Alain T. Laederach, Ph.D. - Publications

Affiliations: 
2003 Iowa State University, Ames, IA, United States 
Area:
Nuclear magnetic resonance, Macromolecular structure and recognition

56 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
2016 Mucaki EJ, Caminsky NG, Perri AM, Lu R, Laederach A, Halvorsen M, Knoll JHM, Rogan PK. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer Bmc Medical Genomics. 9. DOI: 10.1186/s12920-016-0178-5  0.72
2015 Solem A, Laederach A. RNA folding: A clear path to RNA catalysis Nature Chemical Biology. 11: 906-908. PMID 26575236 DOI: 10.1038/nchembio.1954  0.72
2015 Blanco MR, Martin JS, Kahlscheuer ML, Krishnan R, Abelson J, Laederach A, Walter NG. Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics. Nature Methods. 12: 1077-84. PMID 26414013 DOI: 10.1038/nmeth.3602  0.72
2015 Kutchko KM, Sanders W, Ziehr B, Phillips G, Solem A, Halvorsen M, Weeks KM, Moorman N, Laederach A. Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR. Rna (New York, N.Y.). 21: 1274-85. PMID 25999316 DOI: 10.1261/rna.049221.114  0.72
2015 Corley M, Solem A, Qu K, Chang HY, Laederach A. Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. Nucleic Acids Research. 43: 1859-68. PMID 25618847 DOI: 10.1093/nar/gkv010  0.72
2015 Lackey L, McArthur E, Laederach A. Increased transcript complexity in genes associated with chronic obstructive pulmonary disease Plos One. 10. DOI: 10.1371/journal.pone.0140885  0.72
2015 Solem AC, Halvorsen M, Ramos SBV, Laederach A. The potential of the riboSNitch in personalized medicine Wiley Interdisciplinary Reviews: Rna. 6: 517-532. DOI: 10.1002/wrna.1291  0.72
2014 Schlatterer JC, Martin JS, Laederach A, Brenowitz M. Mapping the kinetic barriers of a large RNA molecule's folding landscape Plos One. 9. PMID 24586236 DOI: 10.1371/journal.pone.0085041  0.72
2014 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. Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia Human Molecular Genetics. 23: 368-382. PMID 24009312 DOI: 10.1093/hmg/ddt427  0.72
2014 Ramos SBV, Laederach A. Molecular biology: A second layer of information in RNA Nature. 505: 621-622. DOI: 10.1038/505621a  0.72
2013 Chen C, Mitra S, Jonikas M, Martin J, Brenowitz M, Laederach A. Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns. Biophysical Journal. 104: 1326-37. PMID 23528092 DOI: 10.1016/j.bpj.2013.02.007  0.72
2013 Ritz J, Martin JS, Laederach A. Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation Plos Computational Biology. 9. DOI: 10.1371/journal.pcbi.1003152  0.72
2012 Ritz J, Martin JS, Laederach A. Evaluating our ability to predict the structural disruption of RNA by SNPs Bmc Genomics. 13: S6. PMID 22759654  0.72
2012 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, ... ... Laederach A, et al. Toward interoperable bioscience data. Nature Genetics. 44: 121-6. PMID 22281772 DOI: 10.1038/ng.1054  0.72
2012 Martin JS, Halvorsen M, Davis-Neulander L, Ritz J, Gopinath C, Beauregard A, Laederach A. Structural effects of linkage disequilibrium on the transcriptome Rna. 18: 77-87. PMID 22109839 DOI: 10.1261/rna.029900.111  0.72
2011 Pelleymounter LL, Moon I, Johnson JA, Laederach A, Halvorsen M, Eckloff B, Abo R, Rossetti S. 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. Molecular Genetics and Metabolism. 104: 457-69. PMID 21917492 DOI: 10.1016/j.ymgme.2011.08.019  0.72
2011 Mitra S, Laederach A, Golden BL, Altman RB, Brenowitz M. RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. Rna (New York, N.Y.). 17: 1589-603. PMID 21712400 DOI: 10.1261/rna.2694811  0.72
2011 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, et al. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Standards in Genomic Sciences. 4: 252-6. PMID 21677862 DOI: 10.4056/sigs.1724282  0.72
2011 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, ... ... Laederach A, et al. Sharing and archiving nucleic acid structure mapping data. Rna (New York, N.Y.). 17: 1204-12. PMID 21610212 DOI: 10.1261/rna.2753211  0.72
