[Please contribute] Studies that cite ngs.plot

[Li Shen]

I'm collecting a list of papers or any other kinds of materials that cite ngs.plot. Please contribute if you use ngs.plot in your works. Thanks!

1. Yao, B., Lin, L., Street, R.C., Zalewski, Z.A., Galloway, J.N., Wu, H., Nelson, D.L. and Jin, P. (2013) Genome-wide alteration of 5-hydroxymethylcytosine in a mouse model of fragile X-associated tremor/ataxia syndrome, Hum Mol Genet.

2. Kimura, H. (2013) Histone modifications for human epigenome analysis, J Hum Genet, 58, 439-445.

[Li Shen]

ngs.plot on NIH's helix server: http://helix.nih.gov/Applications/ngsplot.html

[Li Shen]

Add this review paper written by ourselves:

Shen, L., Choi, I., Nestler, E.J. and Won, K.-J. (2013) Human Transcriptome and Chromatin Modifications: An ENCODE Perspective, Genomics Inform, 11, 60-67.

[Li Shen]

Our new paper on PNAS uses ngs.plot:

Scobie, K.N., Damez-Werno, D., Sun, H., Shao, N., Gancarz, A., Panganiban, C.H., Dias, C., Koo, J., Caiafa, P., Kaufman, L., Neve, R.L., Dietz, D.M., Shen, L. and Nestler, E.J. (2014) Essential role of poly(ADP-ribosyl)ation in cocaine action, Proceedings of the National Academy of Sciences, 111, 2005-2010.

[Li Shen]

Add a PLOS ONE paper that uses ngs.plot:

Chandler H, Patel H, Palermo R, Brookes S, Matthews N, et al. (2014) Role of Polycomb Group Proteins in the DNA Damage Response – A Reassessment. PLoS ONE 9(7): e102968. doi:10.1371/journal.pone.0102968

[Samad Elka]

Another article in Int J Mol Sci cites ngs.plot (http://www.ncbi.nlm.nih.gov/pubmed/25056547)

DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide.

Int J Mol Sci. 2014 Jul 23;15(7):13111-22. doi: 10.3390/ijms150713111.

Baranello L, Kouzine F, Wojtowicz D, Cui K, Przytycka TM, Zhao K, Levens D.

[Li Shen]

Dear Samad,

Thank you for sharing this! We appreciate it.

Li

--
You received this message because you are subscribed to the Google Groups "ngsplot-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ngsplot-discu...@googlegroups.com.
To post to this group, send email to ngsplot...@googlegroups.com.
Visit this group at http://groups.google.com/group/ngsplot-discuss.

To view this discussion on the web visit https://groups.google.com/d/msgid/ngsplot-discuss/cbc1b412-5d60-4ea8-89d8-54e5e631ea5a%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

--

Li Shen, Ph.D. Computer Science
Assistant Professor
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
New York, NY 10029
#################
ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/

Want ChIP-seq differential analysis? Use: https://code.google.com/p/diffreps/

[archana bhardwaj]

Another article in Nature  cites ngs.plot

Genome-wide characterization of the routes to pluripotency,Nature516,198–206(11 December 2014) doi:10.1038/nature14046

[Li Shen]

Dear Archana,

Thank you for keeping us updated! 

Li

On Wed, Dec 17, 2014 at 2:16 AM, archana bhardwaj <archa...@gmail.com> wrote:

Another article in Nature  cites ngs.plot

Genome-wide characterization of the routes to pluripotency,Nature516,198–206(11 December 2014) doi:10.1038/nature14046

--
You received this message because you are subscribed to the Google Groups "ngsplot-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ngsplot-discu...@googlegroups.com.
To post to this group, send email to ngsplot...@googlegroups.com.
Visit this group at http://groups.google.com/group/ngsplot-discuss.

To view this discussion on the web visit https://groups.google.com/d/msgid/ngsplot-discuss/f86eda5d-f6bc-459a-8dfb-d6618653b44d%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[Bahareh Haddad Derafshi]

hi,

Ngsplot was working for me last year, but now it doesn't work. it constantly gives an error saying: 

"your ngs.plot database may be corrupted".

I download and installed everything many times. i updated python.

can you please help me?

thanks in advance

Bahareh

[MikeD]

Dear Li Shen

I recently cited your excellent software in the supplemental methods section of

Josling GA, et al (2015) A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression. Cell Host Microbe. Jun 10;17(6):741-51. doi: 10.1016/j.chom.2015.05.009. PMID: 26067602

I used  your Plasmodium falciparum plasmodb v12 custom genome. I am now analysing Plasmodium vivax using V11 from plasmodb. Unfortunately it is only available through plasmodb and the pipeline you kindly provide on github for custom genome builds requires a lot of info from ensembl that doesnt exist for this genome. I am a wetlab scientist who can use your excellent tool from the command line but I dont know how to write code. Could you possibly post/email the actual scripts you used to make the Plasmodium falciparum V12 genome so I could try and copy them to make the P vivax V11 genome?

Thanks
Mike