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Items: 1 to 50 of 99

1.

Corrigendum: Independent Evolution of Strychnine Recognition by Bitter Taste Receptor Subtypes.

Xue AY, Di Pizio A, Levit A, Yarnitzky T, Penn O, Pupko T, Niv MY.

Front Mol Biosci. 2018 Sep 11;5:84. doi: 10.3389/fmolb.2018.00084. eCollection 2018.

2.

A simulation-based approach to statistical alignment.

Levy Karin E, Ashkenazy H, Hein J, Pupko T.

Syst Biol. 2018 Sep 15. doi: 10.1093/sysbio/syy059. [Epub ahead of print]

PMID:
30239957
3.

Evolution of the U.S. Biological Select Agent Rathayibacter toxicus.

Davis EW 2nd, Tabima JF, Weisberg AJ, Lopes LD, Wiseman MS, Wiseman MS, Pupko T, Belcher MS, Sechler AJ, Tancos MA, Schroeder BK, Murray TD, Luster DG, Schneider WL, Rogers EE, Andreote FD, Grünwald NJ, Putnam ML, Chang JH.

MBio. 2018 Aug 28;9(4). pii: e01280-18. doi: 10.1128/mBio.01280-18.

4.

ASAP - A Webserver for Immunoglobulin-Sequencing Analysis Pipeline.

Avram O, Vaisman-Mentesh A, Yehezkel D, Ashkenazy H, Pupko T, Wine Y.

Front Immunol. 2018 Jul 30;9:1686. doi: 10.3389/fimmu.2018.01686. eCollection 2018.

5.

Multiple sequence alignment averaging improves phylogeny reconstruction.

Ashkenazy H, Sela I, Levy Karin E, Landan G, Pupko T.

Syst Biol. 2018 May 15. doi: 10.1093/sysbio/syy036. [Epub ahead of print]

PMID:
29771363
6.

The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria.

Lavi B, Levy Karin E, Pupko T, Hazkani-Covo E.

Genome Biol Evol. 2018 Mar 1;10(3):918-927. doi: 10.1093/gbe/evy044.

7.

Independent Evolution of Strychnine Recognition by Bitter Taste Receptor Subtypes.

Xue AY, Di Pizio A, Levit A, Yarnitzky T, Penn O, Pupko T, Niv MY.

Front Mol Biosci. 2018 Mar 2;5:9. doi: 10.3389/fmolb.2018.00009. eCollection 2018. Erratum in: Front Mol Biosci. 2018 Sep 11;5:84.

8.

Interleukin-6 and Interferon-α Signaling via JAK1-STAT Differentially Regulate Oncolytic versus Cytoprotective Antiviral States.

Danziger O, Pupko T, Bacharach E, Ehrlich M.

Front Immunol. 2018 Jan 30;9:94. doi: 10.3389/fimmu.2018.00094. eCollection 2018.

9.

Phage display peptide libraries: deviations from randomness and correctives.

Ryvkin A, Ashkenazy H, Weiss-Ottolenghi Y, Piller C, Pupko T, Gershoni JM.

Nucleic Acids Res. 2018 May 18;46(9):e52. doi: 10.1093/nar/gky077.

10.

Sequence analysis of malacoherpesvirus proteins: Pan-herpesvirus capsid module and replication enzymes with an ancient connection to "Megavirales".

Mushegian A, Karin EL, Pupko T.

Virology. 2018 Jan 1;513:114-128. doi: 10.1016/j.virol.2017.10.009. Epub 2017 Oct 21.

PMID:
29065352
11.

SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm.

Ashkenazy H, Levy Karin E, Mertens Z, Cartwright RA, Pupko T.

Nucleic Acids Res. 2017 Jul 3;45(W1):W453-W457. doi: 10.1093/nar/gkx322.

12.

TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites.

Levy Karin E, Ashkenazy H, Wicke S, Pupko T, Mayrose I.

