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Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006.

Gamez RM, Rodríguez F, Vidal NM, Ramirez S, Vera Alvarez R, Landsman D, Mariño-Ramírez L.

BMC Genomics. 2019 May 14;20(1):378. doi: 10.1186/s12864-019-5763-5.


Molecular recognition of nucleosomes by binding partners.

Kale S, Goncearenco A, Markov Y, Landsman D, Panchenko AR.

Curr Opin Struct Biol. 2019 Apr 13;56:164-170. doi: 10.1016/ [Epub ahead of print] Review.


Role of the pre-initiation complex in Mediator recruitment and dynamics.

Knoll ER, Zhu ZI, Sarkar D, Landsman D, Morse RH.

Elife. 2018 Dec 12;7. pii: e39633. doi: 10.7554/eLife.39633.


Binding of HMGN proteins to cell specific enhancers stabilizes cell identity.

He B, Deng T, Zhu I, Furusawa T, Zhang S, Tang W, Postnikov Y, Ambs S, Li CC, Livak F, Landsman D, Bustin M.

Nat Commun. 2018 Dec 7;9(1):5240. doi: 10.1038/s41467-018-07687-9.


TPMCalculator: one-step software to quantify mRNA abundance of genomic features.

Vera Alvarez R, Pongor LS, Mariño-Ramírez L, Landsman D.

Bioinformatics. 2019 Jun 1;35(11):1960-1962. doi: 10.1093/bioinformatics/bty896.


Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.

Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR.

Nat Protoc. 2018 Nov;13(11):2535-2556. doi: 10.1038/s41596-018-0048-z.


A Genome-Wide Screen Reveals a Role for the HIR Histone Chaperone Complex in Preventing Mislocalization of Budding Yeast CENP-A.

Ciftci-Yilmaz S, Au WC, Mishra PK, Eisenstatt JR, Chang J, Dawson AR, Zhu I, Rahman M, Bilke S, Costanzo M, Baryshnikova A, Myers CL, Meltzer PS, Landsman D, Baker RE, Boone C, Basrai MA.

Genetics. 2018 Sep;210(1):203-218. doi: 10.1534/genetics.118.301305. Epub 2018 Jul 16.


Correction for Deng et al., "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. 2018 May 29;38(12). pii: e00185-18. doi: 10.1128/MCB.00185-18. Print 2018 Jun 15. No abstract available.


The Mediator co-activator complex regulates Ty1 retromobility by controlling the balance between Ty1i and Ty1 promoters.

Salinero AC, Knoll ER, Zhu ZI, Landsman D, Curcio MJ, Morse RH.

PLoS Genet. 2018 Feb 20;14(2):e1007232. doi: 10.1371/journal.pgen.1007232. eCollection 2018 Feb.


Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres.

Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C.

Genes Dev. 2017 Oct 1;31(19):1958-1972. doi: 10.1101/gad.304782.117. Epub 2017 Oct 26.


SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome.

Vera Alvarez R, Li S, Landsman D, Ovcharenko I.

Bioinformatics. 2017 Sep 14. doi: 10.1093/bioinformatics/btx583. [Epub ahead of print]


Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning.

Shaytan AK, Xiao H, Armeev GA, Wu C, Landsman D, Panchenko AR.

Nucleic Acids Res. 2017 Sep 19;45(16):9229-9243. doi: 10.1093/nar/gkx616.


Workflow and web application for annotating NCBI BioProject transcriptome data.

Vera Alvarez R, Medeiros Vidal N, Garzón-Martínez GA, Barrero LS, Landsman D, Mariño-Ramírez L.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax008.


MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.

El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J.

Epigenetics Chromatin. 2017 Jan 10;10:2. doi: 10.1186/s13072-016-0109-x. eCollection 2017.


Quantifying deleterious effects of regulatory variants.

Li S, Alvarez RV, Sharan R, Landsman D, Ovcharenko I.

Nucleic Acids Res. 2017 Mar 17;45(5):2307-2317. doi: 10.1093/nar/gkw1263.


Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.

Acevedo-Luna N, Mariño-Ramírez L, Halbert A, Hansen U, Landsman D, Spouge JL.

BMC Bioinformatics. 2016 Nov 21;17(1):479.


Dataset of Arabidopsis plants that overexpress FT driven by a meristem-specific KNAT1 promoter.

Duplat-Bermúdez L, Ruiz-Medrano R, Landsman D, Mariño-Ramírez L, Xoconostle-Cázares B.

