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The 6th newsletter of the Chromosome-centric Human Proteome Project is now available online, read it here.
In this issue:
The hPOP (Human Personalized Omics Profiling) project is designed to study the variance of molecular markers across a large number of participants. Recent advances in high throughput technologies allow profiling of thousands of analytes within a single experiment. These measurements could potentially be used to diagnose disease early, monitor treatment progression and stratify patient groups to ensure each individual obtains the treatment best suited to their needs. This personalized approach to medicine would include continuous monitoring of thousands of parameters over a whole lifetime. However, in order to be able to interpret such data, we need to have a better understanding of the underlying natural variation of these molecular parameters in health and disease. Only if we know the natural ranges of individual analytes, the expected responses to perturbations and the long-term trends in their levels, can we draw meaningful conclusions from comprehensive personalized profiling.
In this project, we aim to use a multi-omics approach to study the genome, epigenome, transcriptome, proteome and metabolome of a large number of healthy volunteers. The hPOP project will be launched officially at the 2016 HUPO in Taipei where samples from several hundred people will be collected. The current protocol includes sampling of blood, urine and stool after overnight fasting. Additionally, a detailed questionnaire about food habits, personal health, physical activity and stress levels will be filled out by each participant. All data will be made available to the scientific community under public domain which will allow multiple research groups to use the generated data in their own studies and perform their own analysis of the data.
To find out more or to join the hPOP mailing list, visit the website.
Proteogenomics, integration of proteomics, genomics, and transcriptomics, is an emerging approach that promises to advance basic, translational and clinical research. By combining genomic and proteomic information, leading scientists are gaining new insights due to a more complete and unified understanding of complex biological processes.
Advanced bioinformatics approaches are needed to entirely use the complete information spectra acquired in genomics, transcriptomics and proteomics studies. A DREAM Challenge offers a chance to crowdsource the analysis of numerous rich data sets at once (one of the largest public repositories of proteogenomic sequence data) and thereby compare aspects of various methods to better understand biological features that drive early cancer progression.
To this regard, the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, in partnership with DREAM Challenges, announce the NCI-CPTAC DREAM Proteogenomics Challenge (estimated launch date is mid-June). The aim of the challenge is to encourage the generation of computational methods for extracting information from the cancer proteome and for linking those data to genomic and transcriptomic information. The goal is to predict proteomic and phosphoproteomic data from multiple other data types. Method performance will be blindly evaluated using a previously unseen validation dataset generated by CPTAC.
DREAM Challenge will be run in the Google Cloud, and provide a prize award sponsored by the NVIDIA Foundation. Nature Methods also supports the submission of an overview paper of the Challenge, contingent on a standard evaluation process.
For Registration, click here
Please visit the DREAM website for further details on DREAM challenges, including history, previous challenges and FAQs.
Dear HUPO colleagues,
The HPP is reaching out to clinical scientists or clinicians who are using or consider using proteomics for their research projects. HPP is supporting six (6) clinical scientists with a travel grant to attend the 2017 HUPO World Congress in Dublin, Ireland that will take place from September 17-21, 2017.
Travel grant recipients will receive USD $1,000 to offset travel and hotel costs in addition to complimentary congress registration. The recipients are expected to actively participate in the HUPO congress, particularly in the activities and discussions related to the HPP. Further information on the HUPO 2017 congress and HPP activities in Dublin can be found at http://hupo2017.ie/.
Application deadline: Friday, June 30, 2017
For more information and application instructions visit https://hupo.org/HPP-Clinical-Scientist-Travel-Grants.