Nucleic Acids Res. 2017 Jul 3;45(W1):W260-W264. doi: 10.1093/nar/gkx288.

13.

Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation.

Levy Karin E, Shkedy D, Ashkenazy H, Cartwright RA, Pupko T.

Genome Biol Evol. 2017 May 1;9(5):1280-1294. doi: 10.1093/gbe/evx084.

14.

An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution.

Levy Karin E, Wicke S, Pupko T, Mayrose I.

Syst Biol. 2017 Nov 1;66(6):917-933. doi: 10.1093/sysbio/syx032.

PMID:
28177510
15.

Revealing the inventory of type III effectors in Pantoea agglomerans gall-forming pathovars using draft genome sequences and a machine-learning approach.

Nissan G, Gershovits M, Morozov M, Chalupowicz L, Sessa G, Manulis-Sasson S, Barash I, Pupko T.

Mol Plant Pathol. 2018 Feb;19(2):381-392. doi: 10.1111/mpp.12528. Epub 2017 Feb 16.

PMID:
28019708
16.

The Cytoskeleton of Parabasalian Parasites Comprises Proteins that Share Properties Common to Intermediate Filament Proteins.

Preisner H, Karin EL, Poschmann G, Stühler K, Pupko T, Gould SB.

Protist. 2016 Dec;167(6):526-543. doi: 10.1016/j.protis.2016.09.001. Epub 2016 Sep 16.

17.

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.

McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, Sreecharan T, Vehkala M, Välimäki N, Prentice MB, Ashour A, Avram O, Pupko T, Dobrindt U, Literak I, Guenther S, Schaufler K, Wieler LH, Zhiyong Z, Sheppard SK, McInerney JO, Corander J.

PLoS Genet. 2016 Sep 12;12(9):e1006280. doi: 10.1371/journal.pgen.1006280. eCollection 2016 Sep.

18.

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.

Ashkenazy H, Abadi S, Martz E, Chay O, Mayrose I, Pupko T, Ben-Tal N.

Nucleic Acids Res. 2016 Jul 8;44(W1):W344-50. doi: 10.1093/nar/gkw408. Epub 2016 May 10.

19.

Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits.

Eckshtain-Levi N, Shkedy D, Gershovits M, Da Silva GM, Tamir-Ariel D, Walcott R, Pupko T, Burdman S.

Front Microbiol. 2016 Apr 6;7:430. doi: 10.3389/fmicb.2016.00430. eCollection 2016.

20.

Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.

Burstein D, Amaro F, Zusman T, Lifshitz Z, Cohen O, Gilbert JA, Pupko T, Shuman HA, Segal G.

Nat Genet. 2016 Feb;48(2):167-75. doi: 10.1038/ng.3481. Epub 2016 Jan 11.

21.

Regulation of alternative splicing at the single-cell level.

Faigenbloom L, Rubinstein ND, Kloog Y, Mayrose I, Pupko T, Stein R.

Mol Syst Biol. 2015 Dec 28;11(12):845. doi: 10.15252/msb.20156278.

22.

Inferring Indel Parameters using a Simulation-based Approach.

Levy Karin E, Rabin A, Ashkenazy H, Shkedy D, Avram O, Cartwright RA, Pupko T.

Genome Biol Evol. 2015 Nov 3;7(12):3226-38. doi: 10.1093/gbe/evv212.

23.

Assessing the prediction fidelity of ancestral reconstruction by a library approach.

Bar-Rogovsky H, Stern A, Penn O, Kobl I, Pupko T, Tawfik DS.

Protein Eng Des Sel. 2015 Nov;28(11):507-18. doi: 10.1093/protein/gzv038. Epub 2015 Aug 13.

PMID:
26275856
24.

Identification of novel Xanthomonas euvesicatoria type III effector proteins by a machine-learning approach.

Teper D, Burstein D, Salomon D, Gershovitz M, Pupko T, Sessa G.