2011 Sanders W, Laederach A. Membrane RNAs in bacteria Molecular Microbiology. 79: 1-2. PMID 21210530 DOI: 10.1111/j.1365-2958.2010.07438.x  0.72
2011 Poursina M, Bhalerao KD, Flores SC, Anderson KS, Laederach A. Strategies for articulated multibody-based adaptive coarse grain simulation of RNA. Methods in Enzymology. 487: 73-98. PMID 21187222 DOI: 10.1016/B978-0-12-381270-4.00003-2  0.72
2010 Halvorsen M, Martin JS, Broadaway S, Laederach A. Disease-associated mutations that alter the RNA structural ensemble Plos Genetics. 6. PMID 20808897 DOI: 10.1371/journal.pgen.1001074  0.72
2010 Hamza TH, Zabetian CP, Tenesa A, Laederach A, Montimurro J, Yearout D, Kay DM, Doheny KF, Paschall J, Pugh E, Kusel VI, Collura R, Roberts J, Griffith A, Samii A, et al. Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nature Genetics. 42: 781-5. PMID 20711177 DOI: 10.1038/ng.642  0.72
2010 Quarrier S, Martin JS, Davis-Neulander L, Beauregard A, Laederach A. Evaluation of the information content of RNA structure mapping data for secondary structure prediction Rna. 16: 1108-1117. PMID 20413617 DOI: 10.1261/rna.1988510  0.72
2010 Bhalerao KD, Anderson KS, Laederach A. On adaptivity in coarse grain molecular dynamics Proceedings of the Asme International Design Engineering Technical Conferences and Computers and Information in Engineering Conference 2009, Detc2009. 4: 1495-1498.4. DOI: 10.1115/DETC2009-87827  0.72
2009 Simmons K, Martin JS, Shcherbakova I, Laederach A. Rapid quantification and analysis of kinetic •OH radical footprinting data using SAFA. Methods in Enzymology. 468: 47-66. PMID 20946764 DOI: 10.1016/S0076-6879(09)68003-4  0.72
2009 Martin JS, Simmons K, Laederach A. Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding. Algorithms. 2: 200-214. PMID 19865589 DOI: 10.3390/a2010200  0.72
2009 Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. Rna (New York, N.Y.). 15: 189-99. PMID 19144906 DOI: 10.1261/rna.1270809  0.72
2008 Shcherbakova I, Mitra S, Laederach A, Brenowitz M. Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Current Opinion in Chemical Biology. 12: 655-66. PMID 18926923 DOI: 10.1016/j.cbpa.2008.09.017  0.72
2008 Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nature Protocols. 3: 1395-401. PMID 18772866 DOI: 10.1038/nprot.2008.134  0.72
2008 Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A. High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Research. 36: e63. PMID 18477638 DOI: 10.1093/nar/gkn267  0.72
2008 Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America. 105: 4144-9. PMID 18322008 DOI: 10.1073/pnas.0709032105  0.72
2007 Laederach A. Informatics challenges in structured RNA Briefings in Bioinformatics. 8: 294-303. PMID 17611237 DOI: 10.1093/bib/bbm026  0.72
2007 Laederach A, Shcherbakova I, Jonikas MA, Altman RB, Brenowitz M. Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding Proceedings of the National Academy of Sciences of the United States of America. 104: 7045-7050. PMID 17438287 DOI: 10.1073/pnas.0608765104  0.72
2007 Laederach A, Chan JM, Schwartzman A, Willgohs E, Altman RB. Coplanar and coaxial orientations of RNA bases and helices. Rna (New York, N.Y.). 13: 643-50. PMID 17339576 DOI: 10.1261/rna.381407  0.72
2007 Vicens Q, Gooding AR, Laederach A, Cech TR. Local RNA structural changes induced by crystallization are revealed by SHAPE. Rna (New York, N.Y.). 13: 536-48. PMID 17299128 DOI: 10.1261/rna.400207  0.72
2006 Russell R, Das R, Suh H, Travers KJ, Laederach A, Engelhardt MA, Herschlag D. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. Journal of Molecular Biology. 363: 531-44. PMID 16963081 DOI: 10.1016/j.jmb.2006.08.024  0.72
2006 Laederach A, Shcherbakova I, Liang MP, Brenowitz M, Altman RB. Local Kinetic Measures of Macromolecular Structure Reveal Partitioning among Multiple Parallel Pathways from the Earliest Steps in the Folding of a Large RNA Molecule Journal of Molecular Biology. 358: 1179-1190. PMID 16574145 DOI: 10.1016/j.jmb.2006.02.075  0.72
