans. I am eager to contribute to the council's initiatives and mission, working towards advancing the field of proteomics, and am confident that my track record and dedication to the field make me a suitable candidate for this position. Valentina SiinoPrincipal Scientist, Acrivon Therapeutics, Sweden
Being a scientist in the proteomic field for the past 10 years, I truly believe in the proteomic power of un revealing insightful mechanism of actions for drug discovery. I want to get even more involved in the proteomic community, thus I want to support HUPO in their commitment and mission. Yves VandenbrouckResearch Director, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), France  Molecular physiologist (PhD Paris 6 University) and computational biologist (MSc. Institut Pasteur Paris) by training, I have been working in different environment (academic, biotech and software companies), learning at the interface of various disciplines, from Physiology and Cellular biology to Computational Biology applied to Genomics and Proteomics field. I am research director at the CEA (Fundamental Research Division) where I now coordinate research activities for digital health based on multi-omics approaches. My research interests focuses on designing bioinformatics tools and strategies to leverage the ever-increasing wealth and diversity of "omics" data for biomarkers discovery, and for the investigation of physiopathological processes. I served on the Executive Committee of the French Proteomics Society for eight years. As training manager of the French Proteomics Infrastructure, I organized practical sessions in computational proteomics for young as well as experienced researchers. I also contributed to the development of the Galaxy for proteomics (via the ProteoRE application) and to the European Elixir proteomics community, participating in the dissemination of proteomics data analysis pipelines. For many years, I have taken part in HUPO initiatives such as co-PI of c-HPP (Human Proteome Project), co-founder and co-organizer of the "Bioinformatics Hub", as member of the HUPO awards committee and more recently as contributor to the Human Plasma Proteome Project. As a member of the HUPO council, I will continue to promote the use of computational proteomics resources (data, tools, workflows), and facilitate their access and use to non-expert users (e.g. via the Galaxy Training for Proteomics). At last, I am convinced that supporting new talents and stimulating exchange of ideas and interactions between dry and wet lab scientists through dedicated events organized by HUPO are essential to tackle tomorrow's challenges. Through my involvement in these community efforts, I will contribute to initiatives that stimulate excitement for proteomics and extend the outreach of HUPO towards the broader scientific communityMarkku VarjosaloResearch Director/Professor (Tenured), University of Helsinki, Finland 
I am a tenured Research Director and Professor at the Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Finland. With over two decades of experience in molecular systems biology, my career has been dedicated to advancing our understanding of cellular processes and disease mechanisms using omics, with a focus on mass spectrometry-based proteomics. My educational background includes a Ph.D. in Medical Systems Biology and a Docent degree in Molecular Systems Biology from the University of Helsinki, and an M.Sc. in Biochemistry and Biotechnology from the University of Kuopio. Throughout my career, I have led numerous high-impact research projects, secured significant funding, and published over 150 peer-reviewed articles. My work has been recognized with several prestigious awards, including the University of Helsinki's Best Thesis Award and fellowships from HiLIFE, the Research Council of Finland, and the European Union's Marie Curie program for my postdoc at ETH Zurich. I have a proven track record of fostering collaborative research environments and mentoring the next generation of scientists. My leadership roles at the University of Helsinki, HiLIFE, Biocenter Finland, and the Finnish Proteomics Society, as well as my involvement in international consortia and organizations (Instruct-ERIC Executive Committee member, European Proteomics Association (EuPA) Funding Committee member), and editorial boards demonstrate my commitment to scientific excellence and community building. As a candidate for the HUPO Council, I bring a wealth of experience in proteomics, systems biology, and translational research. My expertise in quantitative mass spectrometry and bioinformatics positions me well to contribute to HUPO's mission of advancing the field of proteomics globally. I am passionate about promoting interdisciplinary research and believe in the power of collaborative networks to drive scientific innovation. If elected, I will work tirelessly to support HUPO's initiatives, foster international collaborations, and ensure that our community remains at the forefront of scientific discovery. I am eager to bring my expertise, dedication, and vision to the HUPO Council, contributing to the continued growth and success of our field. Thank you for considering my candidacy. Juan Antonio VizcainoProteomics Team Leader, EMBL-EBI, United Kingdom 
I am leading the Proteomics team at the EMBL-European Bioinformatics Institute (EMBL-EBI, Hinxton, Cambridge, UK). We are responsible for the PRIDE database (https://www.ebi.ac.uk/pride/) and related software tools and resources. Our overall goal is to make proteomics data FAIR (Findable, Accessible, Interoperable and Reusable), including the integration between proteomics data and other omics data types. I have been working as a computational biologist in proteomics for the last 18 years, and before that I was a wet-lab scientist. Over the years, I have participated in several International efforts where the proteomics community has played a key role. First, I co-led the establishment of the Proteome change consortium of proteomics repositories (http://www.proteomexchange.org/) and have coordinated its efforts since 2011, involving members from USA and Asia in addition to PRIDE. A second example is my participation and leadership in the development of open data standard formats and related software under the umbrella of the HUPO-Proteomics Standards Initiative (HUPO-PSI), where I am currently one of the co-Chairs. I have been a member of the HUPO Council since 2022. Additionally, I have held different positions in the management/executive committees of the European Proteomics Association (EuPA) and of the British Society for Proteome Research (BSPR). Due to these various roles, I have established close contacts with a great number of members of the proteomics community worldwide. I would be excited to continue this role in HUPO to help shaping its ambition in the years to come. If you entrust me with your votes, you can rest assured that I will be fully committed to carrying out this work, and that I will do so in an engaged and transparent manner! |
The field of proteomics continues to mature into an indispensable component of life science research. As such, the HUPO mission is more essential than ever. I would like to help to promote this mission in general, and specifically with respect to these topics:
I am the head of the Quantitative Proteomics laboratory at the Charite University Medicine Berlin, Germany. My research group works on proteomics technology development, with a focus on advancing the capabilities of data-independent acquisition (DIA) mass spectrometry towards novel applications that push the limits of throughput and sensitivity, via new workflows as well as computational approaches that we implement in our DIA-NN software suite.
I am writing to express my interest in serving again the HUPO Council. My academic and research background in One Health, microbiology, food and nutrition proteomics, and zoonoses aligns well with the goals of HUPO to embrace more scientists in the community. With over 20 years of focused research experience, I have led studies in proteomics, particularly its intersection with public health and food safety. My work has advanced our understanding of proteomic profiles in zoonotic pathogens and their transmission mechanisms, contributing to the development of improved diagnostic and preventive strategies.
I have worked for many years in academia and now I work in an oncology harma company where I apply proteomics to help and improve patients lives.
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