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humans of hupo

Each month we will highlight a member of HUPO. A diverse group of researchers representing different career stages, disciplines, geographical locations, and ethnicities will be invited to submit a profile for the monthly highlight. This initiative will improve visibility of HUPO members, advertise research and enhance the HUPO community.


Tiannan Guo, Hangzhou China

What is your current position and location?

I am a Principal Investigator and Associate Professor at Proteomic Big Data Lab of School of Life Sciences at Westlake University, located in Hangzhou, China. I am also the Director of iMarker Lab at Westlake Laboratory for Life Science and Biomedicine, and an associate faculty member of Center for Infectious Disease Research and Research Center for Industries of the Future at Westlake University.

How did you get started in the field of proteomics?

Actually, I was intent on becoming a clinician before delving into academic research. Everything changed in 2006 when protein systems first fascinated me when I learned about Gleevec, a drug directed at the BCR-ABL fusion protein for chronic myeloid leukemia. Invention of this drug enabled about 99% of the patients to be cured, turning a previously fatal diagnosis into a chronic disease. I thought then it would be useful to find more drug targets for more types of cancer, which would require understanding the abnormal proteins associated with each disease. My keen interest in proteins and protein systems took me to Singapore for doctoral studies in cancer proteomics at Nanyang Technological University and National Cancer Centre Singapore. After that, I joined the team of Prof. Ruedi Aebersold at ETH Zurich for my postdoctoral research.

What does being a member of HUPO mean to you?

Birds of a feather flock together. Being a HUPO member since my PhD studies has gratified me with a sense of belonging in a scientific and intellectual community that is the most authoritative and influential organization in the world for human proteome research. We can interact with erudite experts and scientists from diverse backgrounds and cultures. This kind of mingling and mutual learning is highly conducive to all the members and I do enjoy every minute of it. Being an active member of HUPO myself, I joined its Marketing and Outreach Committee (MOC) and was honored to be elected as Chair of the Education and Training Committee (ETC). Probably the most impressive experience in HUPO is that occasionally I need to get up at 5 a.m. to attend meetings with colleagues all over the world. We launched the HUPO account in WeChat, a hugely popular social media platform in China, whose 100+ original or translated articles have attracted nearly 1,300 followers. The training courses we organized had a record of over 2,000 concurrent attendees. I am really glad I can help promote HUPO and proteomics in the most populous country in the world. 

What makes your research program exciting and unique?

My field of study, known as proteomic big data, focuses on the intersection between life science and artificial intelligence. We developed the pressure-cycling technology coupled with DIA mass spectrometry for effective proteomic analysis of biopsy tissue specimens. With this technology we can analyze many tissue samples in a relatively short period of time and generate large datasets to help decipher the complex dynamics of protein networks.

We collaborate with clinicians and help them make more exact diagnoses and search for new drug targets. Currently we focus on precision diagnosis of thyroid cancers. There’s a grey area of about 30% of thyroid nodules, where no noninvasive screening exists to accurately determine if there’s cancer, leaving surgical removal of the thyroid gland and subsequent analysis the only option for certainty. Millions of individuals have their thyroid cut out because clinicians cannot tell whether it's malignant or benign. The thyroid secretes hormones vital for human health and life. Losing this organ will force patients into a lifelong regimen of taking artificial hormones, greatly affecting quality of life. So, our goal is to develop a more precise test. Over the past five years, we have identified a shortlist of proteins out of thousands and built a machine learning model for thyroid nodule diagnosis. It has shown about 90% accuracy in the lab in diagnosing thyroid nodules and will undergo further validation in a prospective clinical trial. Hopefully one day, when a patient has thyroid nodule(s), we can offer a new test and give her or him a better and more precise diagnosis.

What are your interests outside of the lab?

I am a huge fan of music. When I walk into my office every day, the very first thing is to turn on the stereo linked to my cellphone and play the music. It is always so nice to start a day with the music I like. Music entertains, enlightens, purifies, and always inspires me.

I am also a voracious reader of not only academic publications in my field, but also a wide array of books. My office is inundated with books and I encourage my students and colleagues to become bookworms as well. It is true that reading serves for delight, for a well-rounded or well-developed personality, and for an expanded world view.

