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Items: 48

1.

New views on an old enzyme: allosteric regulation and evolution of archaeal pyruvate kinases.

Johnsen U, Reinhardt A, Landan G, Tria FDK, Turner JM, Davies C, Schönheit P.

FEBS J. 2019 Jul;286(13):2471-2489. doi: 10.1111/febs.14837. Epub 2019 Apr 26.

PMID:
30945446
2.

Segregational Drift and the Interplay between Plasmid Copy Number and Evolvability.

Ilhan J, Kupczok A, Woehle C, Wein T, Hülter NF, Rosenstiel P, Landan G, Mizrahi I, Dagan T.

Mol Biol Evol. 2019 Mar 1;36(3):472-486. doi: 10.1093/molbev/msy225.

3.

Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction.

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

Syst Biol. 2019 Jan 1;68(1):117-130. doi: 10.1093/sysbio/syy036.

PMID:
29771363
4.

Phylogenetic rooting using minimal ancestor deviation.

Tria FDK, Landan G, Dagan T.

Nat Ecol Evol. 2017 Jun 19;1:193. doi: 10.1038/s41559-017-0193.

PMID:
29388565
5.

Expansion of the redox-sensitive proteome coincides with the plastid endosymbiosis.

Woehle C, Dagan T, Landan G, Vardi A, Rosenwasser S.

Nat Plants. 2017 May 15;3:17066. doi: 10.1038/nplants.2017.66.

6.

Late Mitochondrial Origin Is an Artifact.

Martin WF, Roettger M, Ku C, Garg SG, Nelson-Sathi S, Landan G.

Genome Biol Evol. 2017 Feb 1;9(2):373-379. doi: 10.1093/gbe/evx027.

7.

Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction.

Popa O, Landan G, Dagan T.

ISME J. 2017 Feb;11(2):543-554. doi: 10.1038/ismej.2016.116. Epub 2016 Sep 20.

8.

UMI-4C for quantitative and targeted chromosomal contact profiling.

Schwartzman O, Mukamel Z, Oded-Elkayam N, Olivares-Chauvet P, Lubling Y, Landan G, Izraeli S, Tanay A.

Nat Methods. 2016 Aug;13(8):685-91. doi: 10.1038/nmeth.3922. Epub 2016 Jul 4.

PMID:
27376768
9.

DnaK-Dependent Accelerated Evolutionary Rate in Prokaryotes.

Kadibalban AS, Bogumil D, Landan G, Dagan T.

Genome Biol Evol. 2016 Jun 3;8(5):1590-9. doi: 10.1093/gbe/evw102.

10.

Endosymbiotic origin and differential loss of eukaryotic genes.

Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF.

Nature. 2015 Aug 27;524(7566):427-32. doi: 10.1038/nature14963. Epub 2015 Aug 19.

PMID:
26287458
11.

The Contribution of Genetic Recombination to CRISPR Array Evolution.

Kupczok A, Landan G, Dagan T.

Genome Biol Evol. 2015 Jun 16;7(7):1925-39. doi: 10.1093/gbe/evv113.

12.

Concatenated alignments and the case of the disappearing tree.

Thiergart T, Landan G, Martin WF.

BMC Evol Biol. 2014 Dec 30;14:266. doi: 10.1186/s12862-014-0266-0.

13.

The parasite Trichomonas vaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes.

Woehle C, Kusdian G, Radine C, Graur D, Landan G, Gould SB.

BMC Genomics. 2014 Oct 17;15:906. doi: 10.1186/1471-2164-15-906.

14.

Origins of major archaeal clades correspond to gene acquisitions from bacteria.

Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chávez N, Thiergart T, Janssen A, Bryant D, Landan G, Schönheit P, Siebers B, McInerney JO, Martin WF.

Nature. 2015 Jan 1;517(7532):77-80. doi: 10.1038/nature13805. Epub 2014 Oct 15.

15.

Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells.

Shipony Z, Mukamel Z, Cohen NM, Landan G, Chomsky E, Zeliger SR, Fried YC, Ainbinder E, Friedman N, Tanay A.

Nature. 2014 Sep 4;513(7516):115-9. doi: 10.1038/nature13458. Epub 2014 Jul 13.

PMID:
25043040
16.

The onset of p53 loss of heterozygosity is differentially induced in various stem cell types and may involve the loss of either allele.

Shetzer Y, Kagan S, Koifman G, Sarig R, Kogan-Sakin I, Charni M, Kaufman T, Zapatka M, Molchadsky A, Rivlin N, Dinowitz N, Levin S, Landan G, Goldstein I, Goldfinger N, Pe'er D, Radlwimmer B, Lichter P, Rotter V, Aloni-Grinstein R.

