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1.

TRY plant trait database - enhanced coverage and open access.

Kattge J, Bönisch G, Díaz S, Lavorel S, Prentice IC, Leadley P, Tautenhahn S, Werner GDA, Aakala T, Abedi M, Acosta ATR, Adamidis GC, Adamson K, Aiba M, Albert CH, Alcántara JM, Alcázar C C, Aleixo I, Ali H, Amiaud B, Ammer C, Amoroso MM, Anand M, Anderson C, Anten N, Antos J, Apgaua DMG, Ashman TL, Asmara DH, Asner GP, Aspinwall M, Atkin O, Aubin I, Baastrup-Spohr L, Bahalkeh K, Bahn M, Baker T, Baker WJ, Bakker JP, Baldocchi D, Baltzer J, Banerjee A, Baranger A, Barlow J, Barneche DR, Baruch Z, Bastianelli D, Battles J, Bauerle W, Bauters M, Bazzato E, Beckmann M, Beeckman H, Beierkuhnlein C, Bekker R, Belfry G, Belluau M, Beloiu M, Benavides R, Benomar L, Berdugo-Lattke ML, Berenguer E, Bergamin R, Bergmann J, Bergmann Carlucci M, Berner L, Bernhardt-Römermann M, Bigler C, Bjorkman AD, Blackman C, Blanco C, Blonder B, Blumenthal D, Bocanegra-González KT, Boeckx P, Bohlman S, Böhning-Gaese K, Boisvert-Marsh L, Bond W, Bond-Lamberty B, Boom A, Boonman CCF, Bordin K, Boughton EH, Boukili V, Bowman DMJS, Bravo S, Brendel MR, Broadley MR, Brown KA, Bruelheide H, Brumnich F, Bruun HH, Bruy D, Buchanan SW, Bucher SF, Buchmann N, Buitenwerf R, Bunker DE, Bürger J, Burrascano S, Burslem DFRP, Butterfield BJ, Byun C, Marques M, Scalon MC, Caccianiga M, Cadotte M, Cailleret M, Camac J, Camarero JJ, Campany C, Campetella G, Campos JA, Cano-Arboleda L, Canullo R, Carbognani M, Carvalho F, Casanoves F, Castagneyrol B, Catford JA, Cavender-Bares J, Cerabolini BEL, Cervellini M, Chacón-Madrigal E, Chapin K, Chapin FS, Chelli S, Chen SC, Chen A, Cherubini P, Chianucci F, Choat B, Chung KS, Chytrý M, Ciccarelli D, Coll L, Collins CG, Conti L, Coomes D, Cornelissen JHC, Cornwell WK, Corona P, Coyea M, Craine J, Craven D, Cromsigt JPGM, Csecserits A, Cufar K, Cuntz M, da Silva AC, Dahlin KM, Dainese M, Dalke I, Dalle Fratte M, Dang-Le AT, Danihelka J, Dannoura M, Dawson S, de Beer AJ, De Frutos A, De Long JR, Dechant B, Delagrange S, Delpierre N, Derroire G, Dias AS, Diaz-Toribio MH, Dimitrakopoulos PG, Dobrowolski M, Doktor D, Dřevojan P, Dong N, Dransfield J, Dressler S, Duarte L, Ducouret E, Dullinger S, Durka W, Duursma R, Dymova O, E-Vojtkó A, Eckstein RL, Ejtehadi H, Elser J, Emilio T, Engemann K, Erfanian MB, Erfmeier A, Esquivel-Muelbert A, Esser G, Estiarte M, Domingues TF, Fagan WF, Fagúndez J, Falster DS, Fan Y, Fang J, Farris E, Fazlioglu F, Feng Y, Fernandez-Mendez F, Ferrara C, Ferreira J, Fidelis A, Finegan B, Firn J, Flowers TJ, Flynn DFB, Fontana V, Forey E, Forgiarini C, François L, Frangipani M, Frank D, Frenette-Dussault C, Freschet GT, Fry EL, Fyllas NM, Mazzochini GG, Gachet S, Gallagher R, Ganade G, Ganga F, García-Palacios P, Gargaglione V, Garnier E, Garrido JL, de Gasper