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Publications

For a completely up to date list of our publications either check out Alain Laederach’s My Citations at Google Scholar or perform an author search on Pubmed.

 

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  1. Mustoe AM, Corley M, Laederach A, Weeks KM. (2018) Messenger RNA Structure Regulates Translation Initiation: A Mechanism Exploited from Bacteria to Humans. Biochemistry. 2018 Jul 3;57(26):3537-3539. Epub 2018 Jun 12.
  2. Kutchko KM, Madden EA, Morrison C, Plante KS, Sanders W, Vincent HA, Cruz Cisneros MC, Long KM, Moorman NJ, Heise MT, Laederach A. (2018) Structural divergence creates new functional features in alphavirus genomes. Nucleic Acids Res. 2018 Apr 20;46(7):3657-3670.
  3. Lackey L, Coria A, Woods C, McArthur E, Laederach A. (2018) Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure. Lackey L, Coria A, Woods C, McArthur E, Laederach A. RNA. 2018 Apr;24(4):513-528. Epub 2018 Jan 9.
  4. Corley M, Solem A, Phillips G, Lackey L, Ziehr B, Vincent HA, Mustoe AM, Ramos SBV, Weeks KM, Moorman NJ, Laederach A. (2017) An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression. Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):E10244-E10253, Epub 2017 Nov 6.
  5. Woods CT, Lackey L, Williams B, Dokholyan NV, Gotz D, Laederach A. (2017) Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophys J. 2017 Jul 25;113(2):290-301
  6. Ball CB, Solem AC, Meganck RM, Laederach A, Ramos SBV. (2017) Impact of RNA structure on ZFP36L2 interaction with luteinizing hormone receptor mRNA. RNA. 2017 Aug;23(8):1209-1223
  7. Gamache ER, Doh JH, Ritz J, Laederach A, Bellaousov S, Mathews DH, Curcio MJ (2017) Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA. Viruses. 2017 Apr 26;9(5). pii: E93
  8. Woods CT, Laederach A. (2017) Classification of RNA structure change by ‘gazing’ at experimental data. Bioinformatics. 2017 Jun 1;33(11):1647-1655
  9. Kutchko KM, Laederach A. (2016) Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution. WIREs RNA, Epub ahead of print.
  10. Schulmeyer KH, Diaz MR, Bair TB, Sanders W, Gode CJ, Laederach A, Wolfgang MC, Yahr TL. (2016) Primary and secondary sequence structure requirements for recognition and discrimination of target RNAs by Pseudomonas aeruginosa RsmA and RsmF. Journal of Bacteriology, Epub ahead of print.
  11. Mucaki EJ, Caminsky NG, Perri AM, Lu R, Laederach A, Halvorsen M, Knoll JH, Rogan PK. (2016) A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. BMC Medical Genomics, 9:19.
  12. Lackey L, McArthur E, Laederach A. (2015) Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease. PLOS ONE, 10(10):e0140885.
  13. Blanco MR, Martin JS, Kahlscheuer ML, Krishnan R, Abelson J, Laederach A, Walter NG. (2015) Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics. Nature Methods, 12(11):1077-84.
  14. Solem AC, Halvorsen M, Ramos SB, Laederach A. (2015) The potential of the riboSNitch in personalized medicine. WIREs RNA, 6(5):517-32.
  15. Kutchko KM, Sanders W, Ziehr B, Phillips G, Solem A, Halvorsen M, Weeks KM, Moorman N, Laederach A. (2015) Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR. RNA, 21(7):1274-85.
  16. Corley M, Solem A, Qu K, Chang HY, Laederach A. (2015) Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. Nucleic Acids Research, 43(3):1859-68.
  17. Schlatterer JC, Martin JS, Laederach A, Brenowitz M. (2014) Mapping the kinetic barriers of a Large RNA molecule’s folding landscape. PLOS ONE, 9(2):e85041.