Cell Death Differ. 2014 Sep;21(9):1419-31. doi: 10.1038/cdd.2014.57. Epub 2014 May 16.

17.

Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis.

Bogumil D, Alvarez-Ponce D, Landan G, McInerney JO, Dagan T.

Mol Biol Evol. 2014 Feb;31(2):410-8. doi: 10.1093/molbev/mst212. Epub 2013 Nov 4.

18.

Early bioenergetic evolution.

Sousa FL, Thiergart T, Landan G, Nelson-Sathi S, Pereira IA, Allen JF, Lane N, Martin WF.

Philos Trans R Soc Lond B Biol Sci. 2013 Jun 10;368(1622):20130088. doi: 10.1098/rstb.2013.0088. Print 2013 Jul 19. Review.

19.

Deep sequencing of Trichomonas vaginalis during the early infection of vaginal epithelial cells and amoeboid transition.

Gould SB, Woehle C, Kusdian G, Landan G, Tachezy J, Zimorski V, Martin WF.

Int J Parasitol. 2013 Aug;43(9):707-19. doi: 10.1016/j.ijpara.2013.04.002. Epub 2013 May 18.

PMID:
23688716
20.

Detecting negative selection on recurrent mutations using gene genealogy.

Ezawa K, Landan G, Graur D.

BMC Genet. 2013 May 7;14:37. doi: 10.1186/1471-2156-14-37.

21.

Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids.

Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, Tandeau de Marsac N, Gugger M, Lockhart PJ, Allen JF, Brune I, Maus I, Pühler A, Martin WF.

Genome Biol Evol. 2013;5(1):31-44. doi: 10.1093/gbe/evs117.

22.

Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea.

Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M, McInerney JO, Deppenmeier U, Martin WF.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20537-42. doi: 10.1073/pnas.1209119109. Epub 2012 Nov 26.

23.

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues.

Landan G, Cohen NM, Mukamel Z, Bar A, Molchadsky A, Brosh R, Horn-Saban S, Zalcenstein DA, Goldfinger N, Zundelevich A, Gal-Yam EN, Rotter V, Tanay A.

Nat Genet. 2012 Nov;44(11):1207-14. doi: 10.1038/ng.2442. Epub 2012 Oct 14.

PMID:
23064413
24.

Robust 4C-seq data analysis to screen for regulatory DNA interactions.

van de Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, Splinter E, Valdes-Quezada C, Oz Y, Bouwman BA, Verstegen MJ, de Wit E, Tanay A, de Laat W.

Nat Methods. 2012 Oct;9(10):969-72. doi: 10.1038/nmeth.2173. Epub 2012 Sep 9.

PMID:
22961246
25.

Chaperones divide yeast proteins into classes of expression level and evolutionary rate.

Bogumil D, Landan G, Ilhan J, Dagan T.

Genome Biol Evol. 2012;4(5):618-25. doi: 10.1093/gbe/evs025. Epub 2012 Mar 14.

26.

An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.

Thiergart T, Landan G, Schenk M, Dagan T, Martin WF.

Genome Biol Evol. 2012;4(4):466-85. doi: 10.1093/gbe/evs018. Epub 2012 Feb 21.

27.

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes.

Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T.

Genome Res. 2011 Apr;21(4):599-609. doi: 10.1101/gr.115592.110. Epub 2011 Jan 26.

28.

Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm.

Elhaik E, Graur D, Josić K, Landan G.

Nucleic Acids Res. 2010 Aug;38(15):e158. doi: 10.1093/nar/gkq532. Epub 2010 Jun 22.

29.

GUIDANCE: a web server for assessing alignment confidence scores.

Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W23-8. doi: 10.1093/nar/gkq443. Epub 2010 May 23.

30.

An alignment confidence score capturing robustness to guide tree uncertainty.

Penn O, Privman E, Landan G, Graur D, Pupko T.

Mol Biol Evol. 2010 Aug;27(8):1759-67. doi: 10.1093/molbev/msq066. Epub 2010 Mar 5.

31.

DNA methylation programming and reprogramming in primate embryonic stem cells.

Cohen NM, Dighe V, Landan G, Reynisdóttir S, Palsson A, Mitalipov S, Tanay A.

Genome Res. 2009 Dec;19(12):2193-201. doi: 10.1101/gr.096685.109. Epub 2009 Nov 3.

32.

Functional enhancers at the gene-poor 8q24 cancer-linked locus.

Jia L, Landan G, Pomerantz M, Jaschek R, Herman P, Reich D, Yan C, Khalid O, Kantoff P, Oh W, Manak JR, Berman BP, Henderson BE, Frenkel B, Haiman CA, Freedman M, Tanay A, Coetzee GA.

