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Items: 1 to 50 of 95

1.

Synthetic 5' UTRs Can Either Up- or Downregulate Expression upon RNA-Binding Protein Binding.

Katz N, Cohen R, Solomon O, Kaufmann B, Atar O, Yakhini Z, Goldberg S, Amit R.

Cell Syst. 2019 Jul 24;9(1):93-106.e8. doi: 10.1016/j.cels.2019.04.007. Epub 2019 May 22.

PMID:
31129060
2.

Sparse NIR optimization method (SNIRO) to quantify analyte composition with visible (VIS)/near infrared (NIR) spectroscopy (350 nm-2500 nm).

Peleg Y, Shefer S, Anavy L, Chudnovsky A, Israel A, Golberg A, Yakhini Z.

Anal Chim Acta. 2019 Mar 21;1051:32-40. doi: 10.1016/j.aca.2018.11.038. Epub 2018 Nov 23.

PMID:
30661617
3.

An in Vivo Binding Assay for RNA-Binding Proteins Based on Repression of a Reporter Gene.

Katz N, Cohen R, Solomon O, Kaufmann B, Atar O, Yakhini Z, Goldberg S, Amit R.

ACS Synth Biol. 2018 Dec 21;7(12):2765-2774. doi: 10.1021/acssynbio.8b00378. Epub 2018 Nov 13.

PMID:
30408420
4.

Reciprocal Reprogramming of Cancer Cells and Associated Mesenchymal Stem Cells in Gastric Cancer.

Shamai Y, Alperovich DC, Yakhini Z, Skorecki K, Tzukerman M.

Stem Cells. 2019 Feb;37(2):176-189. doi: 10.1002/stem.2942. Epub 2018 Nov 23.

PMID:
30379370
5.

Genome-wide analysis of fitness data and its application to improve metabolic models.

Vitkin E, Solomon O, Sultan S, Yakhini Z.

BMC Bioinformatics. 2018 Oct 10;19(1):368. doi: 10.1186/s12859-018-2341-9.

6.

SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data.

Polishchuk M, Paz I, Yakhini Z, Mandel-Gutfreund Y.

Nucleic Acids Res. 2018 Jul 2;46(W1):W221-W228. doi: 10.1093/nar/gky453.

7.

Design and Analysis of Offshore Macroalgae Biorefineries.

Golberg A, Liberzon A, Vitkin E, Yakhini Z.

Methods Mol Biol. 2018 Mar 15. doi: 10.1007/7651_2018_127. [Epub ahead of print]

PMID:
29542056
8.

Prediction of Scar Size in Rats Six Months after Burns Based on Early Post-injury Polarization-Sensitive Optical Frequency Domain Imaging.

Kravez E, Villiger M, Bouma B, Yarmush M, Yakhini Z, Golberg A.

Front Physiol. 2017 Dec 1;8:967. doi: 10.3389/fphys.2017.00967. eCollection 2017.

9.

A Synthetic Oligo Library and Sequencing Approach Reveals an Insulation Mechanism Encoded within Bacterial σ54 Promoters.

Levy L, Anavy L, Solomon O, Cohen R, Brunwasser-Meirom M, Ohayon S, Atar O, Goldberg S, Yakhini Z, Amit R.

Cell Rep. 2017 Oct 17;21(3):845-858. doi: 10.1016/j.celrep.2017.09.063.

10.

Optimizing Analytical Depth and Cost Efficiency of IEF-LC/MS Proteomics.

Kifer I, Branca RM, Ben-Dor A, Zhai L, Xu P, Lehtio J, Yakhini Z.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):272-281. doi: 10.1109/TCBB.2015.2452901.

PMID:
28368805
11.

A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data.

Polishchuk M, Paz I, Kohen R, Mesika R, Yakhini Z, Mandel-Gutfreund Y.

Methods. 2017 Apr 15;118-119:73-81. doi: 10.1016/j.ymeth.2017.03.003. Epub 2017 Mar 6.

PMID:
28274760
12.

Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays.

Levo M, Avnit-Sagi T, Lotan-Pompan M, Kalma Y, Weinberger A, Yakhini Z, Segal E.

Mol Cell. 2017 Feb 16;65(4):604-617.e6. doi: 10.1016/j.molcel.2017.01.007.

13.

Mutual enrichment in aggregated ranked lists with applications to gene expression regulation.

Cohn-Alperovich D, Rabner A, Kifer I, Mandel-Gutfreund Y, Yakhini Z.

Bioinformatics. 2017 Feb 1;33(3):470. doi: 10.1093/bioinformatics/btw727. No abstract available.

14.

Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data.

