My Bibliography

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Zhu I, Song W, Ovcharenko I, Landsman D. A model of active transcription hubs that unifies the roles of active promoters and enhancers. Nucleic Acids Res. 2021 May 7;49(8):4493-4505. doi: 10.1093/nar/gkab235. PubMed PMID: 33872375; PubMed Central PMCID: PMC8096258.

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Zhu I, Landsman D. Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes. Genome Res. 2023 Oct;33(10):1662-1672. doi: 10.1101/gr.278130.123. Epub 2023 Oct 26. PubMed PMID: 37884340; PubMed Central PMCID: PMC10691539.

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Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y. Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4. Mol Cell. 2024 Aug 22;84(16):3061-3079.e10. doi: 10.1016/j.molcel.2024.07.016. Epub 2024 Aug 8. PubMed PMID: 39121853; PubMed Central PMCID: PMC11344660.

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Zhang YM, Dawson SC, Landsman D, Lane HC, Salzman NP. Persistence of four related human immunodeficiency virus subtypes during the course of zidovudine therapy: relationship between virion RNA and proviral DNA. J Virol. 1994 Jan;68(1):425-32. doi: 10.1128/JVI.68.1.425-432.1994. PubMed PMID: 8254752; PubMed Central PMCID: PMC236302.

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Zhang S, Zhu I, Deng T, Furusawa T, Rochman M, Vacchio MS, Bosselut R, Yamane A, Casellas R, Landsman D, Bustin M. HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells. Nucleic Acids Res. 2016 Sep 6;44(15):7144-58. doi: 10.1093/nar/gkw323. Epub 2016 Apr 25. PubMed PMID: 27112571; PubMed Central PMCID: PMC5009722.

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Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF. Log-odds sequence logos. Bioinformatics. 2015 Feb 1;31(3):324-31. doi: 10.1093/bioinformatics/btu634. Epub 2014 Oct 6. PubMed PMID: 25294922; PubMed Central PMCID: PMC4318935.

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Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C. Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres. Genes Dev. 2017 Oct 1;31(19):1958-1972. doi: 10.1101/gad.304782.117. Epub 2017 Oct 26. PubMed PMID: 29074736; PubMed Central PMCID: PMC5710141.

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Wolfsberg TG, Gabrielian AE, Campbell MJ, Cho RJ, Spouge JL, Landsman D. Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae. Genome Res. 1999 Aug;9(8):775-92. PubMed PMID: 10447512; PubMed Central PMCID: PMC310804.

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Wolfsberg TG, Landsman D. Expressed sequence tags (ESTs). Methods Biochem Anal. 2001;43:283-301. doi: 10.1002/0471223921.ch12. PubMed PMID: 11449729.

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Wolfsberg TG, Landsman D. A comparison of expressed sequence tags (ESTs) to human genomic sequences. Nucleic Acids Res. 1997 Apr 15;25(8):1626-32. doi: 10.1093/nar/25.8.1626. PubMed PMID: 9092672; PubMed Central PMCID: PMC146621.

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Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21. doi: 10.1093/nar/gkm1000. Epub 2007 Nov 27. PubMed PMID: 18045790; PubMed Central PMCID: PMC2238880.

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Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2007 Jan;35(Database issue):D5-12. doi: 10.1093/nar/gkl1031. Epub 2006 Dec 14. PubMed PMID: 17170002; PubMed Central PMCID: PMC1781113.

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Walsh TJ, Kasai M, Francesconi A, Landsman D, Chanock SJ. New evidence that Candida albicans possesses additional ATP-binding cassette MDR-like genes: implications for antifungal azole resistance. J Med Vet Mycol. 1997 Mar-Apr;35(2):133-7. PubMed PMID: 9147273.

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Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JA, Tramontano A, Schneider MV. Ten simple rules for developing a short bioinformatics training course. PLoS Comput Biol. 2011 Oct;7(10):e1002245. doi: 10.1371/journal.pcbi.1002245. Epub 2011 Oct 27. PubMed PMID: 22046119; PubMed Central PMCID: PMC3203054.

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Vera Alvarez R, Medeiros Vidal N, Garzón-Martínez GA, Barrero LS, Landsman D, Mariño-Ramírez L. Workflow and web application for annotating NCBI BioProject transcriptome data. Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax008. PubMed PMID: 28605765; PubMed Central PMCID: PMC5467576.

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Vera Alvarez R, Pongor LS, Mariño-Ramírez L, Landsman D. TPMCalculator: one-step software to quantify mRNA abundance of genomic features. Bioinformatics. 2019 Jun 1;35(11):1960-1962. doi: 10.1093/bioinformatics/bty896. PubMed PMID: 30379987; PubMed Central PMCID: PMC6546121.

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Vera Alvarez R, Pongor L, Mariño-Ramírez L, Landsman D. PM4NGS, a project management framework for next-generation sequencing data analysis. Gigascience. 2021 Jan 7;10(1). doi: 10.1093/gigascience/giaa141. PubMed PMID: 33410471; PubMed Central PMCID: PMC7788391.

