Thanks Google Scholar Updates for new article to read .. wish you had an #openaccess only setting

I have a new friend in Google Scholar Updates

I have written about the Updates system before and if you want more information please see this post: The Tree of Life: Wow – Google Scholar “Updates” a big step forward …

Alas, it is imperfect in my mind for I went to try to read this article and boom – $32 for a day’s access

Now I am really wishing Google Scholar had an “show me only open access” articles option.

Wow – Google Scholar "Updates" a big step forward in sifting through the scientific literature

I logged on to Google Scholar a few minutes ago and discovered something very new

This “updates” thing was not there earlier in the day.  So I clicked on the link and got to this page: Scholar Updates: Making New Connections – Google Scholar Blog where James Connor from Google reports

Since Google Scholar launched nearly eight years ago, we’ve been helping people find the research they’re looking for.  But often the spark for discovery comes from making a new connection or looking in a direction that you hadn’t yet considered and that — before your aha! moment — you wouldn’t have known to look for.  Today we hope to start fostering these new connections with Scholar Updates. 

We analyze your articles (as identified in your Scholar profile), scan the entire web looking for new articles relevant to your research, and then show you the most relevant articles when you visit Scholar.  We determine relevance using a statistical model that incorporates what your work is about, the citation graph between articles, the fact that interests can change over time, and the authors you work with and cite.  You don’t need to configure updates or enter any queries.  We’ll notify you about new updates by displaying a preview on the homepage and highlighting a bell icon on search results pages: …

To get article updates relevant to your work, all you need to do is create a public Scholar profile. Article updates will automatically start to appear within a few days. 

Wow.  Completely awesome if it works well.  So, well, let’s see if it works well.  For me the system recommends the following

Evolutionary Diversity of the Mitochondrial Calcium UniporterAG Bick, SE Calvo… – Science, 2012 

REGEN: Ancestral Genome Reconstruction for BacteriaK Yang, LS Heath… – Genes, 2012

Both have some relevance to me.  The first one is about evolution of a gene family and has a line in the abstract that clearly might have driven the automated suggestion: “Here, we characterize the phylogenomic distribution of the uniporter’s membrane-spanning pore subunit (MCU) and regulatory partner (MICU1).” But, well, I am not too interested in this paper.  Not really my thing.

But paper number 2 seems a bit closer to my heart: REGEN: Ancestral Genome Reconstruction for Bacteria.  And bonus – it is freely available.  And so, well, I read over it.  And it is definitely related to what I do and I probably would not have seen it without this notification.  Cool.
So I give Scholar Updates a 1.5 / 2 score which translates to a 7.5 out of 10.  Not bad.  But could be better.  So I clicked on the “See all Updates” link to see what else was there.  And this was a pleasant surprise.  Here is what I got (showing the first page).
50 papers in all with the “Top” selection selected at the top of the page.  And some even come with a comment like Cites A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea or 
The first 25 of the papers are listed below:
  1. Defining the human microbiome
  2. Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities
  3. VIROME: a standard operating procedure for analysis of viral metagenome sequences
  4. Complete Genome Sequence of Paenibacillus strain Y4. 12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park
  5. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat
  6. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov.
  7. Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov.
  8. Complete genome sequence of Pyrobaculum oguniense
  9. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NALT)
  10. The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness
  11. Complete genome sequence of the aromatic-degrading deep-terrestrial-subsurface alphaproteobacterium Novosphingobium aromaticivorans type strain (F199 T), …
  12. Complete genome sequence of Thauera aminoaromatica strain MZ1T
  13. Non-contiguous finished genome sequence and description of Anaerococcus vaginalis
  14. Non-contiguous finished genome sequence and description of Alistipes senegalensis sp. nov.
  15. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton
  16. Predicting kinase-substrate interactions in the era of proteomics
  17. REGEN: Ancestral Genome Reconstruction for Bacteria
  18. Targeted recovery of novel phylogenetic diversity from next-generation sequence data
  19. A call for an international network of genomic observatories (GOs)
  20. Large and linked in scientific publishing
  21. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
  22. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
  23. Ultrafast clustering algorithms for metagenomic sequence analysis
  24. IMG/M-HMP: A Metagenome Comparative Analysis System for the Human Microbiome Project
  25. Microbiomes
  26. Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan‐Vavilov Deep
  27. Distance-Decay diversity patterns of phyllosphere bacteria on Tamarisk trees across the Sonoran Desert
  28. Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure
  29. Reconstruction of Ribosomal RNA Genes from Metagenomic Data
  30. Genome Sequence of the Unclassified Marine Gammaproteobacterium BDW918
  31. Surprising results on phylogenetic tree building methods based on molecular sequences
  32. Road map of the phylum Actinobacteria
  33. Building non-coding RNA families
  34. Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures
  35. Metagenomic microbial community profiling using unique clade-specific marker genes
  36. Unlocking the potential of metagenomics through replicated experimental design
  37. Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem
  38. Minimizing the average distance to a closest leaf in a phylogenetic tree
  39. Parallel-META: efficient metagenomic data analysis based on high-performance computation
  40. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to “Dehalococcoides” strains
  41. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT)
  42. Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15T
  43. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)
  44. Evolutionary Diversity of the Mitochondrial Calcium Uniporter
  45. Phylogenetic Clustering Reveals Selective Events Driving the Turnover of Bacterial Community in Alpine Tundra Soils
  46. A comparative evaluation of sequence classification programs
  47. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1T)
  48. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as …
  49. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4T)
  50. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1)
And well, I’ll be damned.  I kind of want to read almost all of them.  Son based on the top 50 I would give Scholar Updates a score of something like 47/50 or 9.4 / 10.  Many have complained about the limited developments in Google Scholar over the years but this is definitely a nice development.  I hope it means Google will be putting more effort into other developments.
Now – off to read some papers.  And if you do not have a Google Scholar page – you should definitely think about making one now as this is how you open up this feature.

