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What Matters: Balance Between Coverage and Sequencing Costs (Sebastian Jünemann, 18 September 2014)

Nice and very interesting paper! We agree on everything especially on the performance of the assemblers and the observed sub-sampling effects. Hence, we want highlight that we just published a de novo assembler comparison, which are corroborating your conclusions [PLoS ONE 9(9): e107014, 2014]. Albeit we didn't have the opportunity to include the PacBio system in our study, we used a wider range of assemblers, three different bacterial references, and more data... read full comment

Comment on: Miyamoto et al. BMC Genomics, 15:699

Correction to article title in citation 13, Peterlongo et al. (Dan MacLean, 09 July 2014)

The correct citation for Peterlongo et al, [13] in this article is    Peterlongo, P., Schnel, N., Pisanti, N., Sagot, M.-F., Lacroix, V.: Identifying SNPs without a reference genome by comparing raw reads. In: Chavez, E., Lonardi, S. (eds.) String Processing and Information Retrieval. Lecture Notes in Computer Science, Springer Berlin Heidelberg, vol. 6393, pp. 147–158 (2010) read full comment

Comment on: Leggett et al. BMC Genomics, 15:S10

Correction on Matsumoto et al, BMC Genomics, 14: 808 (Tetsuya Yomo, 24 March 2014)

A mistake in the order of the data sets was found. Re-analyses were performed to verify all the results and conclusions presented in the paper. The corrections in the numbers of the genes in C1, C2 and C3, along with some statistic values were made. Some figures and tables were revised accordingly. There are no changes in the interpretation of the results and conclusions. A revised version of the paper can be found in the following pages.
http://www-symbio.ist.osaka-u.ac.jp/en/publications/articles/Comment_on_Matsumoto_2013.pdf read full comment

Comment on: Matsumoto et al. BMC Genomics, 14:808

Correction for paclitaxel extraction (Deyou Qiu, 24 March 2014)

Culture broth was extracted with dichloromethane and mycelia was freeze-dried, pulverized and extracted with dichloromethane. Solvent was removed by reduced pressure at 36°C and the extracts were pooled. To the final crude extract, 0.344 g, 50 mL of water was added, and the mixture separated on C-18 cartridge (Fisher) with vacuum. Methanol was used to rinse the C-18 cartridge and elute the solution that contains paclitaxel. The methanol solution was dried (0.256 g) and dissolved in methanol or acetonitrile to 200 μg/μL after which it was filtered through a 0.45 nm filter. read full comment

Comment on: Yang et al. BMC Genomics, 15:69

Figure 1 legend (Aaron Liston, 11 March 2014)

Both the x and y axes in Figure 1A & B are labelled "replicate 1".  Shouldn't one axis be "replicate 2"?   read full comment

Comment on: Busby et al. BMC Genomics, 12:635

Minor modifications to text (Philipp Schiffer, 03 March 2014)

The article should be changed at two points:
1. The sentence
Genomic DNA was extracted from several hundred, mixed-sex, adult R. culicivorax specimens from a culture first established in Ed Platzer’s laboratory in Riverside, California.
should read
Genomic DNA was extracted from several hundred, mixed-sex, adult R. culicivorax specimens from a culture first established in Edward Platzer’s laboratory, University of California, Riverside.
2. The sentence
We are indebted to E. Platzer, Riverside, for the continuous supply with R. culcivorax nematodes.
should read
We are indepted to Dr. E. Platzer, University of California, Riverside, Dept. of Nematology, for the continuous supply with R. culcivorax... read full comment

Comment on: Schiffer et al. BMC Genomics, 14:923

Citation correction (Kousik Kundu, 05 February 2014)

Unfortunately current reference 42 (Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, Shemesh R, Novik A, Sorek R: Transcription-mediated gene fusion in the human genome.**/Genome Res/ 2006, 16*:*30-6) is wrong. the correct citation would be: Akiva, E., Friedlander, G., Itzhaki, Z., and Margalit, H. (2012). A dynamic view of domain-motif interactions. PLoS Comput Biol, 8(1), e1002341 read full comment

Comment on: Kundu et al. BMC Genomics, 15:S5

CORRECTION FOR DATASET LOCATION IN SRA: BIOPROJECT PRJNA194445 (Heather Rowe, 28 January 2014)

the data are available at http://www.ncbi.nlm.nih.gov/sra/; accessions SRX264824-SRX264835. read full comment

Comment on: Rowe et al. BMC Genomics, 14:342

The interests of data generators should be protected. (Xiaolei Huang, 21 January 2014)

Thanks for bringing this case to light. I agree with you that "the ultimate responsibility should lie with the data... read full comment

Comment on: Nanda et al. BMC Genomics, 15:5

SRST2 (Michael Inouye, 18 November 2013)

There is now a new and improved version, SRST2, which is currently available at:

http://katholt.github.io/srst2/

SRST2 is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.