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Tharakaraman K, Bodenreider O, Landsman D, Spouge JL, Mariño-Ramírez L. The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. Nucleic Acids Res. 2008 May;36(8):2777-86. doi: 10.1093/nar/gkn137. Epub 2008 Mar 26. PubMed PMID: 18367472; PubMed Central PMCID: PMC2377430.

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Tharakaraman K, Mariño-Ramírez L, Sheetlin S, Landsman D, Spouge JL. Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Bioinformatics. 2005 Jun;21 Suppl 1(Suppl 1):i440-8. doi: 10.1093/bioinformatics/bti1028. PubMed PMID: 15961489; PubMed Central PMCID: PMC1317086.

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Tharakaraman K, Mariño-Ramírez L, Sheetlin SL, Landsman D, Spouge JL. Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements. BMC Bioinformatics. 2006 Sep 8;7:408. doi: 10.1186/1471-2105-7-408. PubMed PMID: 16961919; PubMed Central PMCID: PMC1599759.

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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. A unified phylogeny-based nomenclature for histone variants. Epigenetics Chromatin. 2012 Jun 21;5:7. doi: 10.1186/1756-8935-5-7. PubMed PMID: 22650316; PubMed Central PMCID: PMC3380720.

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Szak ST, Pickeral OK, Landsman D, Boeke JD. Identifying related L1 retrotransposons by analyzing 3' transduced sequences. Genome Biol. 2003;4(5):R30. doi: 10.1186/gb-2003-4-5-r30. Epub 2003 Apr 16. PubMed PMID: 12734010; PubMed Central PMCID: PMC156586.

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Szak ST, Pickeral OK, Makalowski W, Boguski MS, Landsman D, Boeke JD. Molecular archeology of L1 insertions in the human genome. Genome Biol. 2002 Sep 19;3(10):research0052. doi: 10.1186/gb-2002-3-10-research0052. Epub 2002 Sep 19. PubMed PMID: 12372140; PubMed Central PMCID: PMC134481.

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Sullivan SA, Landsman D. Characterization of sequence variability in nucleosome core histone folds. Proteins. 2003 Aug 15;52(3):454-65. doi: 10.1002/prot.10441. PubMed PMID: 12866056.

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Sullivan SA, Aravind L, Makalowska I, Baxevanis AD, Landsman D. The histone database: a comprehensive WWW resource for histones and histone fold-containing proteins. Nucleic Acids Res. 2000 Jan 1;28(1):320-2. doi: 10.1093/nar/28.1.320. PubMed PMID: 10592260; PubMed Central PMCID: PMC102427.

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Sullivan SA, Landsman D. Mining core histone sequences from public protein databases. Methods Enzymol. 2004;375:3-20. doi: 10.1016/s0076-6879(03)75001-0. PubMed PMID: 14870656; PubMed Central PMCID: PMC3160111.

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Sullivan S, Sink DW, Trout KL, Makalowska I, Taylor PM, Baxevanis AD, Landsman D. The Histone Database. Nucleic Acids Res. 2002 Jan 1;30(1):341-2. doi: 10.1093/nar/30.1.341. PubMed PMID: 11752331; PubMed Central PMCID: PMC99096.

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Strichman-Almashanu LZ, Bustin M, Landsman D. Retroposed copies of the HMG genes: a window to genome dynamics. Genome Res. 2003 May;13(5):800-12. doi: 10.1101/gr.893803. PubMed PMID: 12727900; PubMed Central PMCID: PMC430908.

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Stepien PP, Margossian SP, Landsman D, Butow RA. The yeast nuclear gene suv3 affecting mitochondrial post-transcriptional processes encodes a putative ATP-dependent RNA helicase. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):6813-7. doi: 10.1073/pnas.89.15.6813. PubMed PMID: 1379722; PubMed Central PMCID: PMC49594.

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Srikantha T, Landsman D, Bustin M. Retropseudogenes for human chromosomal protein HMG-17. J Mol Biol. 1987 Oct 5;197(3):405-13. doi: 10.1016/0022-2836(87)90554-7. PubMed PMID: 3441004.

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Srikantha T, Landsman D, Bustin M. A single copy gene for chicken chromosomal protein HMG-14b has evolutionarily conserved features, has lost one of its introns and codes for a rapidly evolving protein. J Mol Biol. 1990 Jan 5;211(1):49-61. doi: 10.1016/0022-2836(90)90010-J. PubMed PMID: 2153836.

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Srikantha T, Landsman D, Bustin M. Cloning of the chicken chromosomal protein HMG-14 cDNA reveals a unique protein with a conserved DNA binding domain. J Biol Chem. 1988 Sep 25;263(27):13500-3. PubMed PMID: 3417670.

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Shirakawa H, Landsman D, Postnikov YV, Bustin M. NBP-45, a novel nucleosomal binding protein with a tissue-specific and developmentally regulated expression. J Biol Chem. 2000 Mar 3;275(9):6368-74. doi: 10.1074/jbc.275.9.6368. PubMed PMID: 10692437.