AL, Gea-Izquierdo G, Gibson D, Gillison AN, Giroldo A, Glasenhardt MC, Gleason S, Gliesch M, Goldberg E, Göldel B, Gonzalez-Akre E, Gonzalez-Andujar JL, González-Melo A, González-Robles A, Graae BJ, Granda E, Graves S, Green WA, Gregor T, Gross N, Guerin GR, Günther A, Gutiérrez AG, Haddock L, Haines A, Hall J, Hambuckers A, Han W, Harrison SP, Hattingh W, Hawes JE, He T, He P, Heberling JM, Helm A, Hempel S, Hentschel J, Hérault B, Hereş AM, Herz K, Heuertz M, Hickler T, Hietz P, Higuchi P, Hipp AL, Hirons A, Hock M, Hogan JA, Holl K, Honnay O, Hornstein D, Hou E, Hough-Snee N, Hovstad KA, Ichie T, Igić B, Illa E, Isaac M, Ishihara M, Ivanov L, Ivanova L, Iversen CM, Izquierdo J, Jackson RB, Jackson B, Jactel H, Jagodzinski AM, Jandt U, Jansen S, Jenkins T, Jentsch A, Jespersen JRP, Jiang GF, Johansen JL, Johnson D, Jokela EJ, Joly CA, Jordan GJ, Joseph GS, Junaedi D, Junker RR, Justes E, Kabzems R, Kane J, Kaplan Z, Kattenborn T, Kavelenova L, Kearsley E, Kempel A, Kenzo T, Kerkhoff A, Khalil MI, Kinlock NL, Kissling WD, Kitajima K, Kitzberger T, Kjøller R, Klein T, Kleyer M, Klimešová J, Klipel J, Kloeppel B, Klotz S, Knops JMH, Kohyama T, Koike F, Kollmann J, Komac B, Komatsu K, König C, Kraft NJB, Kramer K, Kreft H, Kühn I, Kumarathunge D, Kuppler J, Kurokawa H, Kurosawa Y, Kuyah S, Laclau JP, Lafleur B, Lallai E, Lamb E, Lamprecht A, Larkin DJ, Laughlin D, Le Bagousse-Pinguet Y, le Maire G, le Roux PC, le Roux E, Lee T, Lens F, Lewis SL, Lhotsky B, Li Y, Li X, Lichstein JW, Liebergesell M, Lim JY, Lin YS, Linares JC, Liu C, Liu D, Liu U, Livingstone S, Llusià J, Lohbeck M, López-García Á, Lopez-Gonzalez G, Lososová Z, Louault F, Lukács BA, Lukeš P, Luo Y, Lussu M, Ma S, Maciel Rabelo Pereira C, Mack M, Maire V, Mäkelä A, Mäkinen H, Malhado ACM, Mallik A, Manning P, Manzoni S, Marchetti Z, Marchino L, Marcilio-Silva V, Marcon E, Marignani M, Markesteijn L, Martin A, Martínez-Garza C, Martínez-Vilalta J, Mašková T, Mason K, Mason N, Massad TJ, Masse J, Mayrose I, McCarthy J, McCormack ML, McCulloh K, McFadden IR, McGill BJ, McPartland MY, Medeiros JS, Medlyn B, Meerts P, Mehrabi Z, Meir P, Melo FPL, Mencuccini M, Meredieu C, Messier J, Mészáros I, Metsaranta J, Michaletz ST, Michelaki C, Migalina S, Milla R, Miller JED, Minden V, Ming R, Mokany K, Moles AT, Molnár A 5th, Molofsky J, Molz M, Montgomery RA, Monty A, Moravcová L, Moreno-Martínez A, Moretti M, Mori AS, Mori S, Morris D, Morrison J, Mucina L, Mueller S, Muir CD, Müller SC, Munoz F, Myers-Smith IH, Myster RW, Nagano M, Naidu S, Narayanan A, Natesan B, Negoita L, Nelson AS, Neuschulz EL, Ni J, Niedrist G, Nieto J, Niinemets Ü, Nolan R, Nottebrock H, Nouvellon Y, Novakovskiy A; Nutrient Network, Nystuen KO, O'Grady A, O'Hara K, O'Reilly-Nugent A, Oakley S, Oberhuber W, Ohtsuka T, Oliveira R, Öllerer K, Olson ME, Onipchenko V, Onoda Y, Onstein