Xiang-Jun Lu - Publications

Affiliations: 
Columbia University, New York, NY 

29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ. Towards a mechanistic understanding of DNA methylation readout by transcription factors. Journal of Molecular Biology. PMID 31689433 DOI: 10.1016/J.Jmb.2019.10.021  0.72
2016 Waters JT, Kim HD, Gumbart JC, Lu XJ, Harvey SC. DNA Scrunching in the Packaging of Viral Genomes. The Journal of Physical Chemistry. B. PMID 27214211 DOI: 10.1021/Acs.Jpcb.6B02149  0.36
2016 Waters JT, Lu XJ, Galindo-Murillo R, Gumbart JC, Kim HD, Cheatham TE, Harvey SC. Transitions of Double-Stranded DNA Between the A- and B-Forms. The Journal of Physical Chemistry. B. PMID 27135262 DOI: 10.1021/Acs.Jpcb.6B02155  0.36
2015 Lu XJ, Bussemaker HJ, Olson WK. DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Research. PMID 26184874 DOI: 10.1093/Nar/Gkv716  0.72
2014 Fazlollahi M, Lee E, Muroff I, Lu XJ, Gomez-Alcala P, Causton HC, Bussemaker HJ. Harnessing natural sequence variation to dissect posttranscriptional regulatory networks in yeast. G3 (Bethesda, Md.). 4: 1539-53. PMID 24938291 DOI: 10.1534/G3.114.012039  0.72
2013 Colasanti AV, Grosner MA, Perez PJ, Clauvelin N, Lu XJ, Olson WK. Weak operator binding enhances simulated lac repressor-mediated DNA looping. Biopolymers. 99: 1070-81. PMID 23818216 DOI: 10.1002/Bip.22336  0.36
2013 Colasanti AV, Lu XJ, Olson WK. Analyzing and building nucleic acid structures with 3DNA. Journal of Visualized Experiments : Jove. e4401. PMID 23644419 DOI: 10.3791/4401  0.36
2012 Mládek A, Sponer JE, Kulhánek P, Lu XJ, Olson WK, Sponer J. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. Journal of Chemical Theory and Computation. 8: 335-347. PMID 22712001 DOI: 10.1021/Ct200712B  0.36
2010 Lu XJ, Olson WK, Bussemaker HJ. The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. Nucleic Acids Research. 38: 4868-76. PMID 20223772 DOI: 10.1093/Nar/Gkq155  0.36
2010 Zheng G, Colasanti AV, Lu XJ, Olson WK. 3DNALandscapes: a database for exploring the conformational features of DNA. Nucleic Acids Research. 38: D267-74. PMID 19906722 DOI: 10.1093/Nar/Gkp959  0.36
2009 Zheng G, Lu XJ, Olson WK. Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Research. 37: W240-6. PMID 19474339 DOI: 10.1093/Nar/Gkp358  0.36
2009 Olson WK, Esguerra M, Xin Y, Lu XJ. New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures. Methods (San Diego, Calif.). 47: 177-86. PMID 19150407 DOI: 10.1016/J.Ymeth.2008.12.003  0.36
2008 Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ. Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. Plos One. 3: e3112. PMID 18769540 DOI: 10.1371/Journal.Pone.0003112  0.72
2008 Lu XJ, Olson WK. 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nature Protocols. 3: 1213-27. PMID 18600227 DOI: 10.1038/Nprot.2008.104  0.36
2007 Banerjee A, Misra M, Pai D, Shih LY, Woodley R, Lu XJ, Srinivasan AR, Olson WK, Davé RN, Venanzi CA. Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor. Journal of Chemical Information and Modeling. 47: 2216-27. PMID 17967005 DOI: 10.1021/Ci7001632  0.36
2006 Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, van Steensel B. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 103: 12027-32. PMID 16880385 DOI: 10.1073/Pnas.0605003103  0.36
2006 Halasz G, van Batenburg MF, Perusse J, Hua S, Lu XJ, White KP, Bussemaker HJ. Detecting transcriptionally active regions using genomic tiling arrays. Genome Biology. 7: R59. PMID 16859498 DOI: 10.1186/Gb-2006-7-7-R59  0.36
2005 McLaughlin WA, Kulp DW, De La Cruz J, Lu XJ, Lawson CL, Berman HM. A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction Journal of Structural and Functional Genomics. 5: 255-265. PMID 15704013 DOI: 10.1007/S10969-005-4902-1  0.36
2003 Lu XJ, Olson WK. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Research. 31: 5108-21. PMID 12930962 DOI: 10.1093/Nar/Gkg680  0.36
2002 Kosikov KM, Gorin AA, Lu XJ, Olson WK, Manning GS. Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. Journal of the American Chemical Society. 124: 4838-47. PMID 11971734 DOI: 10.1021/Ja0125218  0.36
2001 Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu XJ, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung CS, Westhof E, Wolberger C, et al. A standard reference frame for the description of nucleic acid base-pair geometry. Journal of Molecular Biology. 313: 229-37. PMID 11601858 DOI: 10.1006/Jmbi.2001.4987  0.36
2001 Ruan Q, Zhuang P, Li S, Perlow R, Srinivasan AR, Lu XJ, Broyde S, Olson WK, Geacintov NE. Base sequence effects in bending induced by bulky carcinogen-DNA adducts: experimental and computational analysis. Biochemistry. 40: 10458-72. PMID 11523987 DOI: 10.1021/Bi002643X  0.36
1999 Lu XJ, Babcock MS, Olson WK. Overview of nucleic acid analysis programs. Journal of Biomolecular Structure & Dynamics. 16: 833-43. PMID 10217453 DOI: 10.1080/07391102.1999.10508296  0.36
1999 Lu XJ, Olson WK. Resolving the discrepancies among nucleic acid conformational analyses. Journal of Molecular Biology. 285: 1563-75. PMID 9917397 DOI: 10.1006/Jmbi.1998.2390  0.36
1998 Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences of the United States of America. 95: 11163-8. PMID 9736707 DOI: 10.1073/Pnas.95.19.11163  0.36
1997 Lu XJ, El Hassan MA, Hunter CA. Structure and conformation of helical nucleic acids: Rebuilding program (SCHNArP) Journal of Molecular Biology. 273: 681-691. PMID 9356256 DOI: 10.1006/Jmbi.1997.1345  0.36
1997 Lu XJ, El Hassan MA, Hunter CA. Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP) Journal of Molecular Biology. 273: 668-680. PMID 9356255 DOI: 10.1006/Jmbi.1997.1346  0.36
1997 Hunter CA, Lu XJ. Construction of double-helical DNA structures based on dinucleotide building blocks Journal of Biomolecular Structure and Dynamics. 14: 747-756. PMID 9195343 DOI: 10.1080/07391102.1997.10508177  0.36
1997 Hunter CA, Lu XJ. DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotide x-ray crystal structures Journal of Molecular Biology. 265: 603-619. PMID 9048952 DOI: 10.1006/Jmbi.1996.0755  0.36
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