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Availability (Karan Uppal, 28 July 2014)

URL: http://sourceforge.net/projects/xmsanalyzer/
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Comment on: Uppal et al. BMC Bioinformatics, 14:15

Full data is now available in a designated site (Assaf Zaritsky, 07 February 2014)

http://www.cs.tau.ac.il/~assafzar/BBBC019v2/BBBC019_rawData.html read full comment

Comment on: Zaritsky et al. BMC Bioinformatics, 14:319

Up-to-date xtal/bio datasets are available at the EPPIC web site (Jose Manuel Duarte, 16 December 2013)

Please note that the manually curated datasets of small biological interfaces and large crystal contacts are also available from the EPPIC web site under the downloads section in plain text files: http://www.eppic-web.org/ewui/#downloads

The datasets in the website will be updated if any issue is found or new data become available. read full comment

Comment on: Duarte et al. BMC Bioinformatics, 13:334

Some remarks (Fabio Fabris, 10 December 2013)

In the 16th page authors state that: "In this case [highly connected genes for both training and testing], there is a clear advantage of using NHMC with ¿ = 0 over using NHMC with ¿ = 0.5."

However, it seems that the second part of table 2 (which should be split in two different tables imho) presents the opposite.

Also, the values on the vertical axis of Figure 2 (varying between 0.2 and 0.4) are inconsistent with the values depicted on the tables.


Thank you! read full comment

Comment on: Stojanova et al. BMC Bioinformatics, 14:285

Softwares for correction of MS data for natural abundance (Pierre Millard, 10 December 2013)

In your manuscript, you state that "only commercial software or user-specific approaches are available for the conversion of mass intensities (provided by the specific software implemented to the mass spectrometer) to the relative and molar isotopomer enrichments", and that "Before the implementation of LS-MIDA, [you] relied on the usage of a lab-specific Excel/Solver-based software". However, a series of free, open source, user friendly, multi-platform softwares for correction of MS-data have been published during the last decade. Among these software there is MSCorr (Wahl et al., Biotech Bioeng, 2004), an algorithm developed in Perl by (Moseley, BMC Bioinformatics, 2010), or IsoCor (Millard et al., Bioinformatics... read full comment

Comment on: Ahmed et al. BMC Bioinformatics, 14:218

Misconceptions about the FCR intervals in the paper "Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes". (Vered Madar, 04 September 2013)

The paper "Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes" argues for the advantages in constructing confidence intervals for selected set of significant log fold changed genes. Bringing convincing arguments along with actual examples in favor of using the adjusted FCR confidence intervals (Benjamini and Yekutieli 2005).... read full comment

Comment on: Jung et al. BMC Bioinformatics, 12:288

Clarification on the name of the software package (Matthew Hayes, 02 July 2013)

Our program should not be confused with the Bellerophon program that was published in 2004 by Huber et al.

http://www.ncbi.nlm.nih.gov/pubmed/15073015 read full comment

Comment on: Hayes et al. BMC Bioinformatics, 14:S6

Update to web-link (Sriganesh Srihari, 02 July 2013)

The MCL-CAw source code and datasets have now been moved to the following website:
https://sites.google.com/site/mclcaw/

The earlier server is no more accessible.

-- Authors. read full comment

Comment on: Srihari et al. BMC Bioinformatics, 11:504

Source code for NetiNeti (Casey Bergman, 18 April 2013)

The source code for NetiNeti is available here: https://github.com/mbl-cli/NetiNeti read full comment

Comment on: Akella et al. BMC Bioinformatics, 13:211

New Links (Terence Sloan, 11 March 2013)

SPRINT is no longer available from the NeSCForge at:

http://tinyurl.com/c6aqodc

Instead it is now available from the Comprehensive R Archive Network(CRAN) at

http://tinyurl.com/cez4q3q

It is also available direct from the SPRINT project team at http://www.r-sprint.org/.

Please also note that in the Acknowledgements section, the edikt2 URL is also no longer valid. The edikt2 URL is now http://www.edikt.org.uk/.

Terence M Sloan, paper co-author read full comment

Comment on: Hill et al. BMC Bioinformatics, 9:558

Coding errors (Prakash joshi, 10 March 2013)

plese help me to out... read full comment

Comment on: Gebäck et al. BMC Bioinformatics, 10:75

JProfileGrid version 2.0 released (Alberto Roca, 10 March 2013)

New JProfileGrid v2.0 can visualize alignments of >100,000 sequences. New features have also been introduced such as sorting and searching the menu list of sequence names for finding a specific homolog to serve as the reference sequence for the ProfileGrid. The new "overview" modes enable the user to visualize the entire MSA within one window as either a ProfileGrid or a stacked sequence. A ProfileGrid can now be exported as a PNG image file. The detailed ProfileGrid window with the character counts has a new second pane that facilitates simultaneous viewing of different parts of the MSA. To focus on rare residues, the "highlight" functionality now identifies residues that occur greater or less than a user-defined threshold of residue frequency. We introduced data sampling to accelerate... read full comment

Comment on: Roca et al. BMC Bioinformatics, 9:554

Important Omission (Dario Strbenac, 10 March 2013)

The authors state that "Currently, HPeak is capable of analyzing ChIP-Seq data collected from human and mouse and can easily be extended to other species.", which is not true. Reading through the function 'realignfileread' in summary.pl, it is evident that the human chromosome names are hard-coded. For users who don't have Perl programming experience, it would be difficult to use for other species. It would be nice if reviewers could verify such broad statements before accepting articles for publication. read full comment

Comment on: Qin et al. BMC Bioinformatics, 11:369

A lot of similarities with our research, BioGraph (Anthony Liekens, 08 March 2013)

There are remarkable similarities between the methods and results presented in this paper and our research on BioGraph (http://www.biograph.be or http://genomebiology.com/content/12/6/R57), which we also adopt for the integration of knowledge sources and predict functional hypotheses with.