RE, Ordonez JC, Osada N, Ostonen I, Ottaviani G, Otto S, Overbeck GE, Ozinga WA, Pahl AT, Paine CET, Pakeman RJ, Papageorgiou AC, Parfionova E, Pärtel M, Patacca M, Paula S, Paule J, Pauli H, Pausas JG, Peco B, Penuelas J, Perea A, Peri PL, Petisco-Souza AC, Petraglia A, Petritan AM, Phillips OL, Pierce S, Pillar VD, Pisek J, Pomogaybin A, Poorter H, Portsmuth A, Poschlod P, Potvin C, Pounds D, Powell AS, Power SA, Prinzing A, Puglielli G, Pyšek P, Raevel V, Rammig A, Ransijn J, Ray CA, Reich PB, Reichstein M, Reid DEB, Réjou-Méchain M, de Dios VR, Ribeiro S, Richardson S, Riibak K, Rillig MC, Riviera F, Robert EMR, Roberts S, Robroek B, Roddy A, Rodrigues AV, Rogers A, Rollinson E, Rolo V, Römermann C, Ronzhina D, Roscher C, Rosell JA, Rosenfield MF, Rossi C, Roy DB, Royer-Tardif S, Rüger N, Ruiz-Peinado R, Rumpf SB, Rusch GM, Ryo M, Sack L, Saldaña A, Salgado-Negret B, Salguero-Gomez R, Santa-Regina I, Santacruz-García AC, Santos J, Sardans J, Schamp B, Scherer-Lorenzen M, Schleuning M, Schmid B, Schmidt M, Schmitt S, Schneider JV, Schowanek SD, Schrader J, Schrodt F, Schuldt B, Schurr F, Selaya Garvizu G, Semchenko M, Seymour C, Sfair JC, Sharpe JM, Sheppard CS, Sheremetiev S, Shiodera S, Shipley B, Shovon TA, Siebenkäs A, Sierra C, Silva V, Silva M, Sitzia T, Sjöman H, Slot M, Smith NG, Sodhi D, Soltis P, Soltis D, Somers B, Sonnier G, Sørensen MV, Sosinski EE Jr, Soudzilovskaia NA, Souza AF, Spasojevic M, Sperandii MG, Stan AB, Stegen J, Steinbauer K, Stephan JG, Sterck F, Stojanovic DB, Strydom T, Suarez ML, Svenning JC, Svitková I, Svitok M, Svoboda M, Swaine E, Swenson N, Tabarelli M, Takagi K, Tappeiner U, Tarifa R, Tauugourdeau S, Tavsanoglu C, Te Beest M, Tedersoo L, Thiffault N, Thom D, Thomas E, Thompson K, Thornton PE, Thuiller W, Tichý L, Tissue D, Tjoelker MG, Tng DYP, Tobias J, Török P, Tarin T, Torres-Ruiz JM, Tóthmérész B, Treurnicht M, Trivellone V, Trolliet F, Trotsiuk V, Tsakalos JL, Tsiripidis I, Tysklind N, Umehara T, Usoltsev V, Vadeboncoeur M, Vaezi J, Valladares F, Vamosi J, van Bodegom PM, van Breugel M, Van Cleemput E, van de Weg M, van der Merwe S, van der Plas F, van der Sande MT, van Kleunen M, Van Meerbeek K, Vanderwel M, Vanselow KA, Vårhammar A, Varone L, Vasquez Valderrama MY, Vassilev K, Vellend M, Veneklaas EJ, Verbeeck H, Verheyen K, Vibrans A, Vieira I, Villacís J, Violle C, Vivek P, Wagner K, Waldram M, Waldron A, Walker AP, Waller M, Walther G, Wang H, Wang F, Wang W, Watkins H, Watkins J, Weber U, Weedon JT, Wei L, Weigelt P, Weiher E, Wells AW, Wellstein C, Wenk E, Westoby M, Westwood A, White PJ, Whitten M, Williams M, Winkler DE, Winter K, Womack C, Wright IJ, Wright SJ, Wright J, Pinho BX, Ximenes F, Yamada T, Yamaji K, Yanai R, Yankov N, Yguel B, Zanini KJ, Zanne AE, Zelený D, Zhao YP, Zheng J, Zheng J, Ziemińska K, Zirbel CR, Zizka G, Zo-Bi IC, Zotz G, Wirth C.

