grnsight 4.0.0 → 6.0.0

package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_manuscript_2016_references.rtf

@@ -1,264 +0,0 @@
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-\par \hich\af0\dbch\af31505\loch\f0 Bostock M., Ogievetsky V., Heer J. 2011. D}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\super\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 3}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 
-\hich\af0\dbch\af31505\loch\f0 : Data-Driven Documents. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 IEEE transactions on visualization and computer graphics}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 
-\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  17:2301\hich\f0 \endash \loch\f0 2309. DOI: 10.1109/TVCG.2011.185.
-\par \hich\af0\dbch\af31505\loch\f0 Brown E. 2014. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Web development with Node and Express}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 
-\hich\af0\dbch\af31505\loch\f0 . Beijing}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \loch\af0\dbch\af31505\hich\f0 \u8239\'3f}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 ; Sebastopol, CA: O
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-978-1-4919-4930-6}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 
-\par \hich\af0\dbch\af31505\loch\f0 Dahlquist KD., Fitzpatrick BG., Camacho ET., Entzminger SD., Wanner NC. 2015. Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharo\hich\af0\dbch\af31505\loch\f0 
-myces cerevisiae. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Bulletin of Mathematical Biology}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  77:1457
-\hich\f0 \endash \loch\f0 1492. DOI: 10.1007/s11538-015-0092-6.
-\par \hich\af0\dbch\af31505\loch\f0 Dionisio JDN., Dahlquist KD. 2008. Improving the computer science in bioinformatics through open source pedagogy. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 
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-Franz M., Lopes CT., Huck G., Dong Y., Sumer O., Bader GD. 2016. Cytoscape.js: a graph theory library for visualisation and analysis. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid9068137\charrsid9068137 \hich\af0\dbch\af31505\loch\f0 
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-\par }\pard \ltrpar\ql \fi-720\li720\ri0\sl480\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin720\itap0 {\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Gostner R., Baldacci B., Mor\hich\af0\dbch\af31505\loch\f0 
-ine MJ., Priami C. 2014. Graphical Modeling Tools for Systems Biology. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 ACM Computing Surveys}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 
-\hich\af0\dbch\af31505\loch\f0  47:1\hich\f0 \endash \loch\f0 21. DOI: 10.1145/2633461.
-\par \hich\af0\dbch\af31505\loch\f0 Harbison CT., Gordon DB., Lee TI., Rinaldi NJ., Macisaac KD., Danford TW., Hannett NM., Tagne J-B., Reynolds DB., Yoo J., Jennings E\hich\af0\dbch\af31505\loch\f0 
-G., Zeitlinger J., Pokholok DK., Kellis M., Rolfe PA., Takusagawa KT., Lander ES., Gifford DK., Fraenkel E., Young RA. 2004. Transcriptional regulatory code of a eukaryotic genome. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 
-\hich\af0\dbch\af31505\loch\f0 Nature}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  431:99\hich\f0 \endash \loch\f0 104. DOI: 10.1038/nature02800.
-\par \hich\af0\dbch\af31505\loch\f0 Lawlor B., Walsh P. 2015. Engi\hich\af0\dbch\af31505\loch\f0 neering bioinformatics: building reliability, performance and productivity into bioinformatics software. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 
-\i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Bioengineered}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  6:193\hich\f0 \endash \loch\f0 203. DOI: 10.1080/21655979.2015.1050162.
-\par \hich\af0\dbch\af31505\loch\f0 Lee TI., Rinaldi NJ., Robert F., Odom DT., Bar-Joseph Z., Gerber GK., Hannett NM., Harbiso\hich\af0\dbch\af31505\loch\f0 
-n CT., Thompson CM., Simon I., Zeitlinger J., Jennings EG., Murray HL., Gordon DB., Ren B., Wyrick JJ., Tagne J-B., Volkert TL., Fraenkel E., Gifford DK., Young RA. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. }{\rtlch\fcs1 
-\ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Science (New York, N\hich\af0\dbch\af31505\loch\f0 .Y.)}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  298:799\hich\f0 
-\endash \loch\f0 804. DOI: 10.1126/science.1075090.
