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Items: 1 to 50 of 63

1.

The bio.tools registry of software tools and data resources for the life sciences.

Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S.

Genome Biol. 2019 Aug 12;20(1):164. doi: 10.1186/s13059-019-1772-6.

2.

The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community.

Darde TA, Lecluze E, Lardenois A, Stévant I, Alary N, Tüttelmann F, Collin O, Nef S, Jégou B, Rolland AD, Chalmel F.

Bioinformatics. 2019 Jan 22. doi: 10.1093/bioinformatics/btz047. [Epub ahead of print]

PMID:
30668675
3.

TOXsIgN: a cross-species repository for toxicogenomic signatures.

Darde TA, Gaudriault P, Beranger R, Lancien C, Caillarec-Joly A, Sallou O, Bonvallot N, Chevrier C, Mazaud-Guittot S, Jégou B, Collin O, Becker E, Rolland AD, Chalmel F.

Bioinformatics. 2018 Jun 15;34(12):2116-2122. doi: 10.1093/bioinformatics/bty040.

4.

Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Apr 4;18(1):63. doi: 10.1186/s13059-017-1202-6. No abstract available.

5.

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Feb 13;18(1):27. doi: 10.1186/s13059-016-1145-3. Erratum in: Genome Biol. 2017 Apr 4;18(1):63.

6.

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective.

Cvijovic M, Höfer T, Aćimović J, Alberghina L, Almaas E, Besozzi D, Blomberg A, Bretschneider T, Cascante M, Collin O, de Atauri P, Depner C, Dickinson R, Dobrzynski M, Fleck C, Garcia-Ojalvo J, Gonze D, Hahn J, Hess HM, Hollmann S, Krantz M, Kummer U, Lundh T, Martial G, Dos Santos VM, Mauer-Oberthür A, Regierer B, Skene B, Stalidzans E, Stelling J, Teusink B, Workman CT, Hohmann S.

NPJ Syst Biol Appl. 2016 May 26;2:16011. doi: 10.1038/npjsba.2016.11. eCollection 2016.

7.

PepPSy: a web server to prioritize gene products in experimental and biocuration workflows.

Sallou O, Duek PD, Darde TA, Collin O, Lane L, Chalmel F.

Database (Oxford). 2016 May 12;2016. pii: baw070. doi: 10.1093/database/baw070. Print 2016.

8.

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

Moreews F, Sallou O, Ménager H, Le Bras Y, Monjeaud C, Blanchet C, Collin O.

F1000Res. 2015 Dec 14;4:1443. doi: 10.12688/f1000research.7536.1. eCollection 2015.

9.

Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.

Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals É, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P.

Gigascience. 2016 Feb 11;5:9. doi: 10.1186/s13742-015-0105-2. eCollection 2016.

10.

BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ.

Bretaudeau A, Monjeaud C, Le Bras Y, Legeai F, Collin O.

Gigascience. 2015 May 9;4:22. doi: 10.1186/s13742-015-0063-8. eCollection 2015.

11.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A.

Nucleic Acids Res. 2015 Jul 1;43(W1):W589-98. doi: 10.1093/nar/gkv350. Epub 2015 Apr 20.

12.

The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community.

Darde TA, Sallou O, Becker E, Evrard B, Monjeaud C, Le Bras Y, Jégou B, Collin O, Rolland AD, Chalmel F.

Nucleic Acids Res. 2015 Jul 1;43(W1):W109-16. doi: 10.1093/nar/gkv345. Epub 2015 Apr 16.

13.

High-resolution profiling of novel transcribed regions during rat spermatogenesis.

Chalmel F, Lardenois A, Evrard B, Rolland AD, Sallou O, Dumargne MC, Coiffec I, Collin O, Primig M, Jégou B.

Biol Reprod. 2014 Jul;91(1):5. doi: 10.1095/biolreprod.114.118166. Epub 2014 Apr 16.

PMID:
24740603
14.

LIMLE, a new molecule over-expressed following activation, is involved in the stimulatory properties of dendritic cells.

Le Texier L, Durand J, Lavault A, Hulin P, Collin O, Le Bras Y, Cuturi MC, Chiffoleau E.

PLoS One. 2014 Apr 4;9(4):e93894. doi: 10.1371/journal.pone.0093894. eCollection 2014.

15.

Migration of dendritic cells: physical principles, molecular mechanisms, and functional implications.

Heuzé ML, Vargas P, Chabaud M, Le Berre M, Liu YJ, Collin O, Solanes P, Voituriez R, Piel M, Lennon-Duménil AM.

Immunol Rev. 2013 Nov;256(1):240-54. doi: 10.1111/imr.12108. Review.

PMID:
24117825
16.

FISH-quant: automatic counting of transcripts in 3D FISH images.

