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Bryan Kolaczkowski, Ph.D. - Publications

Affiliations: 
2010- University of Florida, Gainesville, Gainesville, FL, United States 
Website:
https://microcell.ufl.edu/people/faculty-directory/kolaczkowski/
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34 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
2022 Garcia AK, Kolaczkowski B, Kaçar B. Reconstruction of nitrogenase predecessors suggests origin from maturase-like proteins. Genome Biology and Evolution. PMID 35179578 DOI: 10.1093/gbe/evac031  0.336
2021 Jia H, Aadland K, Kolaczkowski O, Kolaczkowski B. Direct molecular evidence for an ancient, conserved developmental toolkit controlling post-transcriptional gene regulation in land plants. Molecular Biology and Evolution. PMID 34196710 DOI: 10.1093/molbev/msab201  0.702
2021 Neuwald AF, Kolaczkowski BD, Altschul SF. eCOMPASS: evaluative comparison of multiple protein alignments by statistical score. Bioinformatics (Oxford, England). PMID 33983436 DOI: 10.1093/bioinformatics/btab374  0.348
2020 Aadland K, Kolaczkowski B. Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy. Genome Biology and Evolution. PMID 32785673 DOI: 10.1093/Gbe/Evaa164  0.749
2020 Garcia AK, McShea H, Kolaczkowski B, Kaçar B. Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum-cofactor utilization. Geobiology. PMID 32065506 DOI: 10.1111/Gbi.12381  0.426
2019 Roesch LFW, Dobbler PT, Pylro VS, Kolaczkowski B, Drew JC, Triplett EW. PIME: A package for discovery of novel differences among microbial communities. Molecular Ecology Resources. PMID 31698527 DOI: 10.1111/1755-0998.13116  0.303
2019 Timilsina S, Pereira-Martin JA, Minsavage GV, Iruegas-Bocardo F, Abrahamian P, Potnis N, Kolaczkowski B, Vallad GE, Goss EM, Jones JB. Multiple Recombination Events Drive the Current Genetic Structure of in Florida. Frontiers in Microbiology. 10: 448. PMID 30930868 DOI: 10.3389/Fmicb.2019.00448  0.387
2019 Sng NJ, Kolaczkowski B, Ferl RJ, Paul AL. A member of the CONSTANS-Like protein family is a putative regulator of reactive oxygen species homeostasis and spaceflight physiological adaptation. Aob Plants. 11: ply075. PMID 30705745 DOI: 10.1093/Aobpla/Ply075  0.329
2019 Aadland K, Pugh C, Kolaczkowski B. High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function. Methods in Molecular Biology (Clifton, N.J.). 1851: 135-170. PMID 30298396 DOI: 10.1007/978-1-4939-8736-8_8  0.744
2017 Jia H, Kolaczkowski O, Rolland J, Kolaczkowski B. Increased Affinity for RNA Targets Evolved Early in Animal and Plant Dicer Lineages through Different Structural Mechanisms. Molecular Biology and Evolution. PMID 29106606 DOI: 10.1093/Molbev/Msx187  0.424
2017 Dias R, Kolaczkowski B. Improving the accuracy of high-throughput protein-protein affinity prediction may require better training data. Bmc Bioinformatics. 18: 102. PMID 28361672 DOI: 10.1186/S12859-017-1533-Z  0.317
2017 Dias R, Manny A, Kolaczkowski O, Kolaczkowski B. Convergence of domain architecture, structure and ligand affinity in animal and plant RNA-binding proteins. Molecular Biology and Evolution. PMID 28333205 DOI: 10.1093/Molbev/Msx090  0.416
2016 Pugh C, Kolaczkowski O, Manny A, Korithoski B, Kolaczkowski B. Resurrecting ancestral structural dynamics of an antiviral immune receptor: adaptive binding pocket reorganization repeatedly shifts RNA preference. Bmc Evolutionary Biology. 16: 241. PMID 27825296 DOI: 10.1186/S12862-016-0818-6  0.336
2016 Zallot R, Harrison KJ, Kolaczkowski B, de Crécy-Lagard V. Functional Annotations of Paralogs: A Blessing and a Curse. Life (Basel, Switzerland). 6. PMID 27618105 DOI: 10.3390/Life6030039  0.409
2015 Zere TR, Vakulskas CA, Leng Y, Pannuri A, Potts AH, Dias R, Tang D, Kolaczkowski B, Georgellis D, Ahmer BM, Romeo T. Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems. Plos One. 10: e0145035. PMID 26673755 DOI: 10.1371/Journal.Pone.0145035  0.363
