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The September HUPOST is now available! Lots of exciting and interesting info - Congress updates, EC Elections, ECR News, B/D HPP info and more!
See our exciting program information below. All times are US Eastern Time.
10:00 am Matthias Mann, "Ultra-high sensitivity for precision oncology"
10:30 am Erwin Schoof, "Leveraging advanced latest-generation acquisition and MS instrument architecture for improving single cell proteomics experiments"
11:00 am Roman Zubarev, "Since cell proteomics - some considerations from the chemical proteomics point of view"
11:30 am Claudia Ctortecka, "Variations of the proteoCHIP - a high-throughput sample preparation approach for single-cell proteomics"
12:00 pm Ying Zhu, "Enhancing single cell proteomics and tissue proteome mapping with ion mobility filtering"
12:30 pm Ryan Kelly, "Advanced separations and data acquisitions strategies for in-depth single-cell proteomics"
13:00 pm Closing remarks
Organized by the B/D-HPP Single Cell Initiative. Please contact Initiative Chair Dr. Bogdan Budnik (Bogdan.Budnik@wyss.harvard.edu) with any questions or if you want more info!
Livia Rosa-Fernandes is part of Prof. Marinho’s research team at The Institute of Biomedical Sciences of the University of São Paulo and a Research Fellow in Neuroproteomics at Macquarie University Centre for Motor Neuron Disease Research. She received her Ph.D. in Medical Sciences from USP Medical School (2015). During her Ph.D., she had the opportunity to work at Brigham and Women´s Hospital-Harvard Medical School (USA), as part of the Postgraduate Research Exchange Program. In 2016, Livia moved to Denmark, where she worked as a post-doctoral researcher both at the Department of Biochemistry and Molecular Biology and the Institute of Molecular Medicine, at the University of Southern Denmark. From 2019, she was enrolled as a post-doctoral fellow at the Institute of Biomedical Sciences, USP (Brazil).
Over time, Livia has gathered experience using in vivo and in vitro models together with molecular tools to study biological processes focusing on disease progression, cellular communication, and its microenvironment. MS-based proteomics and data analytics play a key role in her research as powerful tools to better understand a biological event. Her scientific production reflects an effort to engage in multidisciplinary fields and strengthen a collaborative approach to science. She is also part of the Brazilian Proteomics Society council and is engaged in several initiatives to promote knowledge transfer and increase access to scientific education.
With the recent refresh of the HUPO Biology/Disease-driven Human Proteome Project (B/D-HPP) Executive Committee, we took the opportunity to get the thoughts of several members of the committee who completed their tenure. Drs. Corrales, Deutsch, Omenn, and Schmidt have all given their valuable time and leadership to the HUPO mission and have been critical to the continued growth of the B/D-HPP initiatives and the continued adoption of proteomics advances toward understanding pressing questions in health and life sciences. We asked them what they would like to share with the HUPO community on this occasion.
Dr. Fernando Corrales served as co-chair, chair, and past-chair of the B/D-HPP from 2015–2021. As the Human Liver Proteome Project (HLPP) chair, he also has led the HLPP since 2014. Regarding what he sees as the importance of the B/D-HPP at large, the former chair said that it has represented to him an “opportunity to translate the essence of proteomics” and particularly into “functional understanding of biological systems.” Dr. Corrales, who is Professor at the Spanish National Centre for Biotechnology, sees the B/D-HPP as the masterpiece of the upcoming Grand Project once it is integrated with the other resources of the HPP. The experience sharing the coordination of the B/D-HPP with Drs. Jenny van Eyk and Ileana Cristea has been outstanding and the efforts of all persons on board during these years have been generous, says Dr. Corrales.
“Defining protein function is something clearly dependent on the biological environment where proteins develop their activity and B/D Teams integrate an ideal research network to dissect so far hidden functionalities and place them into the adequate physiological and/or pathological framework." – Fernando Corrales
Dr. Eric Deutsch, who served on the executive committee for five years, agrees on the importance of ensuring B/D-HPP initiatives receive continued community support. “I wish the new committee well in working to increase active participation of all B/D-HPP initiatives”, adds the longtime HUPO leader and Principal Scientist at the Institute of Systems Biology.
Dr. Gil Omenn is the Harold T. Shapiro Distinguished University Professor at University of Michigan and a longtime chair of the HUPO Human Proteome Project (HPP). He served on the B/D-HPP executive committee for a decade alongside Drs. Ruedi Aebersold, Jenny van Eyk, Fernando Corrales, Ileana Cristea, and now Nicki Packer as chairs, and chaired the Human Plasma Proteome Project from the launch of HUPO in 2002. Under his leadership, the Plasma, Brain, Liver, Cancer, and Cardiovascular Proteome Projects were brought together with many emerging projects to form the B/D-HPP in 2011 and join the Chromosome-centric C-HPP in the HUPO HPP. This year, Dr. Omenn has rotated off the B/D-HPP executive committee after a successful term that saw him continue to lead the executive committee with his vision, which culminated in an HPP Metrics of the Human Proteome paper in the annual special issues of the Journal of Proteome Research and a special perspective article in Molecular & Cellular Proteomics.
“The B/D-HPP teams have made important contributions to the global explosion of research utilizing proteomics to reveal pathways, networks, mechanisms, and biomarkers underlying a great range of biological processes and diseases,” – Gil Omenn
Dr. Frank Schmidt is an active leader in the B/D-HPP community and served on the executive committee. As his term concludes, Dr. Schmidt said he will remember his time with the committee “very positively”. The transition to the digital age during the COVID-19 pandemic was especially memorable, "when we successfully held our first professional webinars and were able to push new ideas under the excellent leadership of Ileana [Cristea] and Fernando [Corrales]”, reminisces Dr. Schmidt, who is Professor at Weill Cornell Medicine-Qatar. He wishes the new committee good luck as a new crop of members from the proteomics community continue the initiative missions.
We look forward to continuing the work of the HUPO B/D-HPP in engaging the proteomics community and promoting the adaption of proteomics advances toward life and medical sciences. We welcome the new and continuing HUPO B/D-HPP Executive Committee members for 2022–2023:
 Omenn GS et al. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res. 2020 Dec 4; 19(12): 4735–4746. PMID: 32931287
 Omenn GS. Reflections on the HUPO Human Proteome Project, the flagship project of the Human Proteome Organization, at 10 years. Mol Cell Proteomics. 2021 Feb 26;20:100062. PMID: 33640492.
Devon Kohler1, Mateusz Staniak4, Olga Vitek1
1Khoury College of Computer Science, Northeastern University, Boston, MA, USA; 4University of Wroc law, Wroc law, Poland
The MSstats ecosystem is a family of open-source R/Bioconductor packages implementing statistical methods for quantitative mass spectrometry-based proteomic experiments. Here we review its recent developments, as well as advances in previously available methods and implementations.
Read full article here.....
The August HUPOST is here! See the latest info about the HUPO 2022 World Congress, Education and Training Committee (ETC) activities, ECR Initiative and an update from the HPP.
The July HUPOST is now available! Be sure to have a look at the HUPO 2022 World Congress updates, ECR and MOC news, Humans of HUPO and Job Opportunities!
The June HUPOST is now available....See important information about HUPO's Statement on Ukraine, World Congress, Awards Deadline, ETC and ECR updates....and much more!
Blandine Chazarin, PhD is currently a postdoctoral scientist in Jennifer Van Eyk's lab at Cedars-Sinai Medical Center in Los Angeles (CA, USA). Previously she studied biology at Paul Sabatier University (Toulouse, France) prior advanced training in proteomics and mass spectrometry at Lille 1 University (Lille, France). She obtained a PhD using mass spectrometry to better understand hibernating brown bear physiology to path the way of therapeutic against muscle atrophy at LSMBO (Strasbourg, France). She is the former president of the youth club of the proteomic French Society and organized yearly meeting dedicated to young scientists in proteomics. Now, she is involved in postdoctoral scientist society at Cedars-Sinai and developed single cell proteomic approach applied to cardiac cells proteome analysis.
Vision for ETC: Being an early career scientist can be challenging and Universities are not teaching how to evolve in science. It’s time to form our next generations of scientists by sharing trainings, advertising incoming meetings and provide additional information about grants and networking.
Ben Collins, PhD is currently a Reader (equiv. Assoc. Prof.) in the School of Biological Sciences, Queen’s University of Belfast, UK (since 2019). His research focuses on broadly on 3 topics: (i) method development and applications in data independent acquisition mass spectrometry; (ii) method development and applications in the analysis of protein interaction networks and protein complexes; and (iii) applications of these strategies in host-pathogen biology and innate immunity. Ben Collins’s PhD was completed at University College Dublin in 2009 where he remained for 1 year as the Agilent Technologies Newman Fellow (postdoctoral) in Quantitative Proteomics. He moved to the Institute of Molecular Systems Biology at ETH Zurich in Autumn 2010 as postdoctoral researcher under the supervision of Prof. Ruedi Aebersold, where his research focused on the application of quantitative interaction proteomics in signaling and the development of DIA/SWATH mass spectrometry. Following this Ben Collins was a Group Leader and SNF Ambizione Fellow at IMSB, ETH Zurich with a focus on applying methods developed as a postdoc to relevant problems in host-pathogen biology.