Where do you envision the field of proteomics in the next 10 years?

I think of proteomics just like a fast-growing adolescent who will inevitably encounter some growing pains, but I believe it has great potential for very brilliant prospects. The cost of measuring one protein using mass spectrometry (MS) has plummeted from around 3 USD in 2006 to roughly 0.1 USD in 2020, greatly enhancing the affordability of proteomics. In the next ten years, I confidently anticipate the routine diagnosis of many diseases will be dependent on biomarkers discovered by MS-based proteomics, and perhaps drugs discovered using proteomics will be adopted for clinical therapy.

Besides, AI-empowered big data technologies are a powerful game changer in many fields but not yet in proteomics. In the next ten years, I think proteomic big data will be of comparable volume to other big data such as texts, photos, and videos. Accumulation of proteomic big data will open a new window for us to understand what’s happening in the micro-world of life activities.

Ruth Hüttenhain, USA

What is your current position and location?

I am an Assistant Adjunct Professor at the University of Californian in San Francisco (UCSF) in the Department of Cellular and Molecular Pharmacology.

How did you get started in the field of proteomics?

In 2005 as part of my masters degree, I performed a research project at National Institute of Health under the supervision of Dr. Sonja Hess, for which I characterized hemoglobin variants using a combination of top down and bottom up proteomics approaches. This experience was transforming for me in many ways. Given my prior training in pharmaceutical sciences I had mainly worked on small molecules and became fascinated by the power and versatility of mass spectrometry to study proteins. It also was the first time that I was exposed to the international scientific community and opened my eyes about possible exciting career trajectories. As a result I decided instead of following my occupation as pharmacist to pursue a career in science and to learn more about mass spectrometry-based proteomics, which I have continued doing since then.

What does being a member of HUPO mean to you?

I love being part of HUPO because it integrates diverse scientists from all over the world that share their passion for proteomics technology development and its application to basic biological and clinical questions. Noticing how integral being part of this international community was in the early stages of my career and in fact still today, I decided to join the Early Career Researcher Initiative of HUPO with the goal to foster and grow an international community of young proteomics researchers that provides networking and career development opportunities and promotes diversity, equity and inclusion within the field of proteomics.

What makes your research program exciting and unique?

In my group, we study mechanisms of intracellular signal integration, currently with a focus on G protein coupled receptors (GPCRs). We develop and apply quantitative proteomic approaches to delineate GPCR interaction and signaling networks, their spatial organization within the cell, and their dynamic adaptations to diverse ligands. Ultimately, we hope that this knowledge will not only translate to a better understanding of GPCR signaling, but might provide a solid foundation for the design and testing of novel therapeutics targeting GPCRs with higher specificity and efficacy by monitoring their effects on a whole signaling network.

What are your interests outside of the lab?

Outside the lab, I love spending as much time as possible with my son. I like to explore the outdoors either by hiking, climbing, biking or running. Throughout my career these activities have always been the best way to find a balance during stressful times at work. Additionally, I like to travel around the globe to immerse in different cultures, explore new food and discover novel places.

Where do you envision the field of proteomics in the next 10 years?

This is not an easy question to answer, since I envision developments in many directions. I hope that proteomics will become more user friendly in terms of instrument operation and computational tools to analyze and interpret complex proteomic datasets, enabling its application in the wider scientific community. I believe there will be a continued improvement in the sensitivity of instrumentation and development of novel acquisition principles to a level that allows reliable quantification of thousands of proteins and PTMs extracted from single cells. However, over the last years also alternative technologies to mass spectrometry have started to emerge for measuring proteins. I believe that this is only the beginning and we will see more of these exciting developments in the next decade.

Christian Moritz, France

What is your current position and location?

My contract says “Research Engineer” and I am working for the University Hospital of Saint-Étienne and the Universities of Saint-Étienne and Lyon in France.

How did you get started in the field of proteomics?

Around 15 years ago, during my final years studying biology in Kaiserslautern, Germany, I got a student assistant job in a neuroscience lab. I was part of a proteomics project for which I was applying 2D gel electrophoresis and MALDI MS to study the auditory brainstem. I continued to do similar projects for my master and PhD thesis later on.

What does being a member of HUPO mean to you?