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Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID. Nat Protoc. 2018 Nov;13(11):2535-2556. doi: 10.1038/s41596-018-0048-z. PubMed PMID: 30341436; PubMed Central PMCID: PMC6322412.

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Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles. Data Brief. 2016 Jun;7:1678-81. doi: 10.1016/j.dib.2016.04.073. eCollection 2016 Jun. PubMed PMID: 27222871; PubMed Central PMCID: PMC4872717.

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Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions. J Mol Biol. 2016 Jan 16;428(1):221-237. doi: 10.1016/j.jmb.2015.12.004. Epub 2015 Dec 14. PubMed PMID: 26699921; PubMed Central PMCID: PMC4738025.

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Shaytan AK, Landsman D, Panchenko AR. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers. Curr Opin Struct Biol. 2015 Jun;32:48-57. doi: 10.1016/j.sbi.2015.02.004. Epub 2015 Feb 27. Review. PubMed PMID: 25731851; PubMed Central PMCID: PMC4512853.

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Shaytan AK, Xiao H, Armeev GA, Wu C, Landsman D, Panchenko AR. Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning. Nucleic Acids Res. 2017 Sep 19;45(16):9229-9243. doi: 10.1093/nar/gkx616. PubMed PMID: 28934480; PubMed Central PMCID: PMC5765820.

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Seal RL, Denny P, Bruford EA, Gribkova AK, Landsman D, Marzluff WF, McAndrews M, Panchenko AR, Shaytan AK, Talbert PB. A standardized nomenclature for mammalian histone genes. Epigenetics Chromatin. 2022 Oct 1;15(1):34. doi: 10.1186/s13072-022-00467-2. Review. PubMed PMID: 36180920; PubMed Central PMCID: PMC9526256.

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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, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, 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. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51. doi: 10.1093/nar/gkq1172. Epub 2010 Nov 21. PubMed PMID: 21097890; PubMed Central PMCID: PMC3013733.

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Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16. doi: 10.1093/nar/gkp967. Epub 2009 Nov 12. PubMed PMID: 19910364; PubMed Central PMCID: PMC2808881.

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Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15. doi: 10.1093/nar/gkn741. Epub 2008 Oct 21. PubMed PMID: 18940862; PubMed Central PMCID: PMC2686545.

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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. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2012 Jan;40(Database issue):D13-25. doi: 10.1093/nar/gkr1184. Epub 2011 Dec 2. PubMed PMID: 22140104; PubMed Central PMCID: PMC3245031.

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Sarkar D, Zhu ZI, Knoll ER, Paul E, Landsman D, Morse RH. Mediator dynamics during heat shock in budding yeast. Genome Res. 2022 Jan;32(1):111-123. doi: 10.1101/gr.275750.121. Epub 2021 Nov 16. PubMed PMID: 34785526; PubMed Central PMCID: PMC8744673.

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Salinero AC, Knoll ER, Zhu ZI, Landsman D, Curcio MJ, Morse RH. The Mediator co-activator complex regulates Ty1 retromobility by controlling the balance between Ty1i and Ty1 promoters. PLoS Genet. 2018 Feb;14(2):e1007232. doi: 10.1371/journal.pgen.1007232. eCollection 2018 Feb. PubMed PMID: 29462141; PubMed Central PMCID: PMC5834202.

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Roh TY, Ngau WC, Cui K, Landsman D, Zhao K. High-resolution genome-wide mapping of histone modifications. Nat Biotechnol. 2004 Aug;22(8):1013-6. doi: 10.1038/nbt990. Epub 2004 Jul 4. PubMed PMID: 15235610.

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Rochman M, Taher L, Kurahashi T, Cherukuri S, Uversky VN, Landsman D, Ovcharenko I, Bustin M. Effects of HMGN variants on the cellular transcription profile. Nucleic Acids Res. 2011 May;39(10):4076-87. doi: 10.1093/nar/gkq1343. Epub 2011 Jan 28. PubMed PMID: 21278158; PubMed Central PMCID: PMC3105402.

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Riz I, Akimov SS, Eaker SS, Baxter KK, Lee HJ, Mariño-Ramírez L, Landsman D, Hawley TS, Hawley RG. TLX1/HOX11-induced hematopoietic differentiation blockade. Oncogene. 2007 Jun 14;26(28):4115-23. doi: 10.1038/sj.onc.1210185. Epub 2007 Jan 8. PubMed PMID: 17213805; PubMed Central PMCID: PMC1955382.

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Popescu N, Landsman D, Bustin M. Mapping the human gene coding for chromosomal protein HMG-17. Hum Genet. 1990 Aug;85(3):376-8. doi: 10.1007/BF00206764. PubMed PMID: 2394451.

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Pongor S, Landsman D. Bioinformatics and the developing world. Biotechnol Dev Monit. 1999 Dec;40:10-13. PubMed PMID: 25960606; PubMed Central PMCID: PMC4422384.