The document summarizes the editorial process for papers submitted to EMBO Scientific Publishing journals. It discusses how editors read submitted manuscripts in their entirety and make initial decisions based on factors like scope, novelty, and completeness of analysis. If a paper is sent for peer review, referees are selected based on expertise and reputation. Referees provide detailed reports evaluating the work. Editors may invite referee cross-commenting before making a final decision. The process aims to publish papers that will advance science while maintaining scientific integrity.
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EMBO Editorial Process
1. EMBO Scientific Publishing
Thomas Lemberger
Chief Editor, Molecular Systems Biology
Deputy Head of Publications, EMBO
1. Editorial Process
2. Scientific integrity
3. Integrating data in papers
2. Scientific
publishing
“The publication of scientific
information is intended to move
science forward. More
specifically, the act of publishing
is a quid pro quo in which
authors receive credit and
acknowledgment in exchange
for disclosure of their scientific
findings.”
11. EMBO Scientific Publications
• All areas of molecular &
cell biology
• All areas of molecular &
cell biology
• First journal launched by • Short-format papers
EMBO (1982)
• Science & Society
section
• Systems biology,
synthetic biology,
systems medicine
• At the interface between
basic and clinical life
sciences
• Open Access
• Open Access
14. OPEN
ACCESS
R Aebersold
GM Church
E Liu
L Hood
Scope & general
policies
Senior Editors
Advisory Board
P Bork
EMBO Editors:
Thomas Lemberger
Maria Polychronidou
Julie Ahringer
Charles Auffray
Ewan Birney
Tom Blundell
Thomas S. Deisboeck
Jan Ellenberg
Michael Elowitz
Alan Fersht
Stan Fields
Mark Gerstein
Frank Holstege
Sung Hou Kim
Hiroaki Kitano
Doron Lancet
Andrew J. Link
Stephen Oliver
Jeremy Nicholson
Bernhard Palsson
Rama Ranganathan
Uwe Sauer
Luis Serrano
Lucy Shapiro
Pamela Silver
Michael Snyder
Janet Thornton
Masaru Tomita
Marc Vidal
Hans V. Westerhoff
Lothar Willmitzer
John Yates
18. First editorial decision
EMBO editors read the entire manuscript (yes!)
Decision on a balance of multiple factors:
•
•
•
•
•
Scope
Novelty & conceptual advance
Mechanistic, functional, biological insights
Utility of methods, dataset, resource
Completeness and conclusiveness of the analysis
19. In case of doubt...
R Aebersold
GM Church
E Liu
L Hood
Senior Editors
Advisory Board
P Bork
EMBO Editors:
Thomas Lemberger
Maria Polychronidou
Julie Ahringer
Charles Auffray
Ewan Birney
Tom Blundell
Thomas S. Deisboeck
Jan Ellenberg
Michael Elowitz
Alan Fersht
Stan Fields
Mark Gerstein
Frank Holstege
Sung Hou Kim
Hiroaki Kitano
Doron Lancet
Andrew J. Link
Stephen Oliver
Jeremy Nicholson
Bernhard Palsson
Rama Ranganathan
Uwe Sauer
Luis Serrano
Lucy Shapiro
Pamela Silver
Michael Snyder
Janet Thornton
Masaru Tomita
Marc Vidal
Hans V. Westerhoff
Lothar Willmitzer
John Yates
21. To review or not to review...
time
review
editorial
rejection
reject
revise
reject
accept
22. Peer-review
Referees are invited based on:
• Balance of expertise
• Reputation as researcher
• Reputation as reviewer
• No conflict of interest (positive or negative)
3 (4) reviewers / manuscript
24. Referee report
1.
Summary
• Describe your understanding of the story
• What are the key conclusions: findings and concepts
• What are the methodology and model system
2.
General remarks
• Are you convinced of the key conclusions?
• Place the work in its context.
• What is the nature of the advance (conceptual, technical, clinical)?
• How important is the advance as compared to previous knowledge?
• What audience will be interested in this?
3.
Major points
• Specific criticisms related to key conclusions
• Specify experiments or analyses required to demonstrate the conclusions
• Motivate your critique with relevant citations and argumentation
4.