Vision for ETC: Training and education are at the heart of HUPO activities, so I am excited to be involved in the effort to revitalize this initiative. My view is that there are many high-quality educational activities ongoing organized by independent groups and a part of our effort should be to make people aware of these courses in an organized way, and to distribute videos/materials as widely as possible where available. We should also aim to complement the current offerings with HUPO-organized courses on prioritized topics. Key to our success will be to reach proteomics-focused scientists but also beyond into the broader life science community where we can have tremendous impact.
Deepti Jaiswal Kundu, PhD works as a Scientific Curator at EMBL-EBI, Cambridge, UK. Before joining EMBL-EBI, she studied botany, psychology, and bioinformatics in India, before doing a PhD in Cheminformatics in the Czech Republic. After successfully defending her thesis in 2015 Deepti Jaiswal Kundu moved to Cambridge, UK and took a break of briefly 2 years to have daughter. She joined EBI in 2018. As a Scientific Curator, Deepti Jaiswal Kundu is responsible to check and validate new datasets submitted to the PRoteomics IDEntifications Database (PRIDE) - the world’s largest public database dedicated to mass spectrometry-based proteomics. Furthermore, she curates the datasets for further reanalysis and integration to other bioinformatic resources in EBI.
Vision for ETC: I would like ETC to reach more people and encourage students/scientists to participate in training programs, conferences, and meetings.
Qingsong Lin, PhD is a Principal Research Fellow (Research Associate Professor) of the Department of Biological Sciences, National University of Singapore (NUS). He is the Director of the Protein and Proteomics Centre (PPC), NUS. Besides, he is the President of the Singapore Society for Mass Spectrometry (SSMS) since 2017. His expertise lies in applications of mass spectrometry in proteins and proteomics, extended to other biomolecules. His research interests are mainly in disease biomarker discovery and disease mechanism, drug target identification and mechanism of action studies, as well as the application of mass spectrometry and quantitative proteomics technologies to address various biological questions.
Vision for ETC: To grow HUPO ETC as the world’s most comprehensive proteomics resource; to educate and train proteomics scientists from fundamental to advanced levels.
Yansheng Liu, PhD is an Assistant Professor in the Department of Pharmacology at Yale University School of Medicine. His research group is interested in DIA-MS and has combined DIA with SILAC and phosphoproteomics for studying fundamental biological questions in cell signaling.
Vision for ETC: I believe the new HUPO ETC should engage the next generation of scientists and is eager to organize workshops in which young scientists, such as first-authors in manuscripts, can present and learn from each other.
Brian Searle, PhD is an Assistant Professor at the Ohio State University Medical Center in the Department of Biomedical Informatics and a member of the Pelotonia Institute for Immuno-Oncology (PIIO). Brian received his chemistry BA at Reed College in 2001. In 2004, he co-founded Proteome Software with Mark Turner and Dr. Ashley McCormack to produce and distribute cutting-edge data analysis software for proteomicists. In 2014, he returned to academia to earn his PhD with Dr. Michael MacCoss at University of Washington, where he developed methods to detect and quantify proteins and phosphosites using mass spectrometry. His lab at PIIO spans the intersection of proteomics, mass spectrometry, bioinformatics, and technology development to study human genetic variation in the backdrop of cancer.
Vision for ETC: I am excited to see the ETC produce the best available educational resources for proteomicists of all skill levels to learn new technologies, and to give early-career proteomicists a chance to interact with top-level researchers and grow their careers.
Low Teck Yew, PhD is an associate professor and senior research fellow located at the UKM Medical Molecular Biology Institute (UMBI) which is affiliated to the National University of Malaysia (UKM), leading the cancer proteomics and metabolomics group. Before that, he worked at Netherlands Proteomics Centre (NPC) in Utrecht University in the Netherlands. His research interests include bridging (phospho)proteomics with clinics and cancer proteogenomics.
Vision for ETC: I hope to connect researchers in southeast Asia (SEA) to the international community in proteomics research and enhance the exposure of this region with respect to education and training. I also wish to share some of the special research topics in this region, which has its own rich and unique biodiversity, to international researchers.
The HUPO Early Career Researcher (ECR) Initiative is an international community of early career researchers in proteomics, whose mission is to provide networking and career development opportunities for aspiring researchers. To help achieve this, the ECR Initiative organizes panel discussions to foster professional development and a space for mentorship. In the upcoming panel discussion, we will be covering the topic of scientific collaborations.
Scientific collaborations can bridge disciplines, expertise, and countries to produce innovative research. Certainly, the COVID-19 pandemic has highlighted the importance of collaborating and has also changed the way scientists across various disciplines collaborate. But how do you collaborate successfully and effectively?
Join us on Wednesday June 29th at 10:00PM GMT for the HUPO ECR online panel discussion, "Choosing and Managing Collaborations: The Do's and Don'ts". We will be joined by three experienced collaborators who will share valuable lessons learned on collaborating:
They will be sharing their input on how to have a successful career of collaborations. You won’t want to miss it!
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