Glob Chang Biol. 2020 Jan;26(1):119-188. doi: 10.1111/gcb.14904. Epub 2019 Dec 31.

2.

Interaction among ploidy, breeding system and lineage diversification.

Zenil-Ferguson R, Burleigh JG, Freyman WA, Igić B, Mayrose I, Goldberg EE.

New Phytol. 2019 Nov;224(3):1252-1265. doi: 10.1111/nph.16184. Epub 2019 Oct 16.

PMID:
31617595
3.

Model selection may not be a mandatory step for phylogeny reconstruction.

Abadi S, Azouri D, Pupko T, Mayrose I.

Nat Commun. 2019 Feb 25;10(1):934. doi: 10.1038/s41467-019-08822-w.

4.

The global biogeography of polyploid plants.

Rice A, Šmarda P, Novosolov M, Drori M, Glick L, Sabath N, Meiri S, Belmaker J, Mayrose I.

Nat Ecol Evol. 2019 Jan 29;3(2):265-273. doi: 10.1038/s41559-018-0787-9.

PMID:
30697006
5.

Meiotic drive shapes rates of karyotype evolution in mammals.

Blackmon H, Justison J, Mayrose I, Goldberg EE.

Evolution. 2019 Mar;73(3):511-523. doi: 10.1111/evo.13682. Epub 2019 Feb 5.

6.

Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants.

Masrati G, Dwivedi M, Rimon A, Gluck-Margolin Y, Kessel A, Ashkenazy H, Mayrose I, Padan E, Ben-Tal N.

Nat Commun. 2018 Oct 11;9(1):4205. doi: 10.1038/s41467-018-06770-5.

7.

OneTwoTree: An online tool for phylogeny reconstruction.

Drori M, Rice A, Einhorn M, Chay O, Glick L, Mayrose I.

Mol Ecol Resour. 2018 Nov;18(6):1492-1499. doi: 10.1111/1755-0998.12927. Epub 2018 Aug 3.

PMID:
30010236
8.

CRISPys: Optimal sgRNA Design for Editing Multiple Members of a Gene Family Using the CRISPR System.

Hyams G, Abadi S, Lahav S, Avni A, Halperin E, Shani E, Mayrose I.

J Mol Biol. 2018 Jul 20;430(15):2184-2195. doi: 10.1016/j.jmb.2018.03.019. Epub 2018 Apr 3.

PMID:
29625203
9.

Macroevolutionary Patterns of Flowering Plant Speciation and Extinction.

Vamosi JC, Magallón S, Mayrose I, Otto SP, Sauquet H.

Annu Rev Plant Biol. 2018 Apr 29;69:685-706. doi: 10.1146/annurev-arplant-042817-040348. Epub 2018 Feb 28.

PMID:
29489399
10.

A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action.

Abadi S, Yan WX, Amar D, Mayrose I.

PLoS Comput Biol. 2017 Oct 16;13(10):e1005807. doi: 10.1371/journal.pcbi.1005807. eCollection 2017 Oct.

11.

Multispeed genome diploidization and diversification after an ancient allopolyploidization.

Mandáková T, Pouch M, Harmanová K, Zhan SH, Mayrose I, Lysak MA.

Mol Ecol. 2017 Nov;26(22):6445-6462. doi: 10.1111/mec.14379. Epub 2017 Nov 25.

PMID:
29024107
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.

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
14.

Macroevolutionary synthesis of flowering plant sexual systems.

Goldberg EE, Otto SP, Vamosi JC, Mayrose I, Sabath N, Ming R, Ashman TL.

Evolution. 2017 Apr;71(4):898-912. doi: 10.1111/evo.13181. Epub 2017 Feb 8.

PMID:
28085192
15.

Erratum: Sex determination, longevity, and the birth and death of reptilian species.

Sabath N, Itescu Y, Feldman A, Meiri S, Mayrose I, Valenzuela N.

Ecol Evol. 2016 Nov 1;6(21):7939. doi: 10.1002/ece3.2559. eCollection 2016 Nov.