Mueller F, Senecal A, Tantale K, Marie-Nelly H, Ly N, Collin O, Basyuk E, Bertrand E, Darzacq X, Zimmer C.

Nat Methods. 2013 Apr;10(4):277-8. doi: 10.1038/nmeth.2406. No abstract available.

PMID:
23538861
17.

CyanoLyase: a database of phycobilin lyase sequences, motifs and functions.

Bretaudeau A, Coste F, Humily F, Garczarek L, Le Corguillé G, Six C, Ratin M, Collin O, Schluchter WM, Partensky F.

Nucleic Acids Res. 2013 Jan;41(Database issue):D396-401. doi: 10.1093/nar/gks1091. Epub 2012 Nov 21.

18.

PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.

Mahé S, Duhamel M, Le Calvez T, Guillot L, Sarbu L, Bretaudeau A, Collin O, Dufresne A, Kiers ET, Vandenkoornhuyse P.

PLoS One. 2012;7(9):e43117. doi: 10.1371/journal.pone.0043117. Epub 2012 Sep 13.

19.

GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development.

Britto R, Sallou O, Collin O, Michaux G, Primig M, Chalmel F.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W458-65. doi: 10.1093/nar/gks380. Epub 2012 May 8.

20.

Fitness of macrolide resistant Campylobacter coli and Campylobacter jejuni.

Zeitouni S, Collin O, Andraud M, Ermel G, Kempf I.

Microb Drug Resist. 2012 Apr;18(2):101-8. doi: 10.1089/mdr.2011.0188. Epub 2012 Feb 10.

PMID:
22324770
21.

Cell migration in confinement: a micro-channel-based assay.

Heuzé ML, Collin O, Terriac E, Lennon-Duménil AM, Piel M.

Methods Mol Biol. 2011;769:415-34. doi: 10.1007/978-1-61779-207-6_28.

PMID:
21748692
22.

Contractility of the cell rear drives invasion of breast tumor cells in 3D Matrigel.

Poincloux R, Collin O, Lizárraga F, Romao M, Debray M, Piel M, Chavrier P.

Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1943-8. doi: 10.1073/pnas.1010396108. Epub 2011 Jan 18.

23.

GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle.

Lardenois A, Gattiker A, Collin O, Chalmel F, Primig M.

Database (Oxford). 2010 Dec 11;2010:baq030. doi: 10.1093/database/baq030. Print 2010.

24.

Spatiotemporal organization, regulation, and functions of tractions during neutrophil chemotaxis.

Shin ME, He Y, Li D, Na S, Chowdhury F, Poh YC, Collin O, Su P, de Lanerolle P, Schwartz MA, Wang N, Wang F.

Blood. 2010 Oct 28;116(17):3297-310. doi: 10.1182/blood-2009-12-260851. Epub 2010 Jul 8.

25.

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.

Legeai F, Shigenobu S, Gauthier JP, Colbourne J, Rispe C, Collin O, Richards S, Wilson AC, Murphy T, Tagu D.

Insect Mol Biol. 2010 Mar;19 Suppl 2:5-12. doi: 10.1111/j.1365-2583.2009.00930.x.

26.

Metastable atom-activated dissociation mass spectrometry: leucine/isoleucine differentiation and ring cleavage of proline residues.

Cook SL, Collin OL, Jackson GP.

J Mass Spectrom. 2009 Aug;44(8):1211-23. doi: 10.1002/jms.1598.

PMID:
19466707
27.

MIMAS 3.0 is a Multiomics Information Management and Annotation System.

Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M.

BMC Bioinformatics. 2009 May 18;10:151. doi: 10.1186/1471-2105-10-151.

28.

Is cell rheology governed by nonequilibrium-to-equilibrium transition of noncovalent bonds?

Chowdhury F, Na S, Collin O, Tay B, Li F, Tanaka T, Leckband DE, Wang N.

Biophys J. 2008 Dec 15;95(12):5719-27. doi: 10.1529/biophysj.108.139832. Epub 2008 Oct 3.

29.

Self-organized podosomes are dynamic mechanosensors.

Collin O, Na S, Chowdhury F, Hong M, Shin ME, Wang F, Wang N.

Curr Biol. 2008 Sep 9;18(17):1288-94. doi: 10.1016/j.cub.2008.07.046. Epub 2008 Aug 28.

30.

BioMAJ: a flexible framework for databanks synchronization and processing.

Filangi O, Beausse Y, Assi A, Legrand L, Larré JM, Martin V, Collin O, Caron C, Leroy H, Allouche D.

Bioinformatics. 2008 Aug 15;24(16):1823-5. doi: 10.1093/bioinformatics/btn325. Epub 2008 Jun 30.

31.

A survey of background levels of explosives and related compounds in the environment.

