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Items: 19

1.

Best practice data life cycle approaches for the life sciences.

Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV.

Version 2. F1000Res. 2017 Aug 31 [revised 2018 Jan 1];6:1618. doi: 10.12688/f1000research.12344.2. eCollection 2017.

2.

Genome-wide meta-analysis of cognitive empathy: heritability, and correlates with sex, neuropsychiatric conditions and cognition.

Warrier V, Grasby KL, Uzefovsky F, Toro R, Smith P, Chakrabarti B, Khadake J, Mawbey-Adamson E, Litterman N, Hottenga JJ, Lubke G, Boomsma DI, Martin NG, Hatemi PK, Medland SE, Hinds DA, Bourgeron T, Baron-Cohen S.

Mol Psychiatry. 2018 Jun;23(6):1402-1409. doi: 10.1038/mp.2017.122. Epub 2017 Jun 6.

3.

Further studies of the down-regulation by Factor I of the C3b feedback cycle using endotoxin as a soluble activator and red cells as a source of CR1 on sera of different complotype.

Lachmann PJ, Lay E, Seilly DJ, Buchberger A, Schwaeble W, Khadake J.

Clin Exp Immunol. 2016 Jan;183(1):150-6. doi: 10.1111/cei.12714. Epub 2015 Nov 5.

4.

VRK1 interacts with p53 forming a basal complex that is activated by UV-induced DNA damage.

López-Sánchez I, Valbuena A, Vázquez-Cedeira M, Khadake J, Sanz-García M, Carrillo-Jiménez A, Lazo PA.

FEBS Lett. 2014 Mar 3;588(5):692-700. doi: 10.1016/j.febslet.2014.01.040. Epub 2014 Jan 31.

5.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H.

Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63. doi: 10.1093/nar/gkt1115. Epub 2013 Nov 13.

6.

Regulatory elements associated with paternally-expressed genes in the imprinted murine Angelman/Prader-Willi syndrome domain.

Rodriguez-Jato S, Shan J, Khadake J, Heggestad AD, Ma X, Johnstone KA, Resnick JL, Yang TP.

PLoS One. 2013;8(2):e52390. doi: 10.1371/journal.pone.0052390. Epub 2013 Feb 4.

7.

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.

Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H.

Nat Methods. 2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931. Erratum in: Nat Methods. 2012 Jun;9(6):626. Brinkman, Fiona [corrected to Brinkman, Fiona S L]; Hancock, Robert [corrected to Hancock, Robert E W].

8.

New gene functions in megakaryopoiesis and platelet formation.

Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U, Goodall AH, Labrune Y, Lopez LM, Mägi R, Meacham S, Okada Y, Pirastu N, Sorice R, Teumer A, Voss K, Zhang W, Ramirez-Solis R, Bis JC, Ellinghaus D, Gögele M, Hottenga JJ, Langenberg C, Kovacs P, O'Reilly PF, Shin SY, Esko T, Hartiala J, Kanoni S, Murgia F, Parsa A, Stephens J, van der Harst P, Ellen van der Schoot C, Allayee H, Attwood A, Balkau B, Bastardot F, Basu S, Baumeister SE, Biino G, Bomba L, Bonnefond A, Cambien F, Chambers JC, Cucca F, D'Adamo P, Davies G, de Boer RA, de Geus EJ, Döring A, Elliott P, Erdmann J, Evans DM, Falchi M, Feng W, Folsom AR, Frazer IH, Gibson QD, Glazer NL, Hammond C, Hartikainen AL, Heckbert SR, Hengstenberg C, Hersch M, Illig T, Loos RJ, Jolley J, Khaw KT, Kühnel B, Kyrtsonis MC, Lagou V, Lloyd-Jones H, Lumley T, Mangino M, Maschio A, Mateo Leach I, McKnight B, Memari Y, Mitchell BD, Montgomery GW, Nakamura Y, Nauck M, Navis G, Nöthlings U, Nolte IM, Porteous DJ, Pouta A, Pramstaller PP, Pullat J, Ring SM, Rotter JI, Ruggiero D, Ruokonen A, Sala C, Samani NJ, Sambrook J, Schlessinger D, Schreiber S, Schunkert H, Scott J, Smith NL, Snieder H, Starr JM, Stumvoll M, Takahashi A, Tang WH, Taylor K, Tenesa A, Lay Thein S, Tönjes A, Uda M, Ulivi S, van Veldhuisen DJ, Visscher PM, Völker U, Wichmann HE, Wiggins KL, Willemsen G, Yang TP, Hua Zhao J, Zitting P, Bradley JR, Dedoussis GV, Gasparini P, Hazen SL, Metspalu A, Pirastu M, Shuldiner AR, Joost van Pelt L, Zwaginga JJ, Boomsma DI, Deary IJ, Franke A, Froguel P, Ganesh SK, Jarvelin MR, Martin NG, Meisinger C, Psaty BM, Spector TD, Wareham NJ, Akkerman JW, Ciullo M, Deloukas P, Greinacher A, Jupe S, Kamatani N, Khadake J, Kooner JS, Penninger J, Prokopenko I, Stemple D, Toniolo D, Wernisch L, Sanna S, Hicks AA, Rendon A, Ferreira MA, Ouwehand WH, Soranzo N.

Nature. 2011 Nov 30;480(7376):201-8. doi: 10.1038/nature10659.

9.

The IntAct molecular interaction database in 2012.

Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H.

Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6. doi: 10.1093/nar/gkr1088. Epub 2011 Nov 24.

10.

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.

Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637. No abstract available.

11.

Recurated protein interaction datasets.

Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H.

Nat Methods. 2009 Dec;6(12):860-1. doi: 10.1038/nmeth1209-860. No abstract available.

PMID:
19935838
12.

The IntAct molecular interaction database in 2010.

Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H.

Nucleic Acids Res. 2010 Jan;38(Database issue):D525-31. doi: 10.1093/nar/gkp878. Epub 2009 Oct 22.

13.

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.

Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.

Genome Biol. 2008;9 Suppl 2:S5. doi: 10.1186/gb-2008-9-s2-s5. Epub 2008 Sep 1.

14.

IntAct--open source resource for molecular interaction data.

Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H.

Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5. Epub 2006 Dec 1.

15.

Expression of rat histone H1d in Escherichia coli and its purification.

Bharath MM, Khadake JR, Rao MR.

Protein Expr Purif. 1998 Feb;12(1):38-44.

PMID:
9473455
16.
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19.

Testis-specific histone (H1t) is not phosphorylated and has a weak interaction with chromatin.

Khadake JR, Markose ER, Rao MR.

Indian J Biochem Biophys. 1994 Aug;31(4):335-8.

PMID:
8002017

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