16.

Sex determination, longevity, and the birth and death of reptilian species.

Sabath N, Itescu Y, Feldman A, Meiri S, Mayrose I, Valenzuela N.

Ecol Evol. 2016 Jun 28;6(15):5207-20. doi: 10.1002/ece3.2277. eCollection 2016 Aug. Erratum in: Ecol Evol. 2016 Nov 01;6(21):7939.

17.

Whole-genome duplication as a key factor in crop domestication.

Salman-Minkov A, Sabath N, Mayrose I.

Nat Plants. 2016 Aug 1;2:16115. doi: 10.1038/nplants.2016.115.

PMID:
27479829
18.

Phylogenetic evidence for cladogenetic polyploidization in land plants.

Zhan SH, Drori M, Goldberg EE, Otto SP, Mayrose I.

Am J Bot. 2016 Jul;103(7):1252-8. doi: 10.3732/ajb.1600108. Epub 2016 Jul 27.

19.

Polyploidy and sexual system in angiosperms: Is there an association?

Glick L, Sabath N, Ashman TL, Goldberg E, Mayrose I.

Am J Bot. 2016 Jul;103(7):1223-35. doi: 10.3732/ajb.1500424. Epub 2016 Jun 27.

20.

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.

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.

Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms.

Sabath N, Goldberg EE, Glick L, Einhorn M, Ashman TL, Ming R, Otto SP, Vamosi JC, Mayrose I.

New Phytol. 2016 Feb;209(3):1290-300. doi: 10.1111/nph.13696. Epub 2015 Oct 15.

23.

The Interplay between Scientific Overlap and Cooperation and the Resulting Gain in Co-Authorship Interactions.

Mayrose I, Freilich S.

PLoS One. 2015 Sep 15;10(9):e0137856. doi: 10.1371/journal.pone.0137856. eCollection 2015.

24.

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.

Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I.

Mol Ecol Resour. 2015 Sep;15(5):1179-91. doi: 10.1111/1755-0998.12387. Epub 2015 Feb 27.

25.

Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al. (2014).

Mayrose I, Zhan SH, Rothfels CJ, Arrigo N, Barker MS, Rieseberg LH, Otto SP.

New Phytol. 2015 Apr;206(1):27-35. doi: 10.1111/nph.13192. Epub 2014 Dec 4. No abstract available.

26.

The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers.

Rice A, Glick L, Abadi S, Einhorn M, Kopelman NM, Salman-Minkov A, Mayzel J, Chay O, Mayrose I.

New Phytol. 2015 Apr;206(1):19-26. doi: 10.1111/nph.13191. Epub 2014 Nov 26. No abstract available.

27.

Sex determination: why so many ways of doing it?

Bachtrog D, Mank JE, Peichel CL, Kirkpatrick M, Otto SP, Ashman TL, Hahn MW, Kitano J, Mayrose I, Ming R, Perrin N, Ross L, Valenzuela N, Vamosi JC; Tree of Sex Consortium.

PLoS Biol. 2014 Jul 1;12(7):e1001899. doi: 10.1371/journal.pbio.1001899. eCollection 2014 Jul. Review.

28.

ChromEvol: assessing the pattern of chromosome number evolution and the inference of polyploidy along a phylogeny.

Glick L, Mayrose I.

Mol Biol Evol. 2014 Jul;31(7):1914-22. doi: 10.1093/molbev/msu122. Epub 2014 Apr 7.

PMID:
24710517
29.

Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

Zhan SH, Glick L, Tsigenopoulos CS, Otto SP, Mayrose I.

J Evol Biol. 2014 Feb;27(2):391-403. doi: 10.1111/jeb.12308. Epub 2014 Jan 13.

30.

Karyotypic changes through dysploidy persist longer over evolutionary time than polyploid changes.

Escudero M, Martín-Bravo S, Mayrose I, Fernández-Mazuecos M, Fiz-Palacios O, Hipp AL, Pimentel M, Jiménez-Mejías P, Valcárcel V, Vargas P, Luceño M.

PLoS One. 2014 Jan 9;9(1):e85266. doi: 10.1371/journal.pone.0085266. eCollection 2014.

31.

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.

32.