HUPO 2017 Abstract Extension
Abstract submissions to the 16th Human Proteome Organization World Congress have been extended to 3 May 2017. Read more >
ECR Manuscript Competition
The Early Career Researcher (ECR) Initiative of the Human Proteome Organization is pleased to announce the 3rd ECR Manuscript Competition to take place at HUPO 2017 in Dublin! Deadline 5 June 2017. Read more >
PhD Abstract Competition
Once again, HUPO is holding a PhD Abstract Competition. 8 abstracts will be selected based on excellence to have a short oral presentation at HUPO 2017 in Dublin. Deadline 3 May 2017. Read more >
HUPO is seeking candidates to serve on the HUPO Council for three-year terms beginning January 2018 (2018-2020). We invite you to nominate yourself and other scientists from your region. Deadline 30 April 2017. Read more >
Welcome to the new HUPOST! As Emma Lundberg, our much-appreciated outgoing Editor, announced in the previous HUPOST, we updated the format for 2017. Key points are now included in the email, and our circulation has broadened to reach an even wider audience. HUPOST’s frequency has also increased to every two months, alternating between a short and snappy overview of current news, and an extended version that covers interesting developments in the field of proteomics.
Speaking of interesting developments, allow me to remind you that the HUPO 2017 World Congress in Dublin on 17-21 September is now only 5 months away! Abstract submissions will now be accepted until 3 May, so you can still join us and share your latest work. I very much look forward to hearing about it, and to meeting you, on the Emerald Isle in September!
Meanwhile, enjoy the new HUPOST, and make sure to let us know at email@example.com when you have something to share! As always, you can find us on social media: Facebook, Twitter, and LinkedIn.
Cheers, Lennart Martens - HUPOST Editor
There has never been a more exciting time for proteomics. We can rapidly measure thousands of molecules and posttranslational modifications, and there are large initiatives such as the Cancer Moonshot and Gene-Tissue Expression Project in which proteomics will make an important contribution. As technological advances continue proteomics will play an increasing role in large-scale influential projects.
A valuable part of all of these efforts is the Human Proteome Project (HPP; 1) which aims to map the proteome parts lists: protein coding genes, splice and allelic isoforms. It also aims to advance the proteomics of a wide range of human biology and disease, for example, cardiovascular disease, diabetes, cancer. With respect to the latter, we are assembling a list of popular proteins for each major human disease (2).
The HUPOST is HUPO’s forum for disseminating advances in our field. We hope to keep the community abreast of the latest advances and technologies.
Cheers, Mike Snyder - HUPO President
1) Advances of the HUPO Human Proteome Project with broad applications for life sciences research. Omenn GS. Expert Rev Proteomics. 2017 Feb;14(2):109-111. doi: 10.1080/14789450.2017.1270763. Epub 2016 Dec 22. No abstract available. PMID: 27935328
Dear HUPO Members,
I am seeking candidates to serve on the HUPO Council for a three-year term that will begin January 2018 (2018-2020).
Each Councilor must be a current HUPO member who is a scientist from the public or private sector with at least ten (10) years of professional experience in educational, research or commercial activities related to the purposes of HUPO. We invite you to nominate yourself or other scientists from your region - Central region (Europe/Africa), Eastern region (Asia/Oceania), and Western region (Pan-America). Please check with your nominee to be sure they are willing to stand for election.
To nominate a colleague or yourself please complete the 2017 Elections Nomination Form (available here) and submit it to firstname.lastname@example.org before 30 April 2017.
If you nominate a colleague please note they will be asked to confirm their willingness to stand for election. The current council list can be found here.
Thank you for your support,
Chair, HUPO Nominations and Election Committee
The Human Proteome Organization is pleased to the announce the HUPO-endorsed Cardiovascular Initiative Workshop. The workshop features outstanding scientists from across the HUPO/HPP community. View the programme online.
The workshop takes place on 2 April 2017, during the Proteomic Forum in Potsdam, Germany. For more information, and to register, visit http://www.proteomic-forum.de/ or contact email@example.com.
Chair, HUPO Marketing Committee
The Human Proteome Organization presents awards annually at the World Congress. The HUPO 2017 World Congress is in Dublin from September 17-21. Award recipients will present a brief talk during the Congress award ceremony. These distinguished awards recognize the outstanding efforts of individuals (or groups) advancing the field of proteomics. Nominations are done through an online submission form and no supporting documents or attachments are required.
You are invited to nominate award candidates!
Nomination Deadline: April 17, 2017
HUPO is now accepting nominations for the following awards:
Distinguished Achievement in Proteomic Sciences Award ($3000, sponsored by Journal of Proteome Research - ACS Publications) recognizes a scientist for distinguished scientific achievements in the field of proteomic science.