It means being connected with the proteomics community, although I am not working in a classical proteomics group. Interaction with other scientists is extremely important for science. Especially the work for the HUPO Early Career Initiative means to me 1) networking with other proteomics scientists, 2) getting into touch with the “celebrities” of our community, and 3) contributing to proteomics events.

What makes your research program exciting and unique?

We found biomarkers that are used by clinicians! A rare but exciting success of proteomics. Sometimes I feel that the autoantibody-related field of proteomics offers what we all are searching for: the translation from basic research to clinical application.

Our research program is exciting and unique as it addresses an underrepresented but emerging subdomain of clinical proteomics. I am convinced that the surprisingly large repertoire of autoantibody-targeted antigens in humans (what I call the “autoantigenome” and which is an important part of the proteome) can help understanding disease states.

What are your interests outside of the lab?

I love being in nature with my bike. To me, holidays by bike are perfect to slow down life, because it does not exceed the speed that our brain is adapted to.

Where do you envision the field of proteomics in the next 10 years?

I hope that proteomics is getting closer to clinics. My vision is to use a drop of blood, some proteomics techniques and a machine learning algorithm that assists the clinicians in their decisions. But that’s rather for the next 30 instead of 10 years ;)

Feel free to get into touch via LinkedIn or to follow me on Twitter.


Lydie Lane, Switzerland

What is your current position and location?

I am associate group leader at the SIB Swiss Institute of Bioinformatics and scientific collaborator at the faculty of medicine of the University of Geneva (Switzerland).

How did you get started in the field of proteomics?

In 2004, I was hired as a curator for the Swiss-Prot group, and my main task was to extract PTM information from research papers. At this time, phosphoproteomics and glycoproteomics were emerging technologies and important large scale PTM datasets started to be published. As these datasets tended to be noisy, I worked with data providers in order to better understand the technologies and set criteria to select the most relevant data for integration. Together with Alain Gateau, we developed the first pipeline to automatically annotate PTMs from such large-scale datasets.

What does being a member of HUPO mean to you?

In 2011, we launched the neXtProt database (www.nextprot.org) at the SIB Swiss Institute of Bioinformatics in order to fill the gaps in the annotation of the human proteome. Applying proteomics technologies to human proteins sounded as a very promising approach to attain this goal, so it has been quite natural for me to join HUPO. It has been very exciting to take part in my first HUPO meeting in Geneva and meet all the HUPO people there!

neXtProt soon became the companion database for HPP projects, and all along these years the neXtProt team has been collecting the needs of the HUPO community and trying to answer them by developing specific tools (https://www.tandfonline.com/doi/full/10.1080/14789450.2020.1733418). I have been an active member of various boards within HUPO/HPP and participated in nearly all HUPO and HPP events since 2011– a fantastic journey in a strongly dedicated and fun community!

What makes your research program exciting and unique?

With its specific focus on human proteins, the neXtProt database is more comprehensive in human protein annotation than generalist databases. In addition, neXtProt has a powerful querying system based on semantic technologies that allows users to look for data not only in neXtProt but also in all semantically compatible life science resources; this enables very complex biological questions to be addressed.

The neXtProt platform hosts tools specifically designed for proteomics labs such as the peptide uniqueness checker, as well as third-party tools from the HUPO community. Recently, we launched new function prediction pages for the ~1500 human proteins that still lack functional annotation and are inviting HUPO researchers to share their functional predictions to accelerate their characterization.  See more information here.

What are your interests outside of the lab?

Outside of the lab, I am a professional music production manager (classical and contemporary music).  I also play the cello in various amateur chamber music ensembles.

Where do you envision the field of proteomics in the next 10 years?

Quantitative proteomics, PTM profiling and multi-omics technologies have become quite mature in research settings and have proven to deliver important and complementary information compared to genetic tools. One can expect that these powerful technologies will be more extensively used in clinical applications - especially in the cancer field. This will certainly be quite challenging in terms of procedure standardization. In parallel, protein databases will have to adapt to personalized medicine needs and switch from the concept of a single static human proteome to that of individualized and dynamic human proteomes.

Giuseppe Palmisano, Brazil


What is your current position and location?

I am currently Associate Professor at the Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil and at the Faculty of Natural Sciences, Macquarie University, Australia.

How did you get started in the field of proteomics?

During my Ph.D., I focused on understanding the phosphorylation of the mitochondrial complex I. My supervisor, Prof. Sergio Papa, an expert in mitochondria biology at the University of Bari (Italy) suggested the use of mass spectrometry as a tool to characterize the phosphorylation of specific subunits of complex I. At that time, I had no idea how to do it until I met my mentor Prof. Martin R. Larsen, an expert in PTMs analysis, who kindly hosted me in the Protein research group in Odense (Denmark), in a vibrant and inspiring atmosphere. That was my first “date” with Proteomics and since then, I never left.

What does being a member of HUPO mean to you?

Since 2010, my first HUPO conference, I have felt part of a community with a shared passion for proteomics, from method development to biological and clinical applications. Being a HUPO member means integration between researchers from diverse areas working in different locations worldwide. HUPO is also a community that continuously fosters the development of young researchers through many initiatives, such as the ECR.

What makes your research program exciting and unique?

In my laboratory, we aim at understanding how a pathogen interacts with vertebrate and invertebrate hosts. We focus on viruses and parasites causing (re)emerging diseases affecting people with poor access to infrastructures. My students and I are very excited to discover the language of this interaction using proteomics and other tools. We think there are unique opportunities to identify biomarkers and therapeutic targets for infectious diseases by looking at these biomolecules.

What are your interests outside of the lab?

I enjoy playing music. I am a saxophonist with a passion for jazz, bossa nova, nuevo tango and Italian opera. I can listen for hours to Charlie Parker, Tom Jobim, Astor Piazzolla and Giacomo Puccini’s music.

Where do you envision the field of proteomics in the next 10 years?

In the next ten years, I think that proteomics technologies, MS and beyond, will be more robust, easily accessible, and clinically approved. Seeing more biomarkers approved after proteomics studies will be an achievement with a profound benefit for public health. Moreover, I expect to see proteomics and other omics sciences part of more undergraduate courses to stimulate the interest of young generations.


Sanjeeva Srivastava, India

What is your current position and location?

Hi, I am Sanjeeva Srivastava, a professor at the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India. IIT Bombay is ranked an Institute of Eminence and number 1 rank in India. 

How did you get started in the field of proteomics?

I got into proteomics because I wanted to learn more about life's deepest secrets. The human genome study was getting accomplished just at the beginning of my research career. What surprised me was the genome's remarkably stable nature! There was little difference between the genomes of humans and chimpanzees and much less between individuals. Nonetheless, we see how unique each individual is. I realized that the mysteries of life's variety are embedded in the continually evolving proteome. It's no surprise that I was drawn to proteomics and decided to pursue it as research for my Ph.D. My first brush with proteomics research started during my Ph.D. studies at the University of Alberta (discovery proteomics using 2DE and MS), and later I gained deeper insights during my post-doctoral years with Prof. Joshua LaBaer at Harvard Medical School (functional proteomics using protein microarrays-NAPPA and Surface Plasmon Resonance).  

What does being a member of HUPO mean to you?

To me, HUPO has been instrumental in bringing together this thriving community of scientists with a shared enthusiasm for pushing the envelope of technologies and ideas, and it's an extraordinary feeling to be a part of this development. Most importantly, HUPO helped me embrace the diversity and engaged in scientific cooperation sans borders which are critical components for a scientist to keep innovating and be forward-thinking, both on and off the bench.

What makes your research program exciting and unique?

My research program's USP is willing to engage with real-world issues and understand the problem from a multi-omics perspective. I collaborate with a team of healthcare professionals on the proverbial "burning clinical problems" that our society faces. In our country, infectious disease is a significant problem. To uncover the biomarker candidates for diagnosis and prognosis, as well as the pathways involved for COVID-19, malaria, and dengue pathogenesis, I applied my multi-omics research expertise, mass spec, protein arrays and unique artificial intelligence-driven solutions. During the previous year, I significantly improved our understanding of the severity of COVID-19 in the Indian community. I used a multi-omics approach to unravel the biomarkers and pathways required for the prognostication and distinction of falciparum and vivax malaria from other febrile diseases. I discovered that the metabolite signatures of individuals with malaria and dengue fever may be used to distinguish between the two febrile infectious illnesses. Using metabolome analysis of infected patient sera, I was able to identify important regulatory mechanisms in severe vivax.In addition, I have made significant contributions to cancer proteomics in India. I'm using Artificial Neural Networking to find the most influential protein candidates that might help cancer patients be differentiated. In additional to our ongoing programs on brain tumors, as a part of ICPC, we are now currently engaged in few projects related to breast, cervical and oral cancer proteogenomics projects. 

