Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 29

1.

Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.

Lun XK, Szklarczyk D, Gábor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B.

Mol Cell. 2019 Jun 6;74(5):1086-1102.e5. doi: 10.1016/j.molcel.2019.04.021. Epub 2019 May 14.

2.

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies.

Heller D, Szklarczyk D, Mering CV.

BMC Bioinformatics. 2019 May 6;20(1):228. doi: 10.1186/s12859-019-2828-z.

3.

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV.

Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131.

4.

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314. doi: 10.1093/nar/gky1085.

5.

Viruses.STRING: A Virus-Host Protein-Protein Interaction Database.

Cook HV, Doncheva NT, Szklarczyk D, von Mering C, Jensen LJ.

Viruses. 2018 Sep 23;10(10). pii: E519. doi: 10.3390/v10100519.

6.

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.

Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P.

Mol Biol Evol. 2017 Aug 1;34(8):2115-2122. doi: 10.1093/molbev/msx148.

7.

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368. doi: 10.1093/nar/gkw937. Epub 2016 Oct 18.

8.

Standardized benchmarking in the quest for orthologs.

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.

Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.

9.

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.

Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M.

Nucleic Acids Res. 2016 Jan 4;44(D1):D380-4. doi: 10.1093/nar/gkv1277. Epub 2015 Nov 20.

10.

WeGET: predicting new genes for molecular systems by weighted co-expression.

Szklarczyk R, Megchelenbrink W, Cizek P, Ledent M, Velemans G, Szklarczyk D, Huynen MA.

Nucleic Acids Res. 2016 Jan 4;44(D1):D567-73. doi: 10.1093/nar/gkv1228. Epub 2015 Nov 17.

11.

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D286-93. doi: 10.1093/nar/gkv1248. Epub 2015 Nov 17.

12.

Protein-protein interaction databases.

Szklarczyk D, Jensen LJ.

Methods Mol Biol. 2015;1278:39-56. doi: 10.1007/978-1-4939-2425-7_3.

PMID:
25859942
13.

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

Wang M, Herrmann CJ, Simonovic M, Szklarczyk D, von Mering C.

Proteomics. 2015 Sep;15(18):3163-8. doi: 10.1002/pmic.201400441. Epub 2015 Mar 12.

14.

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52. doi: 10.1093/nar/gku1003. Epub 2014 Oct 28.

15.

eggNOG v4.0: nested orthology inference across 3686 organisms.

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9. doi: 10.1093/nar/gkt1253. Epub 2013 Dec 1.

16.

STITCH 4: integration of protein-chemical interactions with user data.

Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7. doi: 10.1093/nar/gkt1207. Epub 2013 Nov 28.

17.

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.

Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E.

Nature. 2013 Jul 4;499(7456):74-8. doi: 10.1038/nature12323. Epub 2013 Jun 26.

PMID:
23803765
18.

STRING v9.1: protein-protein interaction networks, with increased coverage and integration.

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ.

Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15. doi: 10.1093/nar/gks1094. Epub 2012 Nov 29.

19.

"Orphan" retrogenes in the human genome.

Ciomborowska J, Rosikiewicz W, Szklarczyk D, Makałowski W, Makałowska I.

Mol Biol Evol. 2013 Feb;30(2):384-96. doi: 10.1093/molbev/mss235. Epub 2012 Oct 12.

20.

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs.

Croft L, Szklarczyk D, Jensen LJ, Gorodkin J.

BMC Syst Biol. 2012 Jul 23;6:90. doi: 10.1186/1752-0509-6-90.

21.

Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins.

Cappellini E, Jensen LJ, Szklarczyk D, Ginolhac A, da Fonseca RA, Stafford TW, Holen SR, Collins MJ, Orlando L, Willerslev E, Gilbert MT, Olsen JV.

J Proteome Res. 2012 Feb 3;11(2):917-26. doi: 10.1021/pr200721u. Epub 2011 Dec 14.

PMID:
22103443
22.

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.

Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. doi: 10.1093/nar/gkr1060. Epub 2011 Nov 16.

23.

STITCH 3: zooming in on protein-chemical interactions.

Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P.

Nucleic Acids Res. 2012 Jan;40(Database issue):D876-80. doi: 10.1093/nar/gkr1011. Epub 2011 Nov 9.

24.

Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington.

Waters MR, Stafford TW Jr, McDonald HG, Gustafson C, Rasmussen M, Cappellini E, Olsen JV, Szklarczyk D, Jensen LJ, Gilbert MT, Willerslev E.

Science. 2011 Oct 21;334(6054):351-3. doi: 10.1126/science.1207663.

25.

Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing.

Fedorov O, Huber K, Eisenreich A, Filippakopoulos P, King O, Bullock AN, Szklarczyk D, Jensen LJ, Fabbro D, Trappe J, Rauch U, Bracher F, Knapp S.

Chem Biol. 2011 Jan 28;18(1):67-76. doi: 10.1016/j.chembiol.2010.11.009.

26.

Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.

Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.

Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. doi: 10.1074/mcp.M110.003590. Epub 2010 Dec 7.

27.

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C.

Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8. doi: 10.1093/nar/gkq973. Epub 2010 Nov 2.

28.

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P.

Nucleic Acids Res. 2010 Jan;38(Database issue):D190-5. doi: 10.1093/nar/gkp951. Epub 2009 Nov 9.

29.

STITCH 2: an interaction network database for small molecules and proteins.

Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P.

Nucleic Acids Res. 2010 Jan;38(Database issue):D552-6. doi: 10.1093/nar/gkp937. Epub 2009 Nov 6.

Supplemental Content

Loading ...
Support Center