  18. Rogler LE, Kosmyna B, Moskowitz D, Bebawee R, Rahimzadeh J, Kutchko K, Laederach A, Notarangelo LD, Giliani S, Bouhassira E, Frenette P, Roy-Chowdhury J, Rogler CE. (2014) Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia. Human Molecular Genetics, 23(2):368-82
  19. Ritz J, Martin JS, Laederach A. (2013) Evolutionary evidence for alternative structure in RNA sequence co-variation. PLOS Computational Biology, 9(7): e1003152.
  20. Chen C, Mitra S, Jonikas M, Martin JS, Brenowitz M, Laederach A. (2013) Understanding the Role of Three-Dimensional Topology in Determining the Folding Intermediates of Group I Introns. Biophysical Journal, 106:6, 1326–1337.
  21. Ritz J, Martin JS, Laederach A. (2012) Evaluating our ability to predict the structural disruption of RNA by SNPs. BMC Genomics, 13(Suppl 4):S6
  22. Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W. (2012) Toward interoperable bioscience data. Nat. Genet. Jan 27;44(2):121-6.
  23. Martin JS, Mitiguy P, Laederach A. (2012) Modeling RNA Folding Pathways and Intermediates Using Time-Resolved Hydroxyl Radical Footprinting Data. RNA 3D Structure Analysis and Prediction, 319-334.
  24. Martin JS, Halvorsen M, Davis-Neulander L, Ritz J, Gopinath C, Beauregard A, Laederach A. (2012) Structural effects of linkage disequilibrium on the transcriptome. RNA,18, 77-87.
  25. Pelleymounter LL, Moon I, Johnson JA, Laederach A, Halvorsen M, Eckloff B, Abo R, Rossetti S. (2011) A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: Targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population. Mol Genet Metab. 2011 Aug 24.
  26. Mitra S, Laederach A, Golden BL, Altman RB, Brenowitz M. (2011) RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. RNA. Aug;17(8):1589-603. Epub 2011 Jun 28.
  27. Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, Laederach A. (2011) Meeting report of the RNA Ontology Consortium January 8-9, 2011.Stand Genomic Sci. Apr 29;4(2):252-6.
  28. Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A. (2011) Sharing and archiving nucleic acid structure mapping data. RNA. Jul;17(7):1204-12. Epub 2011 May 24.
  29. Sanders W, Laederach A. (2011) Membrane RNAs in bacteria. Mol Microbiol. Jan;79(1):1-2.
  30. Poursina M, Bhalerao KD, Flores SC, Anderson KS, Laederach A. (2011) Strategies for articulated multibody-based adaptive coarse grain simulation of RNA. Methods Enzymol.487:73-98.
  31. Halvorsen M, Martin JS, Broadaway S, Laederach A. (2010) Disease-associated mutations that alter the RNA structural ensemble. PLoS Genetics, 2010, 6(8).
  32. Martin JS, Quarrier S, Neulander LJ, Beauregard A, Laederach A. (2010) Evaluating the Information Content of RNA Chemical Mapping Data for Secondary Structure Prediction. RNA,16, 1108-1117
  33. Simmons, K., Martin J.S., Shcherbakova, I., Laederach, A. (2009) Rapid Quantification and Analysis of Kinetic OH Radical Footprinting Data using SAFA, Methods in Enzymology, 3 (468), 21-39
  34. Martin, J.S., Simmons, K., Laederach A. (2009) Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding, Algorithms, 2(1), 200-214.
  35. Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA. Feb;15(2):189-99.
  36. Shcherbakova I, Mitra S, Laederach A, Brenowitz M. (2008) Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol. Dec;12(6):655-66.
  37. Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. (2008), Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat Protoc. 2008;3(9):1395-401.
  38. Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A. (2008) High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Research, 2008 Jun;36(11):e63.
  39. Das, R., Kudaravalli, M., Jonikas M., Laederach A., Fong R., Schwans, J.P., Baker D., Piccirilli J.A., Altman R.B., and Herschlag, D. (2008) Structural inference of native and partially folded RNA by high-throughput contact mapping PNAS, 105, 4144-4149.