A manuscript is in preparation. read full comment

Comment on: Inouye et al. BMC Genomics, 13:338

TCGA Data Clarification (Thomas Peterson, 03 September 2013)

The dbGaP accession number for the TCGA data used in this manuscript is phs000178.v8.p7 read full comment

Comment on: Nehrt et al. BMC Genomics, 13:S9

Provide a descriptive title for your comment here...Mirror link (Piotr Pawlowski, 11 July 2013)

Revised version of the manuscript is available at:
http://www.researchgate.net/publication/236051523_A_kinetic_model_of_the_evolution_of_a_protein_interaction_network read full comment

Comment on: Pawlowski et al. BMC Genomics, 14:172

Acknowledgement (Yan Zhou, 11 July 2013)

This work is supported by National Basic Research Program (973 Program) of China (grant number 2011CB111610). read full comment

Comment on: Zhu et al. BMC Genomics, 13:382

New url for the placenta data (Keyan Zhao, 11 July 2013)

Due to our lab relocation to UCLA, the following url are not working any more. http://intron.healthcare.uiowa.edu/placenta/

We host the data on our new lab webpage:
http://www.mimg.ucla.edu/faculty/xing/placenta/

Thanks for your interest in our paper and data. read full comment

Comment on: Kim et al. BMC Genomics, 13:115

Definitions of viruses (Edward Rybicki, 18 April 2013)

A great piece of work - and since I met Dr van Etten in 1982 in Lincoln, after he and co-workers discovered the first PCBV, something I've been waiting quite a long time to see!

I especially like the comment "...which suggests that the recently acquired genes originate from a still largely un-sequenced reservoir of genomes, possibly other unknown viruses that infect the same hosts.", as it meshes really well with what I have been telling students for while now:

"A virus is an infectious acellular entity composed of compatible genomic components derived from a pool of genetic elements." read full comment

Comment on: Jeanniard et al. BMC Genomics, 14:158

Can it really achieve globin switching in vitro within one-phase system? (Wentian Wang, 10 March 2013)

see below read full comment

Comment on: Li et al. BMC Genomics, 13:153

Are assembled data available (Mark Blaxter, 08 March 2013)

I have been unable to access the SRA accession for this report, and wonder if the assemblies are also to be made available? read full comment

Comment on: Xi et al. BMC Genomics, 13:227

Corrected expression values in supplementary tables (Matthias Erwin Futschik, 06 August 2012)

The original supplementary tables 2-5 of this article contained some entries, which were given as date instead as a number (caused by automatic formating in Excel). These entries were corrected in the revised supplementary tables, that can be found at our web-page. read full comment

Comment on: Russ et al. BMC Genomics, 11:305

Incorrect reference for Bland and Altman (Jacob Hurst, 06 August 2012)

<p>The correct reference is given below. <br/> <br/>J MARTIN BLAND and DOUGLAS G ALTMAN <br/>Misleading Statistics: Errors in Textbooks, Software and Manuals <br/>Int. J. Epidemiol. (1988) 17(2): 245-247 doi:10.1093/ije/17.2.245 <br/> <br/><a href='http://ije.oxfordjournals.org/content/17/2.toc'>Here is a link to the journal</a></p> read full comment

Comment on: McIntyre et al. BMC Genomics, 12:293

Brief comparison to Roberts et al. (Jonathan Dreyfuss, 06 August 2012)

<p>I hope you enjoy our article and welcome any... read full comment

Comment on: Dreyfuss et al. BMC Genomics, 13:340

There is a typo (Yuan Zhou, 25 July 2012)

There is a typo in the Table 1, where the protein number of Arabidopsis genome should be 27,169. We regret the confusion caused by this typo. read full comment

Comment on: Zhou et al. BMC Genomics, 12:632

Streptomyces genomics (hang wu, 25 July 2012)

<p>Comparative streptomyces genomics was also described in the published manuscript.</p> read full comment

Comment on: Wu et al. BMC Genomics, 13:337

Correction to error in the caption of Figure 5 (Ainhoa Ruiz-Aracama, 04 July 2012)

The authors reported that the caption of Figure 5 was incorrect in the originally published version. The correct caption is:... read full comment

Comment on: Ruiz-Aracama et al. BMC Genomics, 12:251

Web access to Haloarchaeal Protein Clusters (Shiladitya DasSarma, 17 May 2012)

The protein clusters (cHOGs) reported in this paper are now available to the community on HaloWeb: The Haloarchaeal Genomes Website (URL: Halo3 and Halo4). read full comment

Comment on: Capes et al. BMC Genomics, 13:39

erratum concerning Figure 3 (Marc Robinson-Rechavi, 17 May 2012)

A mistake escaped our attention while correcting the proofs, for which we apologize.

The caption of figure 3B should not be: ("B) immune system co-module containing lymph node and thymus", but rather should be: "(B) co-module containing liver and kidney". read full comment

Comment on: Piasecka et al. BMC Genomics, 13:124