Ben-Elazar S, Chor B, Yakhini Z.

Bioinformatics. 2016 Sep 1;32(17):i559-i566. doi: 10.1093/bioinformatics/btw453.

PMID:
27587675
15.

Mutual enrichment in aggregated ranked lists with applications to gene expression regulation.

Cohn-Alperovich D, Rabner A, Kifer I, Mandel-Gutfreund Y, Yakhini Z.

Bioinformatics. 2016 Sep 1;32(17):i464-i472. doi: 10.1093/bioinformatics/btw435.

PMID:
27587663
16.

LIMT is a novel metastasis inhibiting lncRNA suppressed by EGF and downregulated in aggressive breast cancer.

Sas-Chen A, Aure MR, Leibovich L, Carvalho S, Enuka Y, Körner C, Polycarpou-Schwarz M, Lavi S, Nevo N, Kuznetsov Y, Yuan J, Azuaje F; Oslo Breast Cancer Research Consortium (OSBREAC)SauerTorillGeislerJürgenHofvindSolveigBathenTone FBorgenElinEngebråtenOlavFodstadØysteinGarredØysteinGeitvikGry AarumKåresenRolfNaumeBjørnMælandsmoGunhild MariRussnesHege GSchlichtingEllenSørlieThereseLingjærdeOle ChristianSahlbergKristine KleiviSkjervenHelle KristineFritzmanBritt, Ulitsky I, Diederichs S, Wiemann S, Yakhini Z, Kristensen VN, Børresen-Dale AL, Yarden Y.

EMBO Mol Med. 2016 Sep 1;8(9):1052-64. doi: 10.15252/emmm.201606198. Print 2016 Sep.

17.

Thermochemical hydrolysis of macroalgae Ulva for biorefinery: Taguchi robust design method.

Jiang R, Linzon Y, Vitkin E, Yakhini Z, Chudnovsky A, Golberg A.

Sci Rep. 2016 Jun 13;6:27761. doi: 10.1038/srep27761.

18.

Comparative genetics. Systematic discovery of cap-independent translation sequences in human and viral genomes.

Weingarten-Gabbay S, Elias-Kirma S, Nir R, Gritsenko AA, Stern-Ginossar N, Yakhini Z, Weinberger A, Segal E.

Science. 2016 Jan 15;351(6270). pii: aad4939. doi: 10.1126/science.aad4939. Epub 2016 Jan 14.

19.

Corrigendum: Unraveling determinants of transcription factor binding outside the core binding site.

Levo M, Zalckvar E, Sharon E, Dantas Machado AC, Kalma Y, Lotan-Pompan M, Weinberger A, Yakhini Z, Rohs R, Segal E.

Genome Res. 2015 Sep;25(9):1410.2. No abstract available.

20.

Serum N-glycan analysis in breast cancer patients--Relation to tumour biology and clinical outcome.

Haakensen VD, Steinfeld I, Saldova R, Shehni AA, Kifer I, Naume B, Rudd PM, Børresen-Dale AL, Yakhini Z.

Mol Oncol. 2016 Jan;10(1):59-72. doi: 10.1016/j.molonc.2015.08.002. Epub 2015 Aug 19.

21.

An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding.

Drory Retwitzer M, Kifer I, Sengupta S, Yakhini Z, Barash D.

PLoS One. 2015 Jul 31;10(7):e0134262. doi: 10.1371/journal.pone.0134262. eCollection 2015.

22.

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps.

Drory Retwitzer M, Polishchuk M, Churkin E, Kifer I, Yakhini Z, Barash D.

Nucleic Acids Res. 2015 Jul 1;43(W1):W507-12. doi: 10.1093/nar/gkv435. Epub 2015 May 4.

23.

Systematic dissection of the sequence determinants of gene 3' end mediated expression control.

Shalem O, Sharon E, Lubliner S, Regev I, Lotan-Pompan M, Yakhini Z, Segal E.

PLoS Genet. 2015 Apr 15;11(4):e1005147. doi: 10.1371/journal.pgen.1005147. eCollection 2015 Apr.

24.

Unraveling determinants of transcription factor binding outside the core binding site.

Levo M, Zalckvar E, Sharon E, Dantas Machado AC, Kalma Y, Lotam-Pompan M, Weinberger A, Yakhini Z, Rohs R, Segal E.

Genome Res. 2015 Jul;25(7):1018-29. doi: 10.1101/gr.185033.114. Epub 2015 Mar 11. Erratum in: Genome Res. 2015 Sep;25(9):1410.2.

25.

ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types.

Steinfeld I, Navon R, Creech ML, Yakhini Z, Tsalenko A.