Increased growth in sunflower correlates with reduced defences and altered gene expression in response to biotic and abiotic stress.

Mayrose M, Kane NC, Mayrose I, Dlugosch KM, Rieseberg LH.

Mol Ecol. 2011 Nov;20(22):4683-94. doi: 10.1111/j.1365-294X.2011.05301.x. Epub 2011 Oct 11.

PMID:
21988641
33.

Recently formed polyploid plants diversify at lower rates.

Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, Otto SP.

Science. 2011 Sep 2;333(6047):1257. doi: 10.1126/science.1207205. Epub 2011 Aug 18.

34.

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
35.

A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution.

Mayrose I, Otto SP.

Mol Biol Evol. 2011 Jan;28(1):759-70. doi: 10.1093/molbev/msq263. Epub 2010 Oct 20.

PMID:
20961959
36.

An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes.

Stern A, Mayrose I, Penn O, Shaul S, Gophna U, Pupko T.

Syst Biol. 2010 Mar;59(2):212-25. doi: 10.1093/sysbio/syp104. Epub 2010 Jan 15.

37.

Probabilistic models of chromosome number evolution and the inference of polyploidy.

Mayrose I, Barker MS, Otto SP.

Syst Biol. 2010 Mar;59(2):132-44. doi: 10.1093/sysbio/syp083. Epub 2009 Dec 10.

PMID:
20525626
38.

Epitopia: a web-server for predicting B-cell epitopes.

Rubinstein ND, Mayrose I, Martz E, Pupko T.

BMC Bioinformatics. 2009 Sep 14;10:287. doi: 10.1186/1471-2105-10-287.

39.

The frequency of polyploid speciation in vascular plants.

Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH.

Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13875-9. doi: 10.1073/pnas.0811575106. Epub 2009 Aug 10.

40.

A machine-learning approach for predicting B-cell epitopes.

Rubinstein ND, Mayrose I, Pupko T.

Mol Immunol. 2009 Feb;46(5):840-7. doi: 10.1016/j.molimm.2008.09.009. Epub 2008 Oct 22.

PMID:
18947876
41.

Computational characterization of B-cell epitopes.

Rubinstein ND, Mayrose I, Halperin D, Yekutieli D, Gershoni JM, Pupko T.

Mol Immunol. 2008 Jul;45(12):3477-89. Epub 2007 Nov 26.

PMID:
18023478
42.

Pepitope: epitope mapping from affinity-selected peptides.

Mayrose I, Penn O, Erez E, Rubinstein ND, Shlomi T, Freund NT, Bublil EM, Ruppin E, Sharan R, Gershoni JM, Martz E, Pupko T.

Bioinformatics. 2007 Dec 1;23(23):3244-6. Epub 2007 Oct 31.

PMID:
17977889
43.

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates.

Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T.

Bioinformatics. 2007 Jul 1;23(13):i319-27.

PMID:
17646313
44.

Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm.

Bublil EM, Freund NT, Mayrose I, Penn O, Roitburd-Berman A, Rubinstein ND, Pupko T, Gershoni JM.

Proteins. 2007 Jul 1;68(1):294-304.

PMID:
17427229
45.

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm.

Mayrose I, Shlomi T, Rubinstein ND, Gershoni JM, Ruppin E, Sharan R, Pupko T.

Nucleic Acids Res. 2007;35(1):69-78. Epub 2006 Dec 6.

46.

A gamma mixture model better accounts for among site rate heterogeneity.

Mayrose I, Friedman N, Pupko T.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii151-8.

PMID:
16204095
47.

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.

Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W299-302.

48.

Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account.

Mayrose I, Mitchell A, Pupko T.

J Mol Evol. 2005 Mar;60(3):345-53.

PMID:
15871045
49.

Selecton: a server for detecting evolutionary forces at a single amino-acid site.

Doron-Faigenboim A, Stern A, Mayrose I, Bacharach E, Pupko T.

Bioinformatics. 2005 May 1;21(9):2101-3. Epub 2005 Jan 12.

PMID:
15647294
50.

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.

Mayrose I, Graur D, Ben-Tal N, Pupko T.

Mol Biol Evol. 2004 Sep;21(9):1781-91. Epub 2004 Jun 16.

PMID:
15201400

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