Mol Plant Pathol. 2016 Apr;17(3):398-411. doi: 10.1111/mpp.12288. Epub 2015 Aug 15.

PMID:
26104875
25.

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.

Sela I, Ashkenazy H, Katoh K, Pupko T.

Nucleic Acids Res. 2015 Jul 1;43(W1):W7-14. doi: 10.1093/nar/gkv318. Epub 2015 Apr 16.

26.

Novel type III effectors in Pseudomonas aeruginosa.

Burstein D, Satanower S, Simovitch M, Belnik Y, Zehavi M, Yerushalmi G, Ben-Aroya S, Pupko T, Banin E.

MBio. 2015 Mar 17;6(2):e00161. doi: 10.1128/mBio.00161-15.

27.

Revealing bacterial targets of growth inhibitors encoded by bacteriophage T7.

Molshanski-Mor S, Yosef I, Kiro R, Edgar R, Manor M, Gershovits M, Laserson M, Pupko T, Qimron U.

Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18715-20. doi: 10.1073/pnas.1413271112. Epub 2014 Dec 15.

28.

Indel reliability in indel-based phylogenetic inference.

Ashkenazy H, Cohen O, Pupko T, Huchon D.

Genome Biol Evol. 2014 Nov 18;6(12):3199-209. doi: 10.1093/gbe/evu252.

29.

Transfer of noncoding DNA drives regulatory rewiring in bacteria.

Oren Y, Smith MB, Johns NI, Kaplan Zeevi M, Biran D, Ron EZ, Corander J, Wang HH, Alm EJ, Pupko T.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):16112-7. doi: 10.1073/pnas.1413272111. Epub 2014 Oct 13.

30.

Alignment errors strongly impact likelihood-based tests for comparing topologies.

Levy Karin E, Susko E, Pupko T.

Mol Biol Evol. 2014 Nov;31(11):3057-67. doi: 10.1093/molbev/msu231. Epub 2014 Aug 1.

PMID:
25085999
31.

Identification of novel Coxiella burnetii Icm/Dot effectors and genetic analysis of their involvement in modulating a mitogen-activated protein kinase pathway.

Lifshitz Z, Burstein D, Schwartz K, Shuman HA, Pupko T, Segal G.

Infect Immun. 2014 Sep;82(9):3740-52. doi: 10.1128/IAI.01729-14. Epub 2014 Jun 23.

32.

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array.

Yosef I, Shitrit D, Goren MG, Burstein D, Pupko T, Qimron U.

Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14396-401. doi: 10.1073/pnas.1300108110. Epub 2013 Aug 12.

33.

Synonymous site conservation in the HIV-1 genome.

Mayrose I, Stern A, Burdelova EO, Sabo Y, Laham-Karam N, Zamostiano R, Bacharach E, Pupko T.

BMC Evol Biol. 2013 Aug 4;13:164. doi: 10.1186/1471-2148-13-164.

34.

State-of the art methodologies dictate new standards for phylogenetic analysis.

Anisimova M, Liberles DA, Philippe H, Provan J, Pupko T, von Haeseler A.

BMC Evol Biol. 2013 Aug 1;13:161. doi: 10.1186/1471-2148-13-161. Review.

35.

CoPAP: Coevolution of presence-absence patterns.

Cohen O, Ashkenazy H, Levy Karin E, Burstein D, Pupko T.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W232-7. doi: 10.1093/nar/gkt471. Epub 2013 Jun 8.

36.

Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal.

Lifshitz Z, Burstein D, Peeri M, Zusman T, Schwartz K, Shuman HA, Pupko T, Segal G.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):E707-15. doi: 10.1073/pnas.1215278110. Epub 2013 Feb 4.

37.

Uncovering the co-evolutionary network among prokaryotic genes.

Cohen O, Ashkenazy H, Burstein D, Pupko T.

Bioinformatics. 2012 Sep 15;28(18):i389-i394. doi: 10.1093/bioinformatics/bts396.

38.

