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Alain T. Laederach, Ph.D. - Publications

Affiliations: 
2003 Iowa State University, Ames, IA, United States 
Area:
Nuclear magnetic resonance, Macromolecular structure and recognition
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57 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 Dadonaite B, Gilbertson B, Knight ML, Trifkovic S, Rockman S, Laederach A, Brown LE, Fodor E, Bauer DLV. The structure of the influenza A virus genome. Nature Microbiology. PMID 31332385 DOI: 10.1038/S41564-019-0513-7  0.32
2018 Jain S, Laederach A, V Ramos SB, Schlick T. A pipeline for computational design of novel RNA-like topologies. Nucleic Acids Research. 46: 7040-7051. PMID 30137633 DOI: 10.1093/Nar/Gky524  0.331
2018 Mustoe AM, Corley M, Laederach A, Weeks KM. Messenger RNA Structure Regulates Translation Initiation: A Mechanism Exploited from Bacteria to Humans. Biochemistry. PMID 29894169 DOI: 10.1021/Acs.Biochem.8B00395  0.318
2018 Kutchko KM, Madden EA, Morrison C, Plante KS, Sanders W, Vincent HA, Cruz Cisneros MC, Long KM, Moorman NJ, Heise MT, Laederach A. Structural divergence creates new functional features in alphavirus genomes. Nucleic Acids Research. PMID 29361131 DOI: 10.1093/Nar/Gky012  0.349
2018 Lackey L, Coria A, Woods C, McArthur E, Laederach A. Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure. Rna (New York, N.Y.). PMID 29317542 DOI: 10.1261/Rna.064469.117  0.361
2017 Corley M, Solem A, Phillips G, Lackey L, Ziehr B, Vincent HA, Mustoe AM, Ramos SBV, Weeks KM, Moorman NJ, Laederach A. An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression. Proceedings of the National Academy of Sciences of the United States of America. PMID 29109288 DOI: 10.1073/Pnas.1706539114  0.303
2017 Woods CT, Lackey L, Williams B, Dokholyan NV, Gotz D, Laederach A. Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophysical Journal. PMID 28625696 DOI: 10.1016/J.Bpj.2017.05.031  0.386
2017 Ball CB, Solem AC, Meganck RM, Laederach A, Ramos SB. Impact of RNA structure on ZFP36L2 interaction with Luteinizing Hormone Receptor mRNA. Rna (New York, N.Y.). PMID 28455422 DOI: 10.1261/Rna.060467.116  0.385
2017 Gamache ER, Doh JH, Ritz J, Laederach A, Bellaousov S, Mathews DH, Curcio MJ. Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA. Viruses. 9. PMID 28445416 DOI: 10.3390/V9050093  0.378
2017 Woods CT, Laederach A. Classification of RNA structure change by "gazing" at experimental data. Bioinformatics (Oxford, England). PMID 28130241 DOI: 10.1093/Bioinformatics/Btx041  0.361
2017 Kutchko KM, Laederach A. Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution. Wiley Interdisciplinary Reviews - Rna. 8. PMID 27396578 DOI: 10.1002/Wrna.1374  0.369
2017 Lackey LL, Coria A, Tolson C, McArthur E, Laederach A. Abstract 505: Somatic and inherited riboSnitches inTPT1andLCP1mRNA secondary structures Cancer Research. 77: 505-505. DOI: 10.1158/1538-7445.Am2017-505  0.337
2016 Corley M, Laederach A. Selecting against accidental RNA interactions. Elife. 5. PMID 27642846 DOI: 10.7554/Elife.20686  0.31
2016 Schulmeyer KH, Diaz MR, Bair TB, Sanders W, Gode CJ, Laederach A, Wolfgang MC, Yahr TL. Primary and secondary sequence structure requirements for recognition and discrimination of target RNAs by Pseudomonas aeruginosa RsmA and RsmF. Journal of Bacteriology. PMID 27381913 DOI: 10.1128/Jb.00343-16  0.327
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  0.365
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  0.415
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  0.354
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  0.374
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  0.348
2014 Ramos SBV, Laederach A. Molecular biology: A second layer of information in RNA Nature. 505: 621-622. DOI: 10.1038/505621A  0.375
2013 Ritz J, Martin JS, Laederach A. Evolutionary evidence for alternative structure in RNA sequence co-variation. Plos Computational Biology. 9: e1003152. PMID 23935473 DOI: 10.1371/Journal.Pcbi.1003152  0.393
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  0.393
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 DOI: 10.1186/1471-2164-13-S4-S6  0.372
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  0.35
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  0.405
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  0.308
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  0.305
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  0.341
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  0.301
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  0.356
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  0.356
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  0.316
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  0.334
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  0.369
2009 Martin JS, Schlatterer J, Brenowitz M, Laederach A. Identifying Energy Barriers in RNA Folding Through Kinetic Model Enumeration Biophysical Journal. 96: 9a. DOI: 10.1016/J.Bpj.2008.12.943  0.365
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  0.351
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  0.334
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  0.373
2007 Laederach A. Informatics challenges in structured RNA Briefings in Bioinformatics. 8: 294-303. PMID 17611237 DOI: 10.1093/Bib/Bbm026  0.348
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  0.399
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  0.361
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  0.321
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  0.351
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  0.354
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  0.596
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  0.6
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  0.598
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  0.644
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  0.598
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  0.652
2003 Laederach A, Cradic K, Fulton D, Andreotti A. Txk SH3 domain backbone assignments Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5651  0.612
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  0.629
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  0.719
2002 Laederach A, Andreotti A, Fulton D. Backbone and 1H assignments for Tachyplesin I, phenylalanine mutant Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5488  0.603
2002 Laederach A, Andreotti A, Fulton D. Backbone and 1H assignments for Tachyplesin I, tyrosine mutant Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5487  0.607
2002 Laederach A, Andreotti A, Fulton D. Backbone and 1H assignments for Tachyplesin I, wild type Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5486  0.593
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  0.633
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