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Items: 1 to 20 of 118

1.

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.

Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR.

J Mol Biol. 2016 Jan 16;428(1):221-37. doi: 10.1016/j.jmb.2015.12.004. Epub 2015 Dec 14.

PMID:
26699921
2.

Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Bacillus amyloliquefaciens BS006.

Gamez RM, Rodríguez F, Bernal JF, Agarwala R, Landsman D, Mariño-Ramírez L.

Genome Announc. 2015 Nov 25;3(6). pii: e01391-15. doi: 10.1128/genomeA.01391-15.

3.

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers.

Garzón-Martínez GA, Osorio-Guarín JA, Delgadillo-Durán P, Mayorga F, Enciso-Rodríguez FE, Landsman D, Mariño-Ramírez L, Barrero LS.

Plant Gene. 2015 Dec 1;4:29-37.

4.

Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Paratyphi B (dT+) and Heidelberg Strains from the Colombian Poultry Chain.

Donado-Godoy P, Bernal JF, Rodríguez F, Gomez Y, Agarwala R, Landsman D, Mariño-Ramírez L.

Genome Announc. 2015 Oct 22;3(5). pii: e01265-15. doi: 10.1128/genomeA.01265-15.

5.

Progressive MS: from pathophysiology to drug discovery.

Salvetti M, Landsman D, Schwarz-Lam P, Comi G, Thompson AJ, Fox RJ.

Mult Scler. 2015 Oct;21(11):1376-84. doi: 10.1177/1352458515603802. Epub 2015 Sep 11. Review.

PMID:
26362902
6.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G.

Database (Oxford). 2015 Jul 11;2015:bav063. doi: 10.1093/database/bav063. eCollection 2015.

7.

Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers.

Deng T, Zhu ZI, Zhang S, Postnikov Y, Huang D, Horsch M, Furusawa T, Beckers J, Rozman J, Klingenspor M, Amarie O, Graw J, Rathkolb B, Wolf E, Adler T, Busch DH, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, van der Velde A, Tessarollo L, Ovcherenko I, Landsman D, Bustin M.

Genome Res. 2015 Sep;25(9):1295-308. doi: 10.1101/gr.192229.115. Epub 2015 Jul 8.

PMID:
26156321
8.

6 Combined influence of linker DNA and histone tails on nucleosome dynamics as revealed by microsecond molecular dynamics simulations.

Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR.

J Biomol Struct Dyn. 2015;33 Suppl 1:3. doi: 10.1080/07391102.2015.1032630. No abstract available.

PMID:
26103217
9.

Key challenges for the creation and maintenance of specialist protein resources.

Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A.

Proteins. 2015 Jun;83(6):1005-13. doi: 10.1002/prot.24803. Epub 2015 Apr 22.

10.

Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers.

Shaytan AK, Landsman D, Panchenko AR.

Curr Opin Struct Biol. 2015 Jun;32:48-57. doi: 10.1016/j.sbi.2015.02.004. Epub 2015 Feb 27. Review.

11.

Genome-wide association of mediator and RNA polymerase II in wild-type and mediator mutant yeast.

Paul E, Zhu ZI, Landsman D, Morse RH.

Mol Cell Biol. 2015 Jan;35(1):331-42. doi: 10.1128/MCB.00991-14. Epub 2014 Nov 3.

12.

Log-odds sequence logos.

Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF.

Bioinformatics. 2015 Feb 1;31(3):324-31. doi: 10.1093/bioinformatics/btu634. Epub 2014 Oct 6.

13.

Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways.

Yu W, McIntosh C, Lister R, Zhu I, Han Y, Ren J, Landsman D, Lee E, Briones V, Terashima M, Leighty R, Ecker JR, Muegge K.

Genome Res. 2014 Oct;24(10):1613-23. doi: 10.1101/gr.172015.114. Epub 2014 Aug 28.

14.

Identification of immunity related genes to study the Physalis peruviana--Fusarium oxysporum pathosystem.

Enciso-Rodríguez FE, González C, Rodríguez EA, López CE, Landsman D, Barrero LS, Mariño-Ramírez L.

PLoS One. 2013 Jul 3;8(7):e68500. doi: 10.1371/journal.pone.0068500. Print 2013.

15.

HMGN1 modulates nucleosome occupancy and DNase I hypersensitivity at the CpG island promoters of embryonic stem cells.

Deng T, Zhu ZI, Zhang S, Leng F, Cherukuri S, Hansen L, Mariño-Ramírez L, Meshorer E, Landsman D, Bustin M.

Mol Cell Biol. 2013 Aug;33(16):3377-89. doi: 10.1128/MCB.00435-13. Epub 2013 Jun 17.

16.

Obituary: In memory of Jack Leunissen.

Luo J, Nijveen H, Attwood T, Judge D, Pongor S, Landsman D, Bishop M.

Brief Bioinform. 2013 May;14(3):261-2. doi: 10.1093/bib/bbt036. No abstract available.

17.

In silico identification and characterization of the ion transport specificity for P-type ATPases in the Mycobacterium tuberculosis complex.

Novoa-Aponte L, León-Torres A, Patiño-Ruiz M, Cuesta-Bernal J, Salazar LM, Landsman D, Mariño-Ramírez L, Soto CY.

BMC Struct Biol. 2012 Oct 3;12:25. doi: 10.1186/1472-6807-12-25.

18.

Differences in local genomic context of bound and unbound motifs.

Hansen L, Mariño-Ramírez L, Landsman D.

Gene. 2012 Sep 10;506(1):125-34. doi: 10.1016/j.gene.2012.06.005. Epub 2012 Jun 10.

19.

A unified phylogeny-based nomenclature for histone variants.

Talbert PB, Ahmad K, Almouzni G, Ausió J, Berger F, Bhalla PL, Bonner WM, Cande WZ, Chadwick BP, Chan SW, Cross GA, Cui L, Dimitrov SI, Doenecke D, Eirin-López JM, Gorovsky MA, Hake SB, Hamkalo BA, Holec S, Jacobsen SE, Kamieniarz K, Khochbin S, Ladurner AG, Landsman D, Latham JA, Loppin B, Malik HS, Marzluff WF, Pehrson JR, Postberg J, Schneider R, Singh MB, Smith MM, Thompson E, Torres-Padilla ME, Tremethick DJ, Turner BM, Waterborg JH, Wollmann H, Yelagandula R, Zhu B, Henikoff S.

Epigenetics Chromatin. 2012 Jun 21;5:7. doi: 10.1186/1756-8935-5-7.

20.

The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction.

Garzón-Martínez GA, Zhu ZI, Landsman D, Barrero LS, Mariño-Ramírez L.

BMC Genomics. 2012 Apr 25;13:151. doi: 10.1186/1471-2164-13-151.

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