Discovery in Proteomic Sciences Award ($3000, sponsored by Journal of Proteomics - Elsevier BV) recognizes a scientist for a single discovery in the field of proteomics.
Science and Technology Award ($3000, sponsored by the HUPO Industrial Advisory Board) recognizes an individual, or team (of up to three people) in private industry who played a key role in commercialization of a proteomics technology, product or procedure. The emphasis for the award is on making the technology, product or procedure widely available, which is different from the basic scientific invention.
Clinical and Translational Proteomics Award ($3000, sponsored by Clinical Proteomics - BioMedCentral) recognizes a scientist for distinguished scientific achievements in the field of clinical and translational proteomics.
Distinguished Service Award ($3000, sponsored by HUPO) recognizes an exemplary member of the proteomic research community whose dedicated service has made indispensable contributions to the organization and mission of HUPO.
A real success story of international collaboration through HUPO was the launch of the International Cancer Proteogenome Consortium (ICPC) during the 2016 HUPO Congress in Taipei.
Story by Michelle Hill, B/D-HPP Newsletter Editor
Some of the ICPC representatives at HUPO 2016 in Taipei. From left: Daehee Hwang (South Korea), Ruedi Aebersold (Switzerland), Christoph Borchers (Canada), Henry Rodriguez (USA), Albert Sickmann (Germany), Mark Baker (Australia), Chia-Jung Yu, Yu-Ju Chen, Min Daw Tsai, Chen-Yang Shen (Taiwan).
This exciting development was grounded on ongoing collaboration between the Cancer Initiative of the B/D-HPP and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of The United States National Cancer Institute (NCI), and nurtured through years of work at HUPO Congresses. Following the first announcement in Australia in July 2016, an additional 7 countries now joins the initiative to form the International Cancer Proteogenome Consortium (ICPC). This is a real success story of international collaboration catalyzed by HUPO. Two of the leaders tell of the story.
Read the full story in the B/D-HPP Newsletter | Issue 1, 2017
Media Release from Macquarie University - 23 January 2017
Much remains to be understood about how proteins in the human body works in unison; however a newly developed resource is giving scientists a more complete picture of how the proteome makes us uniquely human. MissingProteinPedia, a database developed by a collaborative research group lead by scientists at Macquarie University, could not only help researchers learn more about the location and use – termed ‘expression’ – of specific proteins in the body but also how they interact to make us human. It will also help to pin down those proteins which are still ‘in the shadows’, with implications for several diseases.
Dr Shoba Ranganathan and Dr Mark S Baker
Photographer credit: Paul Wright
“While we know a lot about individual proteins, the larger picture of how these proteins work together to make an individual person is a difficult concept to explore. Although we are developing new technologies to test when, where, why and how proteins are expressed, we still need some way of tying all the biological information together so that we get a clearer picture of how proteins work together to turn us into an individual human being,” explained Professor Mark Baker, lead author of the missing protein study.
“Our team developed MissingProteinPedia to gather all the scattered and incomplete information about what the Human Proteome Project calls missing proteins. This includes the 2,949 proteins that, despite rigorous testing, are still ‘in the shadows’ and haven’t yet been proven to exist,” he added.
The tool accelerates the discovery of many missing proteins, particularly those in elusive protein families, with potentially vast consequences for human disease.
“In order to understand how a disease progresses we need a detailed picture of how all proteins work in a healthy individual, so that we can understand what triggers the development of diseases,” explained senior author Professor Shoba Ranganathan.
“MissingProteinPedia has uncovered substantial evidence for many hard-to-detect proteins for which small amounts of information have taken years to gather. The very fact that we have come so far in such a short time bodes well for our understanding of complex human diseases such as cancer,” she added.
The researchers will make the database a community-driven, citizen-science project where everyone can help in the discovery of human missing proteins and their role in health and disease.
Media Contact: Dr Megan Wright | T: +61 (2) 9850 1055 | E: megan.wright(at)mq.edu.au | A copy of this release will be available online at www.mq.edu.au/newsroom
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