Hippocamplus My Second Memory

Journal comparison

Feb 23 2018 pub

Edit Feb 24: Added variance graph and some examples of suspiciously fast publications.

Edit Feb 25: Added script and data to GitHub.

Some info about journals in my field.

Summary table

Journal Co. IF OA APC Other fees Pub/year Received-to-accepted in days. median (75th perc.)
F1000Research - 1.2 Y 1000 USD -
PeerJ - 2.2 Y 1095 USD - ~1290 ~88 (139)
eLife - 7.8 Y 2500 USD - 1018 121 (155)
GigaScience OUP 4.9 Y 2050 USD - ~50 ~126 (195)
PLoS One PLoS 2.8 Y 1495 USD - ~22K ~122 (182)
PLoS Comp Bio PLoS 4.5 Y 2250 USD - ~550 ~159 (217)
PLoS Genetics PLoS 6.1 Y 2250 USD - 644 150 (202)
PLoS Biology PLoS 9.8 Y 2900 USD - ~176 ~141 (175)
BMC Bioinformatics BMC/S 2.5 Y 2145 USD - ~333 ~169 (231)
BMC Genomics BMC/S 3.7 Y 2145 USD - ~985 ~138 (190)
BMC Biology BMC/S 6.8 Y 2785 USD - ~85 ~70 (108)
Genome Biology BMC/S 11.9 Y 2975 USD - ~156 ~106 (143)
Cell Reports Els 8.3 Y 5000 USD - ~1005 ~168 (241)
Scientific Reports Spr 4.3 Y 1760 USD - ~20K ~104 (151)
Nature Communications Spr 12.1 Y 5200 USD - ~3519 ~168 (228)
NAR OUP 10.2 Y 2770 USD pp9 ~1359 ~82 (131)
Genetics - 4.6 12m/+ 2000 USD pp/pf/psf ~374 ~104 (163)
AJHG Els 9.0 6m/+ 5000 USD 850 USD + pf 237 89 (121)
PNAS HWP 9.7 6m/+ 1450 USD 1700 USD
Genome Research CSH 11.9 6m/+ 2500 USD 2500 USD ~179 ~188 (242)
Cell Els 30.4 (12m/+) 5000 USD pf ~351 ~149 (193)
Lancet Els 47.8 6m/+ 5000 USD
Science AAAS 37.2 12m - surprise ~720 ~112 (162)
Bioinformatics OUP 7.3 + 3000 USD pp7/pf ~868 ~126 (180)
New England Journal Of Medicine - 72.4 6m -
Nature Methods_ Spr 25.1 N - pf ~130 ~146 (187)
Nature Genetics Spr 28.0 N - pf 202 147 (203)
Nature Biotech Spr 41.7 N - pp5/pf 80 202 (262)
Nature Spr 40.1 N - ~855 ~175 (246)

Open Access (OA) journal:

  • Y: Yes.
  • +: Authors can pay additional Article Processing Charges (column APC) to make it accessible immediately upon publication.
  • 12m: Articles are accessible after 12 months, either from the journal or PubMed Central/
  • 6m: Articles are accessible after 6 months, either from the journal or PubMed Central.
  • (): Depending on the funding agencies.
  • N: No.

Fees:

  • pp: Per page.
  • ppX: Per pages in excess of X (if more than X pages).
  • pf: Per figure.
  • psf: Per supplementary file.

Sources

Received-to-accepted time and Pub/year are based on articles published in 2016. After a PubMed search, the publication web-page was crawled to get the article type and dates of reception/acceptance. I considered research articles/letters/methods/reports but not reviews/editorial/perspective/erratum/opinion. Sometimes the DOI was not present in the PubMed results or there was a lot of publications to crawl so I analyzed a subset and extrapolated the numbers (~ marks approximated numbers). I still see some suspicious numbers (articles with very short/negative acceptance time). Hopefully the medians are still close to reality but these numbers should be taken with a grain of salt.

Some data has been produced, now it’s graph time !