Minor points
• Easily addressable points
• Presentation and style
• Trivial mistakes
27. Cross-commenting
Ref #3
Ref #2
Ref #1
Ref #2 cross-comments
“…[it] settles a controversy in the field which has been going
on for more than ten years. In summary, this is a landmark
paper. I cannot support publication in your journal strongly
enough!”
“As written, the paper is focused on the methods, which is
fine given that's where it makes its most substantial
contribution. But the writing is quite technical and could
benefit from more explanation of the high-level logic of their
approach.”
“After reading through this nicely-executed technical work,
one is left with an impression that after all we really have not
gained much new mechanistic insights.
…in addition to the XXX data that should be generated
under their current framework…”
…Each reviewer has numerous suggestions about how to
do this. It will likely be impossible to incorporate them all
while retaining a coherent narrative. […]
Reviewer 3 also calls for an additional experiment including XXX stains in the current dataset. To incorporate
this into their current analytical framework, the authors
would have to find parameters and reagents to allow
simultaneous imaging of 5 genes (not just the 4 presented
here). Moreover, they would then have to reacquire all
images using the 5-stain protocol.
While I agree that it would be useful to have XXX data
included, I also believe that this is beyond the scope of this
paper.
29. Transparent Process
• Transparent Anonymous Peer Review:
Anonymous referee reports and editorial correspondence are published alongside papers
• Single Round of Major Revision:
More than 90% of invited revisions are published at Molecular Systems Biology
• Referee Discussion before Decision:
Referees are invited to comment on each other's reports before the editor makes a decision
• Scooping Protection:
Findings that are published by others during review or revision are not a criterion for rejection
• Source Data for Figures:
Authors can archive and make available the data underlying their published figures
• Flexible Formatting:
No journal-specific formatting required at submission
30. Scientific
publishing
“The publication of scientific
information is intended to move
science forward. More
specifically, the act of publishing
is a quid pro quo in which
authors receive credit and
acknowledgment in exchange
for disclosure of their scientific
findings.”
31. Scientific publishing
The publication of scientific information is intended to
move science forward. More specifically, the act of
publishing is a quid pro quo in which authors receive
credit and acknowledgment in exchange for
disclosure of their scientific findings.
Implies:
• Originality
• Integrity
• Authenticity
Respect of:
• Laws and ethics
• Safety and security
• Societal context
32. Data integrity
Beautification
• Clarification
• Aesthetics
Selective reporting
• Misrepresentation of the
data
• Biasing data to fit a
particular hypothesis
Fabrication
• Deliberate
manufacturin of
data
45. Seoul National University's report on Dr. Hwang Woo Suk:
The data in the 2005 article including test results from
• DNA fingerprinting,
• photographs of teratoma,
• embryoid bodies,
• MHC-HLA isotype matches and
• karyotyping
have all been fabricated.
http://www.useoul.edu/snunews?bm=v&bbsidx=71494&page=63
46. Figure 2F
Figure 6D
(F) NT-ESC colony with typical
morphology derived from a caffeinetreated SCNT human blastocyst.
(D) Human NT-ESCs expressed standard pluripotency
markers detected by immunocytochemistry for
antibodies against OCT4, NANOG, SOX2, SSEA-4,
TRA-1–60, and TRA-1–81. Original magnification, ×200;
Ph, phase contrast.
47. In Figures 2F and S5 (upper-right), we presented two phase-contrast photos of fields of cells, correctly labeled as SCNT-derived
hESO-NT1 and IVF-derived hESO-7, respectively. These images are the same fields of cells shown in the top two images of
Figure 6D; however, in Figure 6D, we inadvertently switched the labels on the images. This re-use of the images was intentional,
but we should have indicated this in the original legend for Figure 6. We have corrected the labeling error in Figure 6D.
We would also like to note that the Scientific Integrity Committee at Oregon Health & Science University has carefully assessed
the paper and the errors and has concluded that there is no evidence of fabrication, falsification, or plagiarism that would warrant
further inquiry or investigation into research misconduct.
Figure 2F
Figure 6D
(F) NT-ESC colony with typical
morphology derived from a caffeinetreated SCNT human blastocyst.
(D) Human NT-ESCs expressed standard pluripotency
markers detected by immunocytochemistry for
antibodies against OCT4, NANOG, SOX2, SSEA-4,
TRA-1–60, and TRA-1–81. Original magnification, ×200;
Ph, phase contrast. Note that the upper-left image for
hESO-NT1 is the same shown in Figure 2F.