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-\f0\fs24\insrsid8587810\charrsid8587810 \hich\af0\dbch\af31505\loch\f0 . Upper Saddle River, NJ: Prentice Hall.}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12797383 \hich\af0\dbch\af31505\loch\f0  ISBN: }{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 
-\f0\fs24\insrsid12797383\charrsid12797383 \hich\af0\dbch\af31505\loch\f0 978-0-13-235088-4}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid8587810\charrsid8587810 
-\par \hich\af0\dbch\af31505\loch\f0 Nielsen J. 1993. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid8587810\charrsid8587810 \hich\af0\dbch\af31505\loch\f0 Usability engineering}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 
-\f0\fs24\insrsid8587810\charrsid8587810 \hich\af0\dbch\af31505\loch\f0 . Boston: Academic Press.}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12797383 \hich\af0\dbch\af31505\loch\f0  ISBN: }{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 
-\f0\fs24\insrsid12797383\charrsid12797383 \hich\af0\dbch\af31505\loch\f0 978-0-12-518405-2}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid8587810\charrsid8587810 
-\par }\pard \ltrpar\ql \fi-480\li450\ri0\sl480\slmult1\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin450\itap0\pararsid13566485 {\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid13566485\charrsid13566485 \hich\af0\dbch\af31505\loch\f0 
-Norman DA. 2013. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid13566485\charrsid13566485 \hich\af0\dbch\af31505\loch\f0 The desig\hich\af0\dbch\af31505\loch\f0 n of everyday things}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 
-\f0\fs24\insrsid13566485\charrsid13566485 \hich\af0\dbch\af31505\loch\f0 . New York, New York: Basic Books.}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12797383 \hich\af0\dbch\af31505\loch\f0  ISBN: }{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 
-\f0\fs24\insrsid12797383\charrsid12797383 \hich\af0\dbch\af31505\loch\f0 978-0-465-05065-9}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid13566485\charrsid13566485 
-\par }\pard \ltrpar\ql \fi-720\li720\ri0\sl480\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin720\itap0 {\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 
-Pavlopoulos GA., Malliarakis D., Papanikolaou N., Theodosiou T., Enright AJ., Iliopoulos I. 2015. Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past\hich\af0\dbch\af31505\loch\f0 , present and future. }
-{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 GigaScience}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  4:38. DOI: 10.1186/s13742-015-0077-2.
-\par \hich\af0\dbch\af31505\loch\f0 Salomonis N., Hanspers K., Zambon AC., Vranizan K., Lawlor SC., Dahlquist KD., Doniger SW., Stuart J., Conklin BR., Pico AR. 2007. GenMAPP 2: new features and resources for pathway ana\hich\af0\dbch\af31505\loch\f0 lysis. }{
-\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 BMC bioinformatics}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  8:217. DOI: 10.1186/1471-2105-8-217.
-\par \hich\af0\dbch\af31505\loch\f0 Schade B., Jansen G., Whiteway M., Entian KD., Thomas DY. 2004. Cold adaptation in budding yeast. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 
-Molecular Biology of the Cell}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  15:5492\hich\f0 \endash \loch\f0 5502. DOI: 10.1091/mbc.E04-03-0167.
-\par \hich\af0\dbch\af31505\loch\f0 \hich\f0 Schultheiss SJ., M\'fc\loch\f0 nc\hich\af0\dbch\af31505\loch\f0 \hich\f0 h M-C., Andreeva GD., R\'e4\loch\f0 tsch G. 2011. Persistence and availability of Web services in computational biology. }{\rtlch\fcs1 
-\ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 PloS One}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  6:e24914. DOI: 10.1371/journal.pone.0024914.
-\par \hich\af0\dbch\af31505\loch\f0 Schultheiss SJ. 2011. Ten simple rules for providing a scientific Web resource. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 PLoS computational biology}{\rtlch\fcs1 
-\af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  7:e1001126. DOI: 10.1371/journal.pcbi.1001126.