What are your interests outside of the lab?

I have been very passionate about teaching since the very beginning. Outside of research, I carry on this passion. Teaching becomes a part of my job; however, my true love lies in popularising and demystifying the world of proteomics to resource limited students. India being a diverse country, not all people get access to information as specialized as proteomics. However, with the rapid growth of internet connectivity, I could connect to learners from all around the country. I conduct small training programs for school & college students to experience faculties to help them learn and adopt the new proteomics technologies. Further, I am passionate about proteomics education and outreach using documentary and videos which could be understood by the large audience with audio-visual aids. 

Where do you envision the field of proteomics in the next 10 years?

I anticipate a lot of changes, actually! What history has taught us, we would be doing something very different 10 years hence than what we are doing now. Remember, we primarily used to do gel-based proteomics a decade ago, and the field has changed a lot ever since. Broadly I hope the field is democratized with more labs joining forces, and proteomics no longer remains the fiefdom of a select few. I hope for more and more open-source, user-friendly computational analysis tools within the proteomics community, something like Skyline and MaxQuant. We also need better community-wide data validation methods that are so essential for the science of proteomics to get wider acceptance. Instrumentation wise I see a lot happening in the data collecting field that might ultimately lead to the standardizing experimentation workflows across labs, making data platforms less and less platform-agnostic, allowing proteomics to become as widespread and robust as genomics. However, one challenge that we need to work on is the development of emerging fields like single-cell proteomics and metaproteomics. We need to keep building bridges that would allow for proper integration of genomics, proteomics, and metabolomics datasets for easy and reproducible multi-omics research. Finally, I do see a very promising next decade for the proteomics and multi-omics field. 


Maria Robles, Germany

Photographer: Jan Greune

Website: https://www.imp.med.uni-muenchen.de/research-groups/robles/index.html

What is your current position and location?

I am a tenure-track professor at the Ludwig-Maximilians-University, Munich.

How did you get started in the field of proteomics?

After a postdoc in chronobiology in the lab of Charles Weitz at HMS Boston, I moved to Munich to work with Matthias Mann at the MPIB. I wanted to learn mass spectrometry-based quantitative proteomics and combine it with my interest in circadian biology. At that time, while it was well established that, in cells and tissues, circadian clocks drive rhythms of gene expression, daily dynamics of protein and/or post-translation modification abundance were largely undocumented.     

What does being a member of HUPO mean to you?

Being a HUPO member allows me to keep in contact with the proteomics community, get to know new methods, approaches and having an overview of the general direction in which the field moves.

What makes your research program exciting and unique?

My group is applying mass spectrometry-based quantitative proteomics to answer different questions in the circadian field. For example, we are studying, downstream of transcription, daily dynamics of protein and post-translational modifications shape the temporal compartmentalization of cellular and physiological processes. We are trying to understand how temporal control of protein abundance/function is at the core of rhythmic biological pathways in healthy stage but also how pathological conditions, such as cancer and sleep deprivation, impact protein dynamics and thus circadian fitness. In addition, we are combining temporal and spatial proteomics to investigate rhythms in whole cells/tissue but also in subcellular organelles.

What are your interests outside of the lab?

I dedicate most of the “little” free time I have outside the lab to my children, doing small trips during the weekends and traveling too long distance during our vacations.

Where do you envision the field of proteomics in the next 10 years?

I think the main two areas of proteomics that will greatly advance in the next years, that are already taking over now, are single cell and clinical proteomics.

Brian Searle, USA

Website: http://www.searlelab.org/

What is your current position and location?

I am currently an Assistant Professor in the Department of Biomedical Informatics at The Ohio State University in Columbus, Ohio, and a member of the Pelotonia Institute for Immuno-Oncology (PIIO).