2015 Korithoski B, Kolaczkowski O, Mukherjee K, Kola R, Earl C, Kolaczkowski B. Evolution of a Novel Antiviral Immune-Signaling Interaction by Partial-Gene Duplication. Plos One. 10: e0137276. PMID 26356745 DOI: 10.1371/Journal.Pone.0137276  0.363
2014 Davis-Richardson AG, Ardissone AN, Dias R, Simell V, Leonard MT, Kemppainen KM, Drew JC, Schatz D, Atkinson MA, Kolaczkowski B, Ilonen J, Knip M, Toppari J, Nurminen N, Hyöty H, et al. Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes. Frontiers in Microbiology. 5: 678. PMID 25540641 DOI: 10.3389/Fmicb.2014.00678  0.3
2014 Xiong Y, Mei W, Kim ED, Mukherjee K, Hassanein H, Barbazuk WB, Sung S, Kolaczkowski B, Kang BH. Adaptive expansion of the maize maternally expressed gene (Meg) family involves changes in expression patterns and protein secondary structures of its members Bmc Plant Biology. 14. PMID 25084677 DOI: 10.1186/S12870-014-0204-8  0.38
2014 Reinhardt JA, Kolaczkowski B, Jones CD, Begun DJ, Kern AD. Parallel geographic variation in Drosophila melanogaster. Genetics. 197: 361-73. PMID 24610860 DOI: 10.1534/Genetics.114.161463  0.716
2014 Mukherjee K, Korithoski B, Kolaczkowski B. Ancient origins of vertebrate-specific innate antiviral immunity Molecular Biology and Evolution. 31: 140-153. PMID 24109602 DOI: 10.1093/Molbev/Mst184  0.315
2013 Mukherjee K, Campos H, Kolaczkowski B. Evolution of animal and plant dicers: Early parallel duplications and recurrent adaptation of antiviral RNA binding in plants Molecular Biology and Evolution. 30: 627-641. PMID 23180579 DOI: 10.1093/Molbev/Mss263  0.385
2012 Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, et al. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 192: 533-98. PMID 22673804 DOI: 10.1534/Genetics.112.142018  0.753
2011 Kolaczkowski B, Kern AD, Holloway AK, Begun DJ. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics. 187: 245-60. PMID 21059887 DOI: 10.1534/Genetics.110.123059  0.726
2011 Kolaczkowski B, Hupalo DN, Kern AD. Recurrent adaptation in RNA interference genes across the Drosophila phylogeny. Molecular Biology and Evolution. 28: 1033-42. PMID 20971974 DOI: 10.1093/Molbev/Msq284  0.741
2010 Hanson-Smith V, Kolaczkowski B, Thornton JW. Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Molecular Biology and Evolution. 27: 1988-99. PMID 20368266 DOI: 10.1093/Molbev/Msq081  0.776
2010 Kolaczkowski B, Thornton JW. Correction: Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics Plos One. 5. DOI: 10.1371/Annotation/93635F70-47D7-4876-84F5-Dd568434C9Ae  0.617
2010 Kolaczkowski B, Thornton JW. Correction: Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics Plos One. 5. DOI: 10.1371/annotation/93635f70-47d7-4876-84f5-dd568434c9ae  0.542
2009 Kolaczkowski B, Thornton JW. Long-branch attraction bias and inconsistency in Bayesian phylogenetics. Plos One. 4: e7891. PMID 20011052 DOI: 10.1371/Journal.Pone.0007891  0.648
2009 Sankararaman S, Kolaczkowski B, Sjölander K. INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. Nucleic Acids Research. 37: W390-5. PMID 19443452 DOI: 10.1093/Nar/Gkp339  0.729
2008 Kolaczkowski B, Thornton JW. A mixed branch length model of heterotachy improves phylogenetic accuracy. Molecular Biology and Evolution. 25: 1054-66. PMID 18319244 DOI: 10.1093/Molbev/Msn042  0.643
2007 Kolaczkowski B, Thornton JW. Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses. Molecular Biology and Evolution. 24: 2108-18. PMID 17636043 DOI: 10.1093/Molbev/Msm141  0.634
2006 Kolaczkowski B, Thornton JW. Is there a star tree paradox? Molecular Biology and Evolution. 23: 1819-23. PMID 16837562 DOI: 10.1093/Molbev/Msl059  0.63
2005 Thornton JW, Kolaczkowski B. No magic pill for phylogenetic error. Trends in Genetics : Tig. 21: 310-1. PMID 15922825 DOI: 10.1016/J.Tig.2005.04.002  0.634
2004 Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature. 431: 980-4. PMID 15496922 DOI: 10.1038/Nature02917  0.66
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