Bioinformatics. 2015 May 15;31(10):1683-5. doi: 10.1093/bioinformatics/btu853. Epub 2015 Jan 9.

26.

Peer group normalization and urine to blood context in steroid metabolomics: the case of CAH and obesity.

Vitkin E, Ben-Dor A, Shmoish M, Hartmann MF, Yakhini Z, Wudy SA, Hochberg Z.

Steroids. 2014 Oct;88:83-9. doi: 10.1016/j.steroids.2014.07.003. Epub 2014 Jul 17.

PMID:
25042470
27.

Probing the effect of promoters on noise in gene expression using thousands of designed sequences.

Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, Yakhini Z, Segal E.

Genome Res. 2014 Oct;24(10):1698-706. doi: 10.1101/gr.168773.113. Epub 2014 Jul 16.

28.

Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs.

Leibovich L, Yakhini Z.

Algorithms Mol Biol. 2014 Apr 5;9(1):11. doi: 10.1186/1748-7188-9-11.

29.

Association of N-glycosylation with breast carcinoma and systemic features using high-resolution quantitative UPLC.

Saldova R, Asadi Shehni A, Haakensen VD, Steinfeld I, Hilliard M, Kifer I, Helland A, Yakhini Z, Børresen-Dale AL, Rudd PM.

J Proteome Res. 2014 May 2;13(5):2314-27. doi: 10.1021/pr401092y. Epub 2014 Apr 11.

PMID:
24669823
30.

Molecular rules governing de novo methylation in cancer.

Nejman D, Straussman R, Steinfeld I, Ruvolo M, Roberts D, Yakhini Z, Cedar H.

Cancer Res. 2014 Mar 1;74(5):1475-83. doi: 10.1158/0008-5472.CAN-13-3042. Epub 2014 Jan 22.

31.

Deregulation of cancer-related miRNAs is a common event in both benign and malignant human breast tumors.

Tahiri A, Leivonen SK, Lüders T, Steinfeld I, Ragle Aure M, Geisler J, Mäkelä R, Nord S, Riis ML, Yakhini Z, Kleivi Sahlberg K, Børresen-Dale AL, Perälä M, Bukholm IR, Kristensen VN.

Carcinogenesis. 2014 Jan;35(1):76-85. doi: 10.1093/carcin/bgt333. Epub 2013 Oct 8.

PMID:
24104550
32.

Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.

Johansson HJ, Sanchez BC, Mundt F, Forshed J, Kovacs A, Panizza E, Hultin-Rosenberg L, Lundgren B, Martens U, Máthé G, Yakhini Z, Helou K, Krawiec K, Kanter L, Hjerpe A, Stål O, Linderholm BK, Lehtiö J.

Nat Commun. 2013;4:2175. doi: 10.1038/ncomms3175.

33.

DRIMust: a web server for discovering rank imbalanced motifs using suffix trees.

Leibovich L, Paz I, Yakhini Z, Mandel-Gutfreund Y.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W174-9. doi: 10.1093/nar/gkt407. Epub 2013 May 17.

34.

Identifying in-trans process associated genes in breast cancer by integrated analysis of copy number and expression data.

Aure MR, Steinfeld I, Baumbusch LO, Liestøl K, Lipson D, Nyberg S, Naume B, Sahlberg KK, Kristensen VN, Børresen-Dale AL, Lingjærde OC, Yakhini Z.

PLoS One. 2013;8(1):e53014. doi: 10.1371/journal.pone.0053014. Epub 2013 Jan 30.

35.

Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome.

Ben-Elazar S, Yakhini Z, Yanai I.

Nucleic Acids Res. 2013 Feb 1;41(4):2191-201. doi: 10.1093/nar/gks1360. Epub 2013 Jan 8.

36.

miRNA target enrichment analysis reveals directly active miRNAs in health and disease.

Steinfeld I, Navon R, Ach R, Yakhini Z.

Nucleic Acids Res. 2013 Feb 1;41(3):e45. doi: 10.1093/nar/gks1142. Epub 2012 Dec 2.

37.

Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.

Farkash-Amar S, David Y, Polten A, Hezroni H, Eldar YC, Meshorer E, Yakhini Z, Simon I.

PLoS One. 2012;7(11):e48986. doi: 10.1371/journal.pone.0048986. Epub 2012 Nov 7.

38.

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters.

Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, Zeevi D, Keren L, Yakhini Z, Weinberger A, Segal E.

Nat Biotechnol. 2012 May 20;30(6):521-30. doi: 10.1038/nbt.2205.

39.

Global methylation patterns in idiopathic pulmonary fibrosis.

