Wednesday, 9 October 2013

My List of Most Influential Authors in Computational Proteomics (according to Articles References, Google Scholar, twitter, Linkedin, Microsoft Academic Search and ResearchGate)

Young researchers starting their careers will often look for reviews, opinions and research manuscripts from the most influential authors of their chosen field. In science, however, unlike many other topics on the Internet, ranked lists or manuscript repositories of top authors sorted by research topic are hard to come by. For some researchers, the idea of such a task brings the words ‘wasted time’ to their minds; the most critical condemn it as a frivolous pursuit. Maybe so. In my opinion, however, it as an excellent starting point.

ResearchGate Home page
Home Page of ResearchGate with more than 3 millions of users

These days, more people than ever are involved in science and research. Just look at ResearchGate’s homepage.  There are over 3 million persons there –and we’re only counting ResearchGate users. Once simple undertakings, such as finding the right manuscript to cite, the most authoritative group on a topic, or the best software application for a specific task, have become increasingly difficult for graduate students navigating this ocean of data, despite the availability of services such as Google Scholar or Pubmed. The situation will only worsen in the future, as is easy to see by simply tallying the number of  published papers in the fields of Proteomics, Genomics, Bioinformatics and Computational Proteomics since 1997:

Number of published manuscripts in Pubmed per year (1997-2012). the statistics was done using the Medline Trend Service http://dan.corlan.net/medline-trend.html

In 2012 alone, over 6,000 and 17,000 manuscripts were published in the fields of proteomics and bioinformatics, respectively. Our young field, computational proteomics, published more than four hundred papers. Perhaps well-established PI’s or Group Leaders can easily tell apart derivative or me-too contributions from groundbreaking work, but young scientists, who spend most of their time implementing someone else’s ideas, can certainly have a hard time doing so. Although technology has come to the rescue with today’s mixture of search engines and social networking tools (ResearchGate, Google Scholar, twitter and LinkedIn among them), the best way to harness its power is, precisely, by starting from a ranked list of the most authoritative voices within a field of research, whose whereabouts can then be traced in the scientific literature, the blogosphere, and anywhere else.




Be forewarned that I work mainly on proteomics data storage and management and peptide/protein identification algorithms, so it will probably be a bit biased. I recently made a simple study about my PhD References and also the references in my published manuscripts.   I developed and used different tools to draw my references network and see the name of my most influential authors in computational proteomics. The analysis gives me a perfect pictures of which authors I follow by topics. For example, Alexey Nesvizhskii was cited in my manuscripts each time that I wrote about proteomics statistics, and peptide/protein validation. The analysis also showed that Professor Aebersold contributed in different sub-networks in computational proteomics (proteomics statistics, proteomics repositories and target Computational Proteomics). Jean-Charles Sanchez connected my electrophoresis networks (Electrophoresis and Isoelectric Point estimation).


Sub-Networks of my PhD Thesis References and manuscripts.



What follows is a list of the most influential authors in computationalproteomics , from my point of view as a PhD student, put together with the help of the fine minds behind Google Scholar and tweaked further with ResearchGate, twitter and LinkedIn. I created the list using an h-index from google scholar and also ISI Web, picking group leaders and, occasionally, some post-docs as well. Here’s hoping that you (the reader) can help me expand it.



Knights of the Round Table


Albert JR Heck
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center and Utrecht Institute
Cited by 16376
h-index: 66
http://bioms.chem.uu.nl/ 
http://en.wikipedia.org/wiki/Albert_J.R._Heck
John R. Yates
The Scripps Research Institute, Department of Chemical Physiology
Cited by 51877 (ISI Web)
h-index: 110     (ISI Web)
fields.scripps.edu/
en.wikipedia.org/wiki/John_R._Yates
Matthias Mann
Director at the Max Planck Institute of Biochemistry
Cited by 121301  
h-index: 163
http://en.wikipedia.org/wiki/Matthias_Mann
http://www.biochem.mpg.de/en/rd/mann
Richard D. Smith
Biological Sciences Division Battelle Fellow Pacific Northwest National Laboratory
Cited by 62357 (ISI Web)
h-index: 112     (ISI Web)
http://www.pnl.gov/science/staff/staff_info.asp?staff_num=5832
http://en.wikipedia.org/wiki/Richard_D._Smith
Ruedi Aebersold
Institute of Molecular Systems Biology
Cited by 61868 (ISI Web)
h-index: 116 (ISI Web)
http://www.imsb.ethz.ch/researchgroup/rudolfa
http://en.wikipedia.org/wiki/Ruedi_Aebersold


Alexey Nesvizhskii
Associate Professor, University of Michigan
Cited by 10501
h-index: 38
http://www.nesvilab.org/
Topics: Peptide/Protein Validation, Protein Inference, PeptideAtlas
Amos Bairoch
Professor of Bioinformatics, University of Geneva and group leader, SIB Swiss Institute of Bioinformatics
Cited by 44700
h-index: 88  
http://en.wikipedia.org/wiki/Amos_Bairoch
http://www.isb-sib.ch/
twitter:@calipho2
Topics:UNIPROT, Expasy, PROSITE

Andrej Shevchenko
MPI of Molecular Cell Biology and Genetics, Dresden
Cited by 33479
h-index: 80

http://www.mpi-cbg.de/research/research-groups/andrej-shevchenko/research-focus.html
Topics: Sequence Tag, Homology Identification, Lipidomics

Bin Ma
Professor of Computer Science, University of Waterloo
Cited by 10713
h-index:33
https://cs.uwaterloo.ca/~binma/
Topics: Homology Search, De novo Sequencing,
Tools: Peaks, PatternHunter

David Fenyo
Associate Professor, New York University Medical Center
Cited by 3164 (ISI Web)
h-index: 30     (ISI Web)
http://www.fenyolab.org/
Topics:Protein Identification, Proteomics Repositories, Tools: X!Tandem, GPMDB,

David L. Tabb
Associate Professor of Biomedical Informatics, Vanderbilt University
Cited by 5576 
h-index: 32
http://fenchurch.mc.vanderbilt.edu/
Topics:Protein Identification, Sequence Tag, Protein/Peptide Validation,
Tools: DirecTag, MyriMatch, IDPicker 3

Eric Deutsch
Institute for Systems Biology
Cited by 7131
h-index:42
http://db.systemsbiology.net/users/edeutsch/ 
Topics: Proteomics Databases, Proteomics Standards, Bioinformatics Workflows
Tools:PeptideAtlas, TPP

Henning Hermjakob
Team Leader Proteomics Services
Cited by 27431
h-index: 46
http://www.ebi.ac.uk/about/people/henning-hermjakob
twitter:@pride_ebi, @intact_project
Topics: PRIDE, INTACT, REACTOME, Proteomics Standards
Jean-Charles Sanchez
Biomedical Proteomics Research Group (BPRG), Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
Cited by *
h-index: *
Topics: Electrophoresis, 2D, Expasy,
Jimmy K. Eng
University of Washington, Proteomics Resource
Cited by 24208
h-index: 64
http://proteomicsresource.washington.edu/index.php
Topics:Protein Identification, MS/MS search, Peptide/Protein validation,
Tools:Sequest 

Juan Antonio Vizcaino
PRIDE Group Coordinator, EMBL-EBI
Cited by 1451
h-index: 21
http://www.ebi.ac.uk/pride/
@juan_vizcaino
Topics: PRIDE, Proteomics Repositories, Quality Control
Tools: PRIDE

Juergen Cox
Max Planck Institute for Biochemistry
Cited by 6802
h-index: 40
http://www.biochem.mpg.de/en/rd/mann
twitter: @maxquant
Topics:Protein Identification , Protein Quantitation
Tools: Andromeda, MaxQuant
Lennart Martens
Professor of Systems Biology, Ghent University and VIB, Ghent, Belgium
Cited by 5004
h-index: 35
http://compomics.com/
twitter: @compomics
Topics: Protein Validation, Repositories, Peptide Centric Databases, Lims, Quality Control, Proteomics Standards

Lukas Käll
Assistant Professor, Royal Institute of Technology (KTH)
Cited by 2392
h-index: 17

Topics: Protein Validation, Repositories
 Percolator







Nuno Bandeira
Executive director, NCRR/NIH Biomedical Technology Research Center for Computational Mass Spectrometry
Cited by 630 (ISI Web)
h-index: 16   (ISI Web)
http://cseweb.ucsd.edu/~nbandeir/
Topics: Spectral Networks, Spectral Dictionaries







Michael MacCoss
Associate Professor of Genome Sciences, University of Washington
Cited by 7895
h-index: 46
http://proteome.gs.washington.edu/
twitter:@mjmaccoss
Topics: Target Proteomics, Quantitation, Protein/Peptide Validation 
Tools: Skyline, Percolator


Paulo Costa Carvalho
Research Scientist at Carlos Chagas Institute, Fiocruz - Paraná, Brazil
Cited by 493
h-index: 12
http://pcarvalho.com/patternlab/
Topics: Peptide/Protein Identification, Bioinformatics Workflow 
Tools: PatternLab

Pavel Pevzner
Professor of Computer Science
Cited by 20575
h-index: 65
http://en.wikipedia.org/wiki/Pavel_A._Pevzner
http://cseweb.ucsd.edu/~ppevzner/
Topics:De novo Sequencing, PTMs Identification, Fragment Assembly


Robert Moritz
Associate Professor, Institute for Systems Biology
Cited by 11605
h-index: 54
http://www.systemsbiology.org/moritz-group 
Topics:PeptideAtlas, Bioinformatics Workflows, Peptide/Protein validation


Ronald Beavis
President Beavis Informatics Ltd
Cited by 7512 (ISI Web)
h-index: 36     (ISI Web)
http://www.beavisinformatics.ca/
twitter: @GPMDB
Topics:Protein Identification, Proteomics Repositories, Tools: X!Tandem, GPMDB,



Ron D. Appel
Executive Director, SIB Swiss Institute of Bioinformatics
Cited by 1196
h-index: 45
http://en.wikipedia.org/wiki/Ron_Appel
http://www.isb-sib.ch/aboutsib/organisation/management.html
Topics: Databases, Proteomic Services, Protein Identification,






Rolf Apweiler
Associate Director and Senior Scientist (EBI)
Cited by 22446
h-index: 62 (ISI Web)
http://www.ebi.ac.uk/about/people/rolf-apweiler
http://www.uniprot.org/help/apweiler
Topics: Databases, Proteomic Services,



Oliver Kohlbacher
Professor for Applied Bioinformatics, University of Tübingen
Cited by 3322
h-index: 31
http://abi.inf.uni-tuebingen.de/ 
Topics: Visualization Omics Data, Bioinformatics Workflows
Tools: OpenMS



William Stafford Noble
Professor of Genome Sciences, University of Washington
Cited by 17430
h-index: 59
http://noble.gs.washington.edu/~wnoble/
Topics: Protein Validation, kernel & SVM Methods, Protein-Protein Interactions


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What do you think?