2006 Laederach A. Docking carbohydrates to proteins: Empirical free energy functions Acs Symposium Series. 930: 258-270.  0.72
2005 Laederach A, Reilly PJ. Modeling protein recognition of carbohydrates Proteins: Structure, Function and Genetics. 60: 591-597. PMID 16001416 DOI: 10.1002/prot.20545  0.72
2005 Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. Rna (New York, N.Y.). 11: 344-54. PMID 15701734 DOI: 10.1261/rna.7214405  0.72
2004 Aikens CL, Laederach A, Reilly PJ. Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking Proteins: Structure, Function and Genetics. 57: 27-35. PMID 15326592 DOI: 10.1002/prot.20180  0.72
2004 Allen MJ, Laederach A, Reilly PJ, Mason RJ, Voelker DR. Arg343 in human surfactant protein D governs discrimination between glucose and N-acetylglucosamine ligands. Glycobiology. 14: 693-700. PMID 15115749 DOI: 10.1093/glycob/cwh088  0.72
2004 Liang MP, Troyanskaya OG, Laederach A, Brutlag DL, Altman RB. Computational functional genomics Ieee Signal Processing Magazine. 21: 62-69. DOI: 10.1109/MSP.2004.1359143  0.72
2003 Breheny PJ, Laederach A, Fulton DB, Andreotti AH. Ligand specificity modulated by prolyl imide bond Cis/Trans isomerization in the Itk SH2 domain: a quantitative NMR study. Journal of the American Chemical Society. 125: 15706-7. PMID 14677936 DOI: 10.1021/ja0375380  0.72
2003 Laederach A, Reilly PJ. Specific Empirical Free Energy Function for Automated Docking of Carbohydrates to Proteins Journal of Computational Chemistry. 24: 1748-1757. PMID 12964193 DOI: 10.1002/jcc.10288  0.72
2003 Laederach A, Cradic KW, Fulton DB, Andreotti AH. Determinants of intra versus intermolecular self-association within the regulatory domains of Rlk and Itk. Journal of Molecular Biology. 329: 1011-20. PMID 12798690 DOI: 10.1016/S0022-2836(03)00531-X  0.72
2002 Laederach A, Andreotti AH, Fulton DB. Solution and micelle-bound structures of tachyplesin I and its active aromatic linear derivatives. Biochemistry. 41: 12359-68. PMID 12369825 DOI: 10.1021/bi026185z  0.72
2002 Laederach A, Cradic KW, Brazin KN, Zamoon J, Fulton DB, Huang XY, Andreotti AH. Competing modes of self-association in the regulatory domains of Bruton's tyrosine kinase: intramolecular contact versus asymmetric homodimerization. Protein Science : a Publication of the Protein Society. 11: 36-45. PMID 11742120 DOI: 10.1110/ps.26702  0.72
2001 Pletneva EV, Laederach AT, Fulton DB, Kostic NM. The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains. Journal of the American Chemical Society. 123: 6232-45. PMID 11427046 DOI: 10.1021/ja010401u  0.72
2001 Allen MJ, Laederach A, Reilly PJ, Mason RJ. Polysaccharide recognition by surfactant protein D: novel interactions of a C-type lectin with nonterminal glucosyl residues. Biochemistry. 40: 7789-98. PMID 11425305 DOI: 10.1021/bi002901q  0.72
2000 Rockey WM, Laederach A, Reilly PJ. Automated docking of alpha-(1-->4)- and alpha-(1-->6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site. Proteins. 40: 299-309. PMID 10842343 DOI: 10.1002/(SICI)1097-0134(20000801)40:2<299::AID-PROT100>3.0.CO;2-G  0.72
1999 Laederach A, Dowd MK, Coutinho PM, Reilly PJ. Automated docking of maltose, 2-deoxymaltose, and maltotetraose into the soybean β-amylase active site Proteins: Structure, Function and Genetics. 37: 166-175. PMID 10584063 DOI: 10.1002/(SICI)1097-0134(19991101)37:2<166::AID-PROT3>3.0.CO;2-E  0.72
1996 Stoeckli HF, Laederach A, Affolter J. On the characterization of industrial carbon blacks by physico-chemical and by empirical parameters Carbon. 34: 135-137. DOI: 10.1016/0008-6223(96)81662-9  0.72
1994 Stoeckli F, Currit L, Laederach A, Centeno TA. Water adsorption in carbons described by the dubinin-astakhov and dubinin-serpinski equations Journal of the Chemical Society, Faraday Transactions. 90: 3689-3691. DOI: 10.1039/FT9949003689  0.72
1994 Stoeckli HF, Huguenin D, Laederach A. On the characterization of carbon blacks by various techniques Carbon. 32: 1359-1362. DOI: 10.1016/0008-6223(94)90122-8  0.72
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