How did you get started in the field of proteomics?

After undergrad, in 2001 I started as a Research Assistant at the Oregon Health and Sciences University under Dr. Srinivasa Nagalla, where I trained under my two mentors, Dr. Ashley McCormack (in mass spectrometry) and Mark Turner (in bioinformatics). Later in 2004, Ashley, Mark, and I started Proteome Software, where we produced the Scaffold software suite for analyzing proteomics data.

What does being a member of HUPO mean to you?

The first time I attended HUPO was in Munich, Germany, in the Fall of 2005. Here I met several scientists, such as the late Al Yergey, who would later become close collaborators and friends. I think that HUPO is an important home for like-minded scientists to meet, organize, and push the science of proteomics to new levels.

What makes your research program exciting and unique?

My lab spans the intersection between diverse aspects of proteomics, including mass spectrometry, bioinformatics, and technology development. We draw on multiple disciplines, often at the same time, to study human genetic variation in the backdrop of cancer. We get excited when we can answer a question about chemistry with bioinformatics or solve a problem in cancer biology with mass spectrometry tech dev.

What are your interests outside of the lab?

I am a ceramics artist and enjoy solo sports such as rock climbing and running. I am highly food motivated and am very susceptible to bribes of coffee and beer.

Where do you envision the field of proteomics in the next 10 years?

In ten years, advances in data acquisition approaches will normalize instruments such that specific measurement platforms will be less important, enabling bulk quantitative proteomics to become as common and as robust as bulk RNA-seq. The challenges over the next ten years will revolve around sensitivity (e.g., single-cell proteomics), sample complexity (e.g., metaproteomics and PTMs), and interpretation alongside other protein- and metabolite-level measurements (e.g., imaging).

Marlene Oeffinger, Canada

Website: oeffingerlab.org

What is your current position and location?

I am an Associated Research Professor at the Institut de recherches cliniques Montréal (IRCM) and Professeure-chercheure agrégée at the département de biochimie et médecine moléculaire, Université de Montréal.

How did you get started in the field of proteomics?

I first attempted proteomics during my PhD in David Tollervey’s lab in Edinburgh. Our initial goal was to characterize pre-ribosomal complexes from yeast by mass spectrometry. But  we weren’t very successful at it back then and the MS facility still in their optimization process. Needless to say, I changed my project. But I picked up those threads again as a post-doc in Mike Rout’s lab at Rockefeller, who had been successful at doing proteomics on the yeast nuclear pore complex. So I joined his lab to adopt and optimize his approaches to RNA-protein complexes, learning hands-on proteomics in Brian Chait’s lab.

What does being a member of HUPO mean to you?

To me, it means being part of a lively community that shares a common interest and excitement about pushing the technology and methods, both experimental and computational. But it also means being part of a community that values diversity, collaboration, and training – all of which, at least for me, are important components of a scientific community that is creative and progressive, on a scientific level and beyond.

What makes your research program exciting and unique?

I don’t know if it is unique, but in the lab, we definitely think it’s exciting.

Our research program is focused on understanding the plasticity and disease etiology of RNA-protein complexes. We are using proteomics to define their heterogenous compositions under ‘normal conditions’ and altered ones in response to external and internal changes or stress. But many of the changes and interactions are extremely dynamic, so we are developing and refining techniques such as crosslinking or differential affinity purification MS approaches to capture subtle changes but also wider interaction networks of cellular crosstalk.

What are your interests outside of the lab?

Reading, cooking, and yoga – in that order. Food and the arts have been important parts of my life, always. I love nothing more than a good book on philosophy, poetry or fiction to relax, or cooking a nice meal with my partner after a busy day. And for over two decades now, yoga has provided me with a great place to rebalance during stressful times. I wouldn’t want to miss it.

Where do you envision the field of proteomics in the next 10 years?

That is a hard question to answer. Within the proteomics community, I think – and hope – there will be more user-friendly computational analysis tools, better ways of data validation the community agrees on as a whole, and, most likely, there will be even more approaches and increasingly sensitive instruments, for better and worse. Within the wider scientific community, I would hope that proteomics loses the labels it has acquired in the past decade, of being risky, too broad, or just the thing core facilities do.





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