PLoS Genet. 2009 Aug;5(8):e1000597. doi: 10.1371/journal.pgen.1000597. Epub 2009 Aug 14.

33.

Can GC content at third-codon positions be used as a proxy for isochore composition?

Elhaik E, Landan G, Graur D.

Mol Biol Evol. 2009 Aug;26(8):1829-33. doi: 10.1093/molbev/msp100. Epub 2009 May 14.

PMID:
19443854
34.

Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment.

Schneider A, Souvorov A, Sabath N, Landan G, Gonnet GH, Graur D.

Genome Biol Evol. 2009 Jun 5;1:114-8. doi: 10.1093/gbe/evp012.

35.

A method for the simultaneous estimation of selection intensities in overlapping genes.

Sabath N, Landan G, Graur D.

PLoS One. 2008;3(12):e3996. doi: 10.1371/journal.pone.0003996. Epub 2008 Dec 22.

36.

p53-Repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation.

Brosh R, Shalgi R, Liran A, Landan G, Korotayev K, Nguyen GH, Enerly E, Johnsen H, Buganim Y, Solomon H, Goldstein I, Madar S, Goldfinger N, Børresen-Dale AL, Ginsberg D, Harris CC, Pilpel Y, Oren M, Rotter V.

Mol Syst Biol. 2008;4:229. doi: 10.1038/msb.2008.65. Epub 2008 Nov 25.

37.

Same-strand overlapping genes in bacteria: compositional determinants of phase bias.

Sabath N, Graur D, Landan G.

Biol Direct. 2008 Aug 21;3:36. doi: 10.1186/1745-6150-3-36.

38.

Characterization of pairwise and multiple sequence alignment errors.

Landan G, Graur D.

Gene. 2009 Jul 15;441(1-2):141-7. doi: 10.1016/j.gene.2008.05.016. Epub 2008 Jun 3.

PMID:
18614299
39.

The genome of the model beetle and pest Tribolium castaneum.

Tribolium Genome Sequencing Consortium, Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, Raible F, Bork P, Friedrich M, Walden KK, Robertson HM, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y, Miller SC, Grossmann D, Bucher G.

Nature. 2008 Apr 24;452(7190):949-55. doi: 10.1038/nature06784. Epub 2008 Mar 23.

PMID:
18362917
40.
41.

Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor.

Deusch O, Landan G, Roettger M, Gruenheit N, Kowallik KV, Allen JF, Martin W, Dagan T.

Mol Biol Evol. 2008 Apr;25(4):748-61. doi: 10.1093/molbev/msn022. Epub 2008 Jan 24.

PMID:
18222943
42.

Prevention of acute graft-versus-host disease by blocking T-cell entry to secondary lymphoid organs.

Beilhack A, Schulz S, Baker J, Beilhack GF, Nishimura R, Baker EM, Landan G, Herman EI, Butcher EC, Contag CH, Negrin RS.

Blood. 2008 Mar 1;111(5):2919-28. Epub 2007 Nov 7.

43.

Heads or tails: a simple reliability check for multiple sequence alignments.

Landan G, Graur D.

Mol Biol Evol. 2007 Jun;24(6):1380-3. Epub 2007 Mar 25.

PMID:
17387100
44.

Alloreactive T-cell trafficking after hematopoietic stem cell transplantation.

Beilhack A, Schulz S, Baker J, Beilhack G, Herman E, Baker E, Landan G, Nishimura R, Butcher E, Contag Ch, Negrin R.

J Stem Cells Regen Med. 2007 May 16;2(1):107. eCollection 2007. No abstract available.

PMID:
24692934
45.

Alloreactive T-cell trafficking after hematopoietic stem cell transplantation.

Beilhack A, Schulz S, Baker J, Beilhack G, Herman E, Baker E, Landan G, Nishimura R, Butcher E, Contag Ch, Negrin R.

J Stem Cells Regen Med. 2007 May 16;2(1):17. eCollection 2007. No abstract available.

PMID:
24692881
46.

Evolution of the sarafotoxin/endothelin superfamily of proteins.

Landan G, Bdolah A, Wollberg Z, Kochva E, Graur D.

Toxicon. 1991;29(2):237-44.

PMID:
2048141
47.

The evolutionary history of the sarafotoxin/endothelin/endothelin-like superfamily.

Landan G, Bdolah A, Wollberg Z, Kochva E, Graur D.

J Cardiovasc Pharmacol. 1991;17 Suppl 7:S517-9.

PMID:
1725430
48.

Evolution of isopenicillin N synthase genes may have involved horizontal gene transfer.

Landan G, Cohen G, Aharonowitz Y, Shuali Y, Graur D, Shiffman D.

Mol Biol Evol. 1990 Sep;7(5):399-406. Review.

PMID:
2263192

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