Deep Panning: steps towards probing the IgOme.

Ryvkin A, Ashkenazy H, Smelyanski L, Kaplan G, Penn O, Weiss-Ottolenghi Y, Privman E, Ngam PB, Woodward JE, May GD, Bell C, Pupko T, Gershoni JM.

PLoS One. 2012;7(8):e41469. doi: 10.1371/journal.pone.0041469. Epub 2012 Aug 1.

39.

Differential GC content between exons and introns establishes distinct strategies of splice-site recognition.

Amit M, Donyo M, Hollander D, Goren A, Kim E, Gelfman S, Lev-Maor G, Burstein D, Schwartz S, Postolsky B, Pupko T, Ast G.

Cell Rep. 2012 May 31;1(5):543-56. doi: 10.1016/j.celrep.2012.03.013. Epub 2012 May 3.

40.

FastML: a web server for probabilistic reconstruction of ancestral sequences.

Ashkenazy H, Penn O, Doron-Faigenboim A, Cohen O, Cannarozzi G, Zomer O, Pupko T.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W580-4. doi: 10.1093/nar/gks498. Epub 2012 May 31.

41.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

42.

A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis.

Burstein D, Gould SB, Zimorski V, Kloesges T, Kiosse F, Major P, Martin WF, Pupko T, Dagan T.

Eukaryot Cell. 2012 Feb;11(2):217-28. doi: 10.1128/EC.05225-11. Epub 2011 Dec 2.

43.

Emergence of an HIV-1 cluster harbouring the major protease L90M mutation among treatment-naïve patients in Tel Aviv, Israel.

Turner D, Amit S, Chalom S, Penn O, Pupko T, Katchman E, Matus N, Tellio H, Katzir M, Avidor B.

HIV Med. 2012 Apr;13(4):202-6. doi: 10.1111/j.1468-1293.2011.00960.x. Epub 2011 Nov 3.

44.

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons.

Gelfman S, Burstein D, Penn O, Savchenko A, Amit M, Schwartz S, Pupko T, Ast G.

Genome Res. 2012 Jan;22(1):35-50. doi: 10.1101/gr.119834.110. Epub 2011 Oct 5.

45.

Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation study.

Cohen O, Pupko T.

Genome Biol Evol. 2011;3:1265-75. doi: 10.1093/gbe/evr101. Epub 2011 Oct 4.

46.

Improving the performance of positive selection inference by filtering unreliable alignment regions.

Privman E, Penn O, Pupko T.

Mol Biol Evol. 2012 Jan;29(1):1-5. doi: 10.1093/molbev/msr177. Epub 2011 Jul 19.

PMID:
21772063
47.

Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection.

Rubinstein ND, Doron-Faigenboim A, Mayrose I, Pupko T.

Mol Biol Evol. 2011 Dec;28(12):3297-308. doi: 10.1093/molbev/msr162. Epub 2011 Jun 20.

PMID:
21690564
48.

The operonic location of auto-transcriptional repressors is highly conserved in bacteria.

Rubinstein ND, Zeevi D, Oren Y, Segal G, Pupko T.

Mol Biol Evol. 2011 Dec;28(12):3309-18. doi: 10.1093/molbev/msr163. Epub 2011 Jun 20.

PMID:
21690561
49.

Native homing endonucleases can target conserved genes in humans and in animal models.

Barzel A, Privman E, Peeri M, Naor A, Shachar E, Burstein D, Lazary R, Gophna U, Pupko T, Kupiec M.

Nucleic Acids Res. 2011 Aug;39(15):6646-59. doi: 10.1093/nar/gkr242. Epub 2011 Apr 27.

50.

Phosphatidylserine increases IKBKAP levels in familial dysautonomia cells.

Keren H, Donyo M, Zeevi D, Maayan C, Pupko T, Ast G.

PLoS One. 2010 Dec 29;5(12):e15884. doi: 10.1371/journal.pone.0015884.

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