  40. Laederach, A. (2007) Informatics Challenges in Structured RNA, Briefings in Bioinformatics, 5, 294-303.
  41. Laederach, A., Shcherbakova, I., Jonikas, M.A., Altman, R.B., Brenowitz, M.(2007) Distinct contribution of electrostatics, initial conformational ensemble and macromolecular stability in RNA folding, PNAS, 104, 7045-50.
  42. Laederach, A., Chan, J.M., Schwartzman, A., Willgohs, E.S., Altman, R.B. (2007) Co-planar and co-axial orientations of RNA bases and helices, RNA 13, 643-50.
  43. Vicens, Q., Gooding A.R., Laederach, A., Cech, T.R. (2006) RNA structure mapping in crystals to reveal lattice contacts. RNA 13, 536-48.
  44. Russell, R., Das, R., Suh H., Travers, K.J., Laederach, A., Engelhardt, M.A., Herschlag D. (2006). The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J. Mol. Biol. 363, 531-544.
  45. Laederach, A., Shcherbakova, I., Liang, M., Brenowitz, M., Altman, R.B. (2006). Local kinetic measures of macromolecular structure reveal multiple parallel folding pathways for a large RNA molecule.  J. Mol.Biol,  358, 1179-1190.
  46. Laederach A., Reilly P. J. (2005) Modeling Protein Recognition of Carbohydrates. Proteins, Structure Function and Genetics, 60, 591-597.
  47. Das, R., Laederach, A. Pearlman, S. M., Herschlag, D, & Altman, R.B. (2005) SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11, 344-354.
  48. Liang M.P., Troyanskaya O. G. , Laederach, A., Brutlag D.L. & Altman, R.B. (2004) Computational Functional Genomics, IEEE Signal Processing, 21, 62-69.
  49. Aikens C.L., Laederach A. & Reilly P. J. (2004) Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking. Proteins 1, 27-35.
  50. Allen M.J., Laederach A., Reilly P. J., Mason R.J. & Voelker D.R. (2004) Arg343 in human surfactant protein D governs discrimination between glucose and N-acetylglucosamine ligands. Glycobiology 14, 693-700.
  51. Breheny, P., Laederach, A., Fulton, D. B. & Andreotti, A. H. (2003). Ligand specificity modulated by prolyl imide bond cis/trans isomerization in the ITK SH2 domain: A quantitative NMR study.J Am Chem Soc 125, 15706-15707.
  52. Laederach, A., Cradic, K. W., Fulton, D. B. & Andreotti, A. H. (2003). Determinants of intra versus intermolecular self-association within the regulatory domains of Rlk and Itk. J Mol Biol 329, 1011-1020.
  53. Laederach, A. & Reilly, P. J. (2003). Specific empirical free energy function for automated docking of carbohydrates to proteins. J Comput Chem 24, 1748-1757.
  54. Laederach, A., Andreotti, A. H. & Fulton, D. B. (2002). Solution and micelle-bound structures of tachyplesin I and its active aromatic linear derivatives. Biochemistry 41, 12359-12368.
  55. Laederach, A., Cradic, K. W., Brazin, K. N., Zamoon, J., Fulton, D. B., Huang, X. Y. & Andreotti, A. H. (2002). Competing modes of self-association in the regulatory domains of Bruton’s tyrosine kinase: intramolecular contact versus asymmetric homodimerization. Protein Sci 11, 36-45.
  56. Allen, M. J., Laederach, A., Reilly, P. J. & Mason, R. J. (2001). Polysaccharide recognition by surfactant protein D: novel interactions of a C-type lectin with nonterminal glucosyl residues. Biochemistry 40, 7789-7798.
  57. Pletneva, E. V., Laederach, A. T., Fulton, D. B. & Kostic, N. M. (2001). The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains. J Am Chem Soc 123, 6232-6245.
  58. Rockey, W. M., Laederach, A. & Reilly, P. J. (2000). Automated docking of a-(1–>4)- and a-(1–>6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site. Proteins 40, 299-309.
  59. Laederach, A., Dowd, M. K., Coutinho, P. M. & Reilly, P. J. (1999). Automated docking of maltose, 2-deoxymaltose, and maltotetraose into the soybean b-amylase active site. Proteins 37, 166-175.