UPDATE 1 8/9 1:45 AM

Just noticed that now in the top of the page when I go to Google Scholar there is also now a link to “Updates”

UPDATE 2: 8/9 10 AM – Some other posts about this

UPDATE 3: 8/9 10 AM – Other stuff from around the web about this

MoreCite Feed from my Google Citations Page

Just got an email from someone at describing a simple widget they have made to display information from one’s Google Citation page. So I took the bait .. and two minutes later I have a feed: This is not an endorsement of MoreCite.Com. I know very little of what they are about. But I like the little widget …

Google scholar missing paper issue clarified, though not corrected, but glad Google responded

Below is a thread relating to a reference missing from Google Scholar

Subject: Missing reference in Google Scholar
Date: Sat, 24 Dec 2011 15:12:07 +0000

The following important and highly cited reference is somehow missing from Google Scholar although it was there a few months ago – it would be useful to have it back:

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana 

Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Eisen JA, Salzberg SL, Fraser CM, Venter JC.

Nature. 1999 Dec 16;402(6763):761-8.

PMID: 10617197 [PubMed – indexed for MEDLINE]

Thanks for your recent email to Google Scholar. We’ve included answers to a number of frequently asked questions in our response below. If you have a question or concern that is not addressed by these answers, please reply to this email for further assistance.

Adding content to Google Scholar:
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Incorrect bibliographic information in Google Scholar results:
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I can’t find my paper anymore! My citation count has gone down!
That can happen because we index scholarly articles available to us on the Web, and the Web changes. Chances are that some website that used to host your paper or papers that cite it no longer do so. Please contact your publisher about adding your papers or correcting their bibliographic data. Unfortunately, we’re unable to include papers that are no longer available on the Web.

Two of my papers are listed as one… Some citations aren’t counted…
Please reply to this message with detailed examples of the problem. Please include the queries you used as well as the specific articles in question. Google Scholar is based on automated indexing algorithms. We’re unable to make individual changes, but specific examples will help improve the automated techniques and will result in improved results for all users.

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We’re working hard to provide easy access to scholarly literature, and your feedback will assist us in improving this program.

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My concern is not addressed by these answers.  My concern is that I am an author on a paper that is listed in Pubmed and used to be listed on Google Scholar but it has disappeared for some reason.  The citation is below.  It is a reasonably important biology paper and thus it would  be good in general (and good for me) if it could be “rescued” and show up in Google Scholar again.  Thanks

Jonathan Eisen

Hello Jonathan,

In this case the clustering algorithm mis-detected two articles with
similar metadata as being the same article, which you can see at:,5

We’re not currently able to perform manual correction on individual
entries in our database since the indexing is done automatically by
robots, but we use examples like this one as we continue to improve the clustering algorithm. Thanks for letting us know about the issue.


The Google Scholar Team