Data Brief. 2016 Jun 8;8:520-8. doi: 10.1016/j.dib.2016.06.002. eCollection 2016 Sep.


Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles.

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

Data Brief. 2016 May 6;7:1678-81. doi: 10.1016/j.dib.2016.04.073. eCollection 2016 Jun.


Transcriptomic analysis of Arabidopsis overexpressing flowering locus T driven by a meristem-specific promoter that induces early flowering.

Duplat-Bermúdez L, Ruiz-Medrano R, Landsman D, Mariño-Ramírez L, Xoconostle-Cázares B.

Gene. 2016 Aug 10;587(2):120-31. doi: 10.1016/j.gene.2016.04.060. Epub 2016 May 3.


Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens PS006.

Gamez RM, Rodríguez F, Ramírez S, Gómez Y, Agarwala R, Landsman D, Mariño-Ramírez L.

Genome Announc. 2016 May 5;4(3). pii: e00329-16. doi: 10.1128/genomeA.00329-16.


HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells.

Zhang S, Zhu I, Deng T, Furusawa T, Rochman M, Vacchio MS, Bosselut R, Yamane A, Casellas R, Landsman D, Bustin M.

Nucleic Acids Res. 2016 Sep 6;44(15):7144-58. doi: 10.1093/nar/gkw323. Epub 2016 Apr 25.


HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants.

Draizen EJ, Shaytan AK, Mariño-Ramírez L, Talbert PB, Landsman D, Panchenko AR.

Database (Oxford). 2016 Mar 17;2016. pii: baw014. doi: 10.1093/database/baw014. Print 2016.


Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial Resistance Monitoring Program in Colombia.

Bernal JF, Donado-Godoy P, Valencia MF, León M, Gómez Y, Rodríguez F, Agarwala R, Landsman D, Mariño-Ramírez L.

Genome Announc. 2016 Mar 17;4(2). pii: e00131-16. doi: 10.1128/genomeA.00131-16.


Whole-Genome Sequence of Multidrug-Resistant Campylobacter coli Strain COL B1-266, Isolated from the Colombian Poultry Chain.

Bernal JF, Donado-Godoy P, Arévalo A, Duarte C, Realpe ME, Díaz PL, Gómez Y, Rodríguez F, Agarwala R, Landsman D, Mariño-Ramírez L.

Genome Announc. 2016 Mar 17;4(2). pii: e00130-16. doi: 10.1128/genomeA.00130-16.


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):221-237. doi: 10.1016/j.jmb.2015.12.004. Epub 2015 Dec 14.


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.


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.


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.


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.


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.


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.


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.


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/ Epub 2015 Feb 27. Review.


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.


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.


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.


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.


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. Erratum in: Mol Cell Biol. 2018 May 29;38(12):.


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.


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.


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.


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.


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.


Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae.

Hansen L, Kim NK, Mariño-Ramírez L, Landsman D.

PLoS One. 2011;6(12):e29711. doi: 10.1371/journal.pone.0029711. Epub 2011 Dec 29.


Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Krasnov S, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Karsch-Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D13-25. doi: 10.1093/nar/gkr1184. Epub 2011 Dec 2.


Ten simple rules for developing a short bioinformatics training course.

Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JA, Tramontano A, Schneider MV.

PLoS Comput Biol. 2011 Oct;7(10):e1002245. doi: 10.1371/journal.pcbi.1002245. Epub 2011 Oct 27. No abstract available.


The Histone Database: an integrated resource for histones and histone fold-containing proteins.

Mariño-Ramírez L, Levine KM, Morales M, Zhang S, Moreland RT, Baxevanis AD, Landsman D.

Database (Oxford). 2011 Oct 23;2011:bar048. doi: 10.1093/database/bar048. Print 2011.


Genome sequence of the Mycobacterium colombiense type strain, CECT 3035.

González-Pérez M, Murcia MI, Landsman D, Jordan IK, Mariño-Ramírez L.

J Bacteriol. 2011 Oct;193(20):5866-7. doi: 10.1128/JB.05928-11.


Effects of HMGN variants on the cellular transcription profile.

Rochman M, Taher L, Kurahashi T, Cherukuri S, Uversky VN, Landsman D, Ovcharenko I, Bustin M.

Nucleic Acids Res. 2011 May;39(10):4076-87. doi: 10.1093/nar/gkq1343. Epub 2011 Jan 28.


Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.

Database (Oxford). 2011 Jan 4;2011:baq027. doi: 10.1093/database/baq027. Print 2011.

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