Rabinovich EI, Kapetanaki MG, Steinfeld I, Gibson KF, Pandit KV, Yu G, Yakhini Z, Kaminski N.

PLoS One. 2012;7(4):e33770. doi: 10.1371/journal.pone.0033770. Epub 2012 Apr 10.

40.

Efficient motif search in ranked lists and applications to variable gap motifs.

Leibovich L, Yakhini Z.

Nucleic Acids Res. 2012 Jul;40(13):5832-47. doi: 10.1093/nar/gks206. Epub 2012 Mar 13.

41.

Deubiquitination of EGFR by Cezanne-1 contributes to cancer progression.

Pareja F, Ferraro DA, Rubin C, Cohen-Dvashi H, Zhang F, Aulmann S, Ben-Chetrit N, Pines G, Navon R, Crosetto N, Köstler W, Carvalho S, Lavi S, Schmitt F, Dikic I, Yakhini Z, Sinn P, Mills GB, Yarden Y.

Oncogene. 2012 Oct 25;31(43):4599-608. doi: 10.1038/onc.2011.587. Epub 2011 Dec 19.

42.

Ischemia caused by time to freezing induces systematic microRNA and mRNA responses in cancer tissue.

Borgan E, Navon R, Vollan HK, Schlichting E, Sauer T, Yakhini Z, Lingjærde OC, Sørlie T, Børresen-Dale AL.

Mol Oncol. 2011 Dec;5(6):564-76. doi: 10.1016/j.molonc.2011.08.004. Epub 2011 Aug 29.

43.

Divergent RNA binding specificity of yeast Puf2p.

Yosefzon Y, Koh YY, Chritton JJ, Lande A, Leibovich L, Barziv L, Petzold C, Yakhini Z, Mandel-Gutfreund Y, Wickens M, Arava Y.

RNA. 2011 Aug;17(8):1479-88. doi: 10.1261/rna.2700311. Epub 2011 Jun 17.

44.

Cancer computational biology.

Yakhini Z, Jurisica I.

BMC Bioinformatics. 2011 Apr 26;12:120. doi: 10.1186/1471-2105-12-120. No abstract available.

45.

miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors.

Enerly E, Steinfeld I, Kleivi K, Leivonen SK, Aure MR, Russnes HG, Rønneberg JA, Johnsen H, Navon R, Rødland E, Mäkelä R, Naume B, Perälä M, Kallioniemi O, Kristensen VN, Yakhini Z, Børresen-Dale AL.

PLoS One. 2011 Feb 22;6(2):e16915. doi: 10.1371/journal.pone.0016915.

46.

A structural-based statistical approach suggests a cooperative activity of PUM1 and miR-410 in human 3'-untranslated regions.

Leibovich L, Mandel-Gutfreund Y, Yakhini Z.

Silence. 2010 Sep 22;1(1):17. doi: 10.1186/1758-907X-1-17.

47.

Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture.

Yaffe E, Farkash-Amar S, Polten A, Yakhini Z, Tanay A, Simon I.

PLoS Genet. 2010 Jul 1;6(7):e1001011. doi: 10.1371/journal.pgen.1001011.

48.

EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors.

Avraham R, Sas-Chen A, Manor O, Steinfeld I, Shalgi R, Tarcic G, Bossel N, Zeisel A, Amit I, Zwang Y, Enerly E, Russnes HG, Biagioni F, Mottolese M, Strano S, Blandino G, Børresen-Dale AL, Pilpel Y, Yakhini Z, Segal E, Yarden Y.

Sci Signal. 2010 Jun 1;3(124):ra43. doi: 10.1126/scisignal.2000876.

49.

A novel translocation breakpoint within the BPTF gene is associated with a pre-malignant phenotype.

Buganim Y, Goldstein I, Lipson D, Milyavsky M, Polak-Charcon S, Mardoukh C, Solomon H, Kalo E, Madar S, Brosh R, Perelman M, Navon R, Goldfinger N, Barshack I, Yakhini Z, Rotter V.

PLoS One. 2010 Mar 11;5(3):e9657. doi: 10.1371/journal.pone.0009657.

50.

SNPs in genes coding for ROS metabolism and signalling in association with docetaxel clearance.

Edvardsen H, Brunsvig PF, Solvang H, Tsalenko A, Andersen A, Syvanen AC, Yakhini Z, Børresen-Dale AL, Olsen H, Aamdal S, Kristensen VN.

Pharmacogenomics J. 2010 Dec;10(6):513-23. doi: 10.1038/tpj.2010.6. Epub 2010 Feb 16.

PMID:
20157331

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