Lahoda KG, Collin OL, Mathis JA, LeClair HE, Wise SH, McCord BR.

J Forensic Sci. 2008 Jul;53(4):802-6. doi: 10.1111/j.1556-4029.2008.00743.x.

PMID:
18537869
32.

Regulation of neuropeptide Y Y1 receptors by testosterone in vascular smooth muscle cells in rat testis.

Kopp J, Collin O, Villar M, Mullins D, Bergh A, Hokfelt T.

Neuroendocrinology. 2008;88(3):216-26. doi: 10.1159/000138250. Epub 2008 Jun 9.

PMID:
18535365
33.

Rapid signal transduction in living cells is a unique feature of mechanotransduction.

Na S, Collin O, Chowdhury F, Tay B, Ouyang M, Wang Y, Wang N.

Proc Natl Acad Sci U S A. 2008 May 6;105(18):6626-31. doi: 10.1073/pnas.0711704105. Epub 2008 May 2.

34.

Dynamic collision-induced dissociation (DCID) in a quadrupole ion trap using a two-frequency excitation waveform: II. Effects of frequency spacing and scan rate.

Laskay UA, Collin OL, Hyland JJ, Nichol B, Jackson GP, Pasilis SP, Duckworth DC.

J Am Soc Mass Spectrom. 2007 Nov;18(11):2017-25. Epub 2007 Aug 29.

35.

Dynamic collision-induced dissociation of peptides in a quadrupole ion trap mass spectrometer.

Collin OL, Beier M, Jackson GP.

Anal Chem. 2007 Jul 15;79(14):5468-73. Epub 2007 Jun 16.

PMID:
17571856
36.

Fast gas chromatography of explosive compounds using a pulsed-discharge electron capture detector.

Collin OL, Niegel C, Derhodes KE, McCord BR, Jackson GP.

J Forensic Sci. 2006 Jul;51(4):815-8.

PMID:
16882225
37.

Spatiotemporal dynamics of actin-rich adhesion microdomains: influence of substrate flexibility.

Collin O, Tracqui P, Stephanou A, Usson Y, Clément-Lacroix J, Planus E.

J Cell Sci. 2006 May 1;119(Pt 9):1914-25.

38.

Effects of haemorrhagic hypotension on the subcapsular artery and microvasculature of the rat testis.

Lissbrant E, Collin O, Damber JE, Bergh A.

Int J Androl. 2006 Jun;29(3):434-40. Epub 2006 Mar 8.

PMID:
16524367
39.

Optical techniques for real-time penetration monitoring for laser welding.

Bardin F, Cobo A, Lopez-Higuera JM, Collin O, Aubry P, Dubois T, Högström M, Nylen P, Jonsson P, Jones JD, Hand DP.

Appl Opt. 2005 Jul 1;44(19):3869-76.

PMID:
16004030
40.
41.

Closed-loop power and focus control of laser welding for full-penetration monitoring.

Bardin F, Cobo A, Lopez-Higuera JM, Collin O, Aubry P, Dubois T, Högström M, Nylen P, Jonsson P, Jones JD, Hand DP.

Appl Opt. 2005 Jan 1;44(1):13-21.

PMID:
15662879
42.

Hormonal regulation and functional role of vascular endothelial growth factor a in the rat testis.

Rudolfsson SH, Wikström P, Jonsson A, Collin O, Bergh A.

Biol Reprod. 2004 Feb;70(2):340-7. Epub 2003 Oct 15.

PMID:
14561656
43.

The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection.

Bailly X, Leroy R, Carney S, Collin O, Zal F, Toulmond A, Jollivet D.

Proc Natl Acad Sci U S A. 2003 May 13;100(10):5885-90. Epub 2003 Apr 29.

44.
45.

Cigarette smoke and hypoxia induce acute changes in the testicular and cerebral microcirculation.

Koskinen LO, Collin O, Bergh A.

Ups J Med Sci. 2000;105(3):215-26.

PMID:
11261607
46.

Testicular vasomotion in different mammals.

Collin O, Zupp JL, Setchell BP.

Asian J Androl. 2000 Dec;2(4):297-300.

47.

Effects of acute graded reductions in testicular blood flow on testicular morphology in the adult rat.

Bergh A, Collin O, Lissbrant E.

Biol Reprod. 2001 Jan;64(1):13-20.

PMID:
11133653
48.

Temporal variations in testicular microcirculation.

Bergh A, Lissbrant E, Collin O.

J Androl. 1999 Nov-Dec;20(6):724-30.

49.

KID, a Kinase Inhibitor Database project.

Collin O, Meijer L.

Pharmacol Ther. 1999 May-Jun;82(2-3):165-8. Review.

PMID:
10454195
50.

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