-\par \hich\af0\dbch\af31505\loch\f0 Shannon P., Markiel A., Ozier O., Baliga NS., Wang JT., Ramage D., Amin N., Schwikowski B., Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular in\hich\af0\dbch\af31505\loch\f0 
-teraction networks. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Genome Research}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  13:2498\hich\f0 \endash 
-\loch\f0 2504. DOI: 10.1101/gr.1239303.
-\par }\pard \ltrpar\ql \fi-750\li720\ri0\sl480\slmult1\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin720\itap0\pararsid8587810 {\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid8587810\charrsid8587810 \hich\af0\dbch\af31505\loch\f0 
-Shneiderman B., Plaisant C., Cohen M., Jacobs SM., Elmqvist N., Diakopoulos N. 2016. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid8587810\charrsid8587810 \hich\af0\dbch\af31505\loch\f0 
-Designing the user interface: strategies for effective human-computer interaction}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid8587810\charrsid8587810 \hich\af0\dbch\af31505\loch\f0 . Hoboken: Pear\hich\af0\dbch\af31505\loch\f0 son.}{\rtlch\fcs1 
-\af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid13203410 \hich\af0\dbch\af31505\loch\f0  ISBN: }{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid13203410\charrsid13203410 \hich\af0\dbch\af31505\loch\f0 978-0-13-438038-4}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 
-\f0\fs24\insrsid8587810\charrsid8587810 
-\par }\pard \ltrpar\ql \fi-720\li720\ri0\sl480\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin720\itap0 {\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 
-Shore D., Nasmyth K. 1987. Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Cell}{
-\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  51:721\hich\f0 \endash \loch\f0 732.
-\par \hich\af0\dbch\af31505\loch\f0 Smoot ME., Ono K., Ruscheinski J., Wang P-L., Ideker T. 2011. Cytoscape 2.\hich\af0\dbch\af31505\loch\f0 8: new features for data integration and network visualization. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 
-\i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Bioinformatics (Oxford, England)}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  27:431\hich\f0 \endash \loch\f0 
-432. DOI: 10.1093/bioinformatics/btq675.
-\par \hich\af0\dbch\af31505\loch\f0 \hich\f0 Teixeira MC., Monteiro PT., Guerreiro JF., Gon\'e7\loch\f0 alves JP., Mira NP., dos Santos SC., Cabrito TR., Palma M., Cost\hich\af0\dbch\af31505\loch\f0 \hich\f0 
-a C., Francisco AP., Madeira SC., Oliveira AL., Freitas AT., S\'e1\loch\f0 -Correia I. 2014. The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. }{\rtlch\fcs1 
-\ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Nucleic Acids Research}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  42:D16\hich\af0\dbch\af31505\loch\f0 1\hich\f0 \endash 
-\loch\f0 166. DOI: 10.1093/nar/gkt1015.
-\par \hich\af0\dbch\af31505\loch\f0 Veretnik S., Fink JL., Bourne PE. 2008. Computational biology resources lack persistence and usability. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 
-PLoS computational biology}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  4:e1000136. DOI: 10.1371/journal.pcbi.1000136.
-\par }\pard \ltrpar\ql \fi-720\li720\ri0\sl480\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin720\itap0\pararsid8587810 {\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0 Wilson G., Aruliah DA., Brown CT., Chue Hong 
-\hich\af0\dbch\af31505\loch\f0 NP., Davis M., Guy RT., Haddock SHD., Huff KD., Mitchell IM., Plumbley MD., Waugh B., White EP., Wilson P. 2014. Best practices for scientific computing. }{\rtlch\fcs1 \ai\af0\afs24 \ltrch\fcs0 \i\f0\fs24\insrsid12058939 
-\hich\af0\dbch\af31505\loch\f0 PLoS biology}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid12058939 \hich\af0\dbch\af31505\loch\f0  12:e1001745. DOI: 10.1371/journal.pbio.1001745.}{\rtlch\fcs1 \af0\afs24 \ltrch\fcs0 \f0\fs24\insrsid8587810 
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