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Items: 26

1.

ResponseNet v.3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues.

Basha O, Mauer O, Simonovsky E, Shpringer R, Yeger-Lotem E.

Nucleic Acids Res. 2019 May 22. pii: gkz421. doi: 10.1093/nar/gkz421. [Epub ahead of print]

PMID:
31114913
2.

Large-scale analysis of human gene expression variability associates highly variable drug targets with lower drug effectiveness and safety.

Simonovsky E, Schuster R, Yeger-Lotem E.

Bioinformatics. 2019 Jan 14. doi: 10.1093/bioinformatics/btz023. [Epub ahead of print]

PMID:
30649201
3.

Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae.

Iacovella MG, Bremang M, Basha O, Giacò L, Carotenuto W, Golfieri C, Szakal B, Dal Maschio M, Infantino V, Beznoussenko GV, Joseph CR, Visintin C, Mironov AA, Visintin R, Branzei D, Ferreira-Cerca S, Yeger-Lotem E, De Wulf P.

Nucleic Acids Res. 2018 Sep 6;46(15):7586-7611. doi: 10.1093/nar/gky618.

4.

Role of duplicate genes in determining the tissue-selectivity of hereditary diseases.

Barshir R, Hekselman I, Shemesh N, Sharon M, Novack L, Yeger-Lotem E.

PLoS Genet. 2018 May 3;14(5):e1007327. doi: 10.1371/journal.pgen.1007327. eCollection 2018 May.

5.

RSRC1 mutation affects intellect and behaviour through aberrant splicing and transcription, downregulating IGFBP3.

Perez Y, Menascu S, Cohen I, Kadir R, Basha O, Shorer Z, Romi H, Meiri G, Rabinski T, Ofir R, Yeger-Lotem E, Birk OS.

Brain. 2018 Apr 1;141(4):961-970. doi: 10.1093/brain/awy045.

PMID:
29522154
6.

The DifferentialNet database of differential protein-protein interactions in human tissues.

Basha O, Shpringer R, Argov CM, Yeger-Lotem E.

Nucleic Acids Res. 2018 Jan 4;46(D1):D522-D526. doi: 10.1093/nar/gkx981.

7.

MotifNet: a web-server for network motif analysis.

Smoly IY, Lerman E, Ziv-Ukelson M, Yeger-Lotem E.

Bioinformatics. 2017 Jun 15;33(12):1907-1909. doi: 10.1093/bioinformatics/btx056.

PMID:
28165111
8.

An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts.

Smoly I, Shemesh N, Ziv-Ukelson M, Ben-Zvi A, Yeger-Lotem E.

PLoS Comput Biol. 2017 Jan 30;13(1):e1005221. doi: 10.1371/journal.pcbi.1005221. eCollection 2017 Jan.

9.

A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans.

Bar-Lavan Y, Shemesh N, Dror S, Ofir R, Yeger-Lotem E, Ben-Zvi A.

PLoS Genet. 2016 Dec 30;12(12):e1006531. doi: 10.1371/journal.pgen.1006531. eCollection 2016 Dec.

10.

The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues.

Basha O, Barshir R, Sharon M, Lerman E, Kirson BF, Hekselman I, Yeger-Lotem E.

Nucleic Acids Res. 2017 Jan 4;45(D1):D427-D431. doi: 10.1093/nar/gkw1088. Epub 2016 Nov 29.

11.

Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns.

Smoly I, Carmel A, Shemer-Avni Y, Yeger-Lotem E, Ziv-Ukelson M.

J Comput Biol. 2016 Mar;23(3):165-79. doi: 10.1089/cmb.2015.0168.

PMID:
26953875
12.

Human protein interaction networks across tissues and diseases.

Yeger-Lotem E, Sharan R.

Front Genet. 2015 Aug 19;6:257. doi: 10.3389/fgene.2015.00257. eCollection 2015. Review.

13.

MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts.

Basha O, Flom D, Barshir R, Smoly I, Tirman S, Yeger-Lotem E.

Nucleic Acids Res. 2015 Jul 1;43(W1):W258-63. doi: 10.1093/nar/gkv515. Epub 2015 May 18.

14.

A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novel Arabidopsis thaliana abiotic stress genes.

Ransbotyn V, Yeger-Lotem E, Basha O, Acuna T, Verduyn C, Gordon M, Chalifa-Caspi V, Hannah MA, Barak S.

Plant Biotechnol J. 2015 May;13(4):501-13. doi: 10.1111/pbi.12274. Epub 2014 Nov 5.

15.

Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases.

Barshir R, Shwartz O, Smoly IY, Yeger-Lotem E.

PLoS Comput Biol. 2014 Jun 12;10(6):e1003632. doi: 10.1371/journal.pcbi.1003632. eCollection 2014 Jun.

16.

Cancer evolution is associated with pervasive positive selection on globally expressed genes.

Ostrow SL, Barshir R, DeGregori J, Yeger-Lotem E, Hershberg R.

PLoS Genet. 2014 Mar 6;10(3):e1004239. doi: 10.1371/journal.pgen.1004239. eCollection 2014 Mar.

17.

A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks.

Lan A, Ziv-Ukelson M, Yeger-Lotem E.

Bioinformatics. 2013 Jul 1;29(13):i210-6. doi: 10.1093/bioinformatics/btt240.

18.

ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data.

Basha O, Tirman S, Eluk A, Yeger-Lotem E.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W198-203. doi: 10.1093/nar/gkt532. Epub 2013 Jun 12.

19.

The TissueNet database of human tissue protein-protein interactions.

Barshir R, Basha O, Eluk A, Smoly IY, Lan A, Yeger-Lotem E.

Nucleic Acids Res. 2013 Jan;41(Database issue):D841-4. doi: 10.1093/nar/gks1198. Epub 2012 Nov 27.

20.

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data.

Lan A, Smoly IY, Rapaport G, Lindquist S, Fraenkel E, Yeger-Lotem E.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W424-9. doi: 10.1093/nar/gkr359. Epub 2011 May 16.

21.

Compounds from an unbiased chemical screen reverse both ER-to-Golgi trafficking defects and mitochondrial dysfunction in Parkinson's disease models.

Su LJ, Auluck PK, Outeiro TF, Yeger-Lotem E, Kritzer JA, Tardiff DF, Strathearn KE, Liu F, Cao S, Hamamichi S, Hill KJ, Caldwell KA, Bell GW, Fraenkel E, Cooper AA, Caldwell GA, McCaffery JM, Rochet JC, Lindquist S.

Dis Model Mech. 2010 Mar-Apr;3(3-4):194-208. doi: 10.1242/dmm.004267. Epub 2009 Dec 28.

22.

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity.

Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar AG, King OD, Auluck PK, Geddie ML, Valastyan JS, Karger DR, Lindquist S, Fraenkel E.

Nat Genet. 2009 Mar;41(3):316-23. doi: 10.1038/ng.337. Epub 2009 Feb 22.

23.

Alignment of metabolic pathways.

Pinter RY, Rokhlenko O, Yeger-Lotem E, Ziv-Ukelson M.

Bioinformatics. 2005 Aug 15;21(16):3401-8. Epub 2005 Jun 28.

PMID:
15985496
24.

Chromosomal organization is shaped by the transcription regulatory network.

Hershberg R, Yeger-Lotem E, Margalit H.

Trends Genet. 2005 Mar;21(3):138-42. Review.

PMID:
15734572
25.

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.

Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H.

Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):5934-9. Epub 2004 Apr 12.

26.

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