Median time to acceptance/publication

Median time to acceptance/publication vs number of article published

Median time to acceptance/publication vs impact factor

I’m curious to see if it takes more time in some cases because a journal is more “picky” ?

The impact factor is not a good indicator of research impact but maybe it can be a proxy for a journal’s pickiness. Looking at the correlation with the impact factor, there’s a trend (with or without the first tier journals). Still, the journals are quite spread out.

Variance in time to acceptance

The ranking using the 75th percentile is not so different than the one using the median.

We see some publications with suspiciously short received-to-accepted times…

Suspiciously short received-to-accepted times

I’m not sure how each journal defines “received”. Some publications have acceptance times too short to be the peer-review time.

I even found two papers that have negative received-to-accepted times… In both the webpage and the PDFs, these papers were published 3 months before they were submitted: 10.1534/genetics.115.183194 and 10.1534/genetics.115.185181.

Anyway, looking at a few examples for each journal, some of the “fast” publications are about resources (databases, portal, websites) which makes sense, others look like research that would require peer-review longer than a few days…

For example, the “fastest” publications for each journal (among the publications I considered):

Days to acceptance Journal Title
1 Genome Biology OncoNEM: inferring tumor evolution from single-cell sequencing data.
3 PLoS Genet. Tbx5 Buffers Inherent Left/Right Asymmetry Ensuring Symmetric Forelimb Formation.
4 eLife Lysosomal membrane glycoproteins bind cholesterol and contribute to lysosomal cholesterol export.
4 PeerJ Ectopic expression of Jatropha curcas APETALA1 (JcAP1) caused early flowering in Arabidopsis, but not in Jatropha.
5 Genetics Identifying Regulators of Morphogenesis Common to Vertebrate Neural Tube Closure and Caenorhabditis elegans Gastrulation.
9 NAR PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
10 GigaScience RES-Scanner: a software package for genome-wide identification of RNA-editing sites.
11 PLoS ONE Time-Resolved Visualisation of Nearly-Native Influenza A Virus Progeny Ribonucleoproteins and Their Individual Components in Live Infected Cells.
15 PLoS Biology The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation.
15 BMC Biology Nuclear fallout provides a new link between aPKC and polarized cell trafficking.
17 Bioinformatics iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition.
19 Science Selective conversion of syngas to light olefins.
20 Am J Hum Genet. The Power of Human Protective Modifiers: PLS3 and CORO1C Unravel Impaired Endocytosis in Spinal Muscular Atrophy and Rescue SMA Phenotype.
20 Cell Reports Structures of NS5 Methyltransferase from Zika Virus.
22 PLoS Comput Biol Direct Correlation between Motile Behavior and Protein Abundance in Single Cells.
22 Nature Communications Switchable friction enabled by nanoscale self-assembly on graphene.
24 Scientific Reports Aero-Thermo-Dynamic Mass Analysis.
25 Nature Non-classical correlations between single photons and phonons from a mechanical oscillator.
26 Cell Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator.
28 Nature Methods ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.
30 BMC Genomics Suboptimal culture conditions induce more deviations in gene expression in male than female bovine blastocysts.
38 Nature Genetics Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley.
43 BMC Bioinformatics ksRepo: a generalized platform for computational drug repositioning.
59 Nature Biotech Blood pressure regulation by CD4(+) lymphocytes expressing choline acetyltransferase.
94 Genome Research Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism.

Script and data

I someone wants to do the same for other journals, I put my script there. The data I used is also there in a TSV file.

“Good” journals

  • eLife is non-profit, open and modern.
  • PLOS the pioneer in open-access.
  • BMC, although it’s owned by Springer Nature publishing group.
  • F1000 where the manuscript is “published” right away and then transparently peer-reviewed. Once peer-reviewed, it is indexed in PubMed etc.
  • PeerJ is about open-access and cost-efficient publishing.

“Evil” publishing companies

  • Elsevier.
  • Springer Nature.