48. What can PIs do?
•
•
•
•
•
•
•
Provide guidance to students and postdocs
View original data
Organize good data management practice
Maintain an open lab environment
Accept only relevant authorship
Cooperate with editors
Retract/correct as appropriate
49. What can journals do?
•
•
•
•
Rigorous peer review
Check by editors before publication
Investigation and retraction policy
Data transparency
55. • Data archival service
• Data‘transparency‟
• Data reuse
• Data-oriented search
56. 15/27
Structured metadata:
„perturbation-observation-assay‟
(Level 0:metadata associated to individual panels.)
Level 1: „object-oriented‟ representation of
experimental variables as a list of chemical
and biological components.
Level 2: represent the causality of the experimental
design: “Measurement of Y as a function of A,
B, C, using assay P in biological system S.”
Level 3: machine-readable representation with
standard identifiers.
experimental system
perturbed
component
measured
component
assayed
property
57. 9/27
SourceData
Tools to publish figures as structured digital objects
that link the human-readable illustrations with
machine-readable metadata and „source data‟ in
order to
•improve data transparency;
•make published data useable;
•enable data-oriented search.
58. 19/27
drug Z
activity
kinase Y
kinase Y
protein X
Paper 3
Paper 2
Paper 1
Data-oriented search
gene x
P
tissue T
disease
D
Resulting hypothesis: test drug Z in disease D.
60. Scientific publishing
• Dominant channel for the
dissemination of peer-reviewed
data.
• Journals function as a proxy for
quality in research assessment
• The rate of publishing keeps
increasing.
• Papers are human-readable but
poorly machine-readable.
62. The Paper of the Future?
Search
<!DOCTYPE article PUBLIC "-//NLM//DTD
Journal Archiving and Interchange DTD v2.3
20070202//EN" "archivearticle.dtd">
<article article-type="researcharticle"><?properties no_embargo?>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Mol Syst
Biol</journal-id>
<journal-title>Molecular Systems
Biology</journal-title>
<issn pub-type="epub">1744-4292</issn>
<publisher>
<publisher-name>Nature Publishing
Group</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-idtype="pmc">2238715</article-id>
Data
Methods
Claims
Authors
Models
63.
64.
65. Future directions in systems biology
• Genome-wide genetics of human diseases
• Translational systems biology or systems
medicine
• Genome-scale engineering & synthetic biology
• Temporal structure of biological processes
• ‘In vivo biochemistry’ with single-cell singlemolecule assays
• Bridge the gap between ‘omics’ and mechanistic
models
66.
67. “How do we get from the
Jimome & Craigome to
systems biology?”
George M Church, Senior Editor
68. Multi-omics data integration
Global analysis of genome, transcriptome and
proteome reveals the response to aneuploidy in
human cells.
Zuzana Storchova, Mol Syst Biol. 2012 8:608.
Integration of clinical data with a genome-scale metabolic model of the
human adipocyte.
Jens Nielsen and colleagues, Mol Syst Biol. 2013;9:649.
69. Comparative omics for functional discoveries
Human disease locus
discovery and mapping to
molecular pathways through
phylogenetic profiling.
Gary Ruvkun and colleagues,
Mol Syst Biol. 2013 9:692
19 017 human genes
Phylogenetic profiles of across 86 eukaryotic genomes.
71. Spatial patterns
Waks et al, 2011 Mol Syst Biol 7:506
Di Vetura and Sourjik , 2011 Mol Syst Biol 7:457
72. Temporal patterns
Promoter decoding of transcription factor dynamics involves a tradeoff between noise and control of gene expression.
Hansen AS, O'Shea EK. Mol Syst Biol. 2013 9:704
73. Cell population & dynamics
Digital cell quantification identifies global immune cell dynamics during influenza
infection.
Ido Amit and colleagues, 2014 Mol Syst Biol. 10:720
74. Microbiome & metagenomics
A top-down systems biology view of microbiomemammalian metabolic interactions in a mouse
model.
J. Nicholson and colleagues, Mol Syst Biol. 2007 3:112.
Toward molecular trait-based ecology through integration of
biogeochemical, geographical and metagenomic data.
Peer Bork and colleagues, Mol Syst Biol. 2011 7:473