I find it unfortunate that our resource is not referenced or used as a comparison in this paper. read full comment

Comment on: Eronen et al. BMC Bioinformatics, 13:119

Misleading representation of existing databases (Philip Zimmermann, 08 March 2013)

The resource presented in this paper is interesting and beneficial for the cancer research community. I would like to thank this team for making it available. It's a pity, however, that the authors have not accurately represented existing databases - ArrayExpress, Oncomine and Genevestigator. For example, the claim that Oncomine and Genevestigator "focus on analyses of subsets of the data and neither fully addresses the problem of integration across studies" is wrong. In fact, Genevestigator data is normalized using a global scheme that allows integration across studies, and its tools are specialized on global type analyzes rather than looking at individual experiments in detail. As far as I know Oncomine also has made a major effort to integrate data across... read full comment

Comment on: Liu et al. BMC Bioinformatics, 12:46

SparSNP is now open source at https://github.com/gabraham/SparSNP (Gad Abraham, 18 January 2013)

SparSNP is now licensed under the GPLv3, and the source code and documentation are available at
https://github.com/gabraham/SparSNP read full comment

Comment on: Abraham et al. BMC Bioinformatics, 13:88

Errors in Table 1. Comparison of common graphical workflow environments (Scott Markel, 11 January 2013)

Thank you for including Pipeline Pilot in your... read full comment

Comment on: Dinov et al. BMC Bioinformatics, 12:304

A slight error in Equation 6 (Hunter Moseley, 26 October 2012)

There is a slight error in Equation 6 in the two summation terms. The summation should be for y = 0; y ≤ j and x = 0; x ≤ i with the following condition (y ≠ j or x ≠ i) that must be satisfied as well. It is easier to describe this summation with a single summation term which includes the conditional, which I have tried to represent below given the limitations of this editor: y ≤ j; x ≤ i; y ≠ j or x ≠ i ∑ y = 0; x = 0 read full comment

Comment on: Moseley BMC Bioinformatics, 11:139

To avoid any confusion (Sofie Van Landeghem, 06 August 2012)

Please note that the Gent Text Mining system, abbreviated to GETM only within this paper to enable comparison to the TEES software, is not to be confused with the GETM system of Gerner et al., 2010. read full comment

Comment on: Van Landeghem et al. BMC Bioinformatics, 13:S6

Introduction of the piRNA cluster - database (David Rosenkranz, 30 May 2012)

For a more comfortable accessibility of the data provided as supplementary material of this paper, all piRNA clusters detected with the proTRAC software are now made available at the piRNA cluster - database.

piRNA cluster - database read full comment

Comment on: Rosenkranz et al. BMC Bioinformatics, 13:5

Formatting problem (Rayan Chikhi, 27 March 2012)

It appears that the provisional PDF suffers from major formatting problems; as our Latex manuscript was converted to a Word document. We are working with the editor to fix it in the final version. read full comment

Comment on: Peterlongo et al. BMC Bioinformatics, 13:48

PubChem links ? (Christopher Southan, 06 March 2012)

I'm sure this has been suggested already but having all those structures mapped into PubChem would be very useful. You could instantiate MetRxn as a new source. read full comment

Comment on: Kumar et al. BMC Bioinformatics, 13:6

Errata to section "Matches as Equivalence Classes" (Manuel Holtgrewe, 05 March 2012)

There is an error in the section "Matches as Equivalence Classes". Particularly, the definition of match equivalence is flawed.

This has been fixed in an erratum which is available on Rabema's project website http://www.seqan.de/projects/rabema.html. This page also contains a document with additional material and extended proofs regarding the valid definitions in the original paper and the changed definition. read full comment

Comment on: Holtgrewe et al. BMC Bioinformatics, 12:210

POSTN expression confirmed by Nature paper (Jim Zheng, 14 February 2012)

POSTN is a consistently differentially expressed gene identified by CDEP. Now it has been shown that POSTN is a stromal niche component that is induced on metastasis formation

Malanchi I, Santamaria-Martínez A, Susanto E, Peng H, Lehr HA, Delaloye JF, Huelsken J.
Interactions between cancer stem cells and their niche govern metastatic colonization. Nature. 2011 Dec 7;481(7379):85-9.
doi:10.1038/nature10694. PubMed PMID: 22158103. read full comment

Comment on: Tsoi et al. BMC Bioinformatics, 12:438

This project has been moved to Google Code (Pengyi Yang, 12 January 2012)

The algorithm and software described in this article have been moved to Google Code.

Please refer to:
http://code.google.com/p/genetic-ensemble-snpx/ read full comment

Comment on: Yang et al. BMC Bioinformatics, 11:524