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Items: 1 to 50 of 57

1.

The relationship between fecal bile acids and microbiome community structure in pediatric Crohn's disease.

Connors J, Dunn KA, Allott J, Bandsma R, Rashid M, Otley AR, Bielawski JP, Van Limbergen J.

ISME J. 2019 Dec 3. doi: 10.1038/s41396-019-0560-3. [Epub ahead of print]

PMID:
31796936
2.

A phenotype-genotype codon model for detecting adaptive evolution.

Jones CT, Youssef N, Susko E, Bielawski JP.

Syst Biol. 2019 Nov 15. pii: syz075. doi: 10.1093/sysbio/syz075. [Epub ahead of print]

PMID:
31730199
3.

Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship Between Model and Data.

Jones CT, Susko E, Bielawski JP.

Methods Mol Biol. 2019;1910:399-426. doi: 10.1007/978-1-4939-9074-0_13.

PMID:
31278672
4.

Introduction to Genome Biology and Diversity.

Youssef N, Budd A, Bielawski JP.

Methods Mol Biol. 2019;1910:3-31. doi: 10.1007/978-1-4939-9074-0_1.

PMID:
31278660
5.

Crohn's Disease Exclusion Diet Plus Partial Enteral Nutrition Induces Sustained Remission in a Randomized Controlled Trial.

Levine A, Wine E, Assa A, Sigall Boneh R, Shaoul R, Kori M, Cohen S, Peleg S, Shamaly H, On A, Millman P, Abramas L, Ziv-Baran T, Grant S, Abitbol G, Dunn KA, Bielawski JP, Van Limbergen J.

Gastroenterology. 2019 Aug;157(2):440-450.e8. doi: 10.1053/j.gastro.2019.04.021. Epub 2019 Jun 4.

PMID:
31170412
6.
7.

ModL: exploring and restoring regularity when testing for positive selection.

Mingrone J, Susko E, Bielawski JP.

Bioinformatics. 2019 Aug 1;35(15):2545-2554. doi: 10.1093/bioinformatics/bty1019.

PMID:
30541063
8.

Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo.

Dunn KA, Andrews K, Bashwih RO, Bielawski JP.

Methods Mol Biol. 2018;1849:267-289. doi: 10.1007/978-1-4939-8728-3_17.

PMID:
30298260
9.

Phenomenological Load on Model Parameters Can Lead to False Biological Conclusions.

Jones CT, Youssef N, Susko E, Bielawski JP.

Mol Biol Evol. 2018 Jun 1;35(6):1473-1488. doi: 10.1093/molbev/msy049.

PMID:
29596684
10.

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn's disease.

Douglas GM, Hansen R, Jones CMA, Dunn KA, Comeau AM, Bielawski JP, Tayler R, El-Omar EM, Russell RK, Hold GL, Langille MGI, Van Limbergen J.

Microbiome. 2018 Jan 15;6(1):13. doi: 10.1186/s40168-018-0398-3.

11.

Shifting Balance on a Static Mutation-Selection Landscape: A Novel Scenario of Positive Selection.

Jones CT, Youssef N, Susko E, Bielawski JP.

Mol Biol Evol. 2017 Feb 1;34(2):391-407. doi: 10.1093/molbev/msw237.

PMID:
28110273
12.

Early Changes in Microbial Community Structure Are Associated with Sustained Remission After Nutritional Treatment of Pediatric Crohn's Disease.

Dunn KA, Moore-Connors J, MacIntyre B, Stadnyk AW, Thomas NA, Noble A, Mahdi G, Rashid M, Otley AR, Bielawski JP, Van Limbergen J.

Inflamm Bowel Dis. 2016 Dec;22(12):2853-2862.

PMID:
27805918
13.

The Gut Microbiome of Pediatric Crohn's Disease Patients Differs from Healthy Controls in Genes That Can Influence the Balance Between a Healthy and Dysregulated Immune Response.

Dunn KA, Moore-Connors J, MacIntyre B, Stadnyk A, Thomas NA, Noble A, Mahdi G, Rashid M, Otley AR, Bielawski JP, Van Limbergen J.

Inflamm Bowel Dis. 2016 Nov;22(11):2607-2618.

PMID:
27760077
14.

Inference of Episodic Changes in Natural Selection Acting on Protein Coding Sequences via CODEML.

Bielawski JP, Baker JL, Mingrone J.

Curr Protoc Bioinformatics. 2016 Jun 20;54:6.15.1-6.15.32. doi: 10.1002/cpbi.2.

PMID:
27322407
15.

Functional Divergence of the Nuclear Receptor NR2C1 as a Modulator of Pluripotentiality During Hominid Evolution.

Baker JL, Dunn KA, Mingrone J, Wood BA, Karpinski BA, Sherwood CC, Wildman DE, Maynard TM, Bielawski JP.

Genetics. 2016 Jun;203(2):905-22. doi: 10.1534/genetics.115.183889. Epub 2016 Apr 13.

16.

Novel Strategies for Applied Metagenomics.

Moore-Connors JM, Dunn KA, Bielawski JP, Van Limbergen J.

Inflamm Bowel Dis. 2016 Mar;22(3):709-18. doi: 10.1097/MIB.0000000000000717. Review.

PMID:
26848519
17.

BioMiCo: a supervised Bayesian model for inference of microbial community structure.

Shafiei M, Dunn KA, Boon E, MacDonald SM, Walsh DA, Gu H, Bielawski JP.

Microbiome. 2015 Mar 10;3:8. doi: 10.1186/s40168-015-0073-x. eCollection 2015.

18.

BiomeNet: a Bayesian model for inference of metabolic divergence among microbial communities.

Shafiei M, Dunn KA, Chipman H, Gu H, Bielawski JP.

PLoS Comput Biol. 2014 Nov 20;10(11):e1003918. doi: 10.1371/journal.pcbi.1003918. eCollection 2014 Nov.

19.

Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton.

El-Swais H, Dunn KA, Bielawski JP, Li WK, Walsh DA.

Environ Microbiol. 2015 Oct;17(10):3642-61. doi: 10.1111/1462-2920.12629. Epub 2015 Jan 30.

PMID:
25244530
20.

Inference of functional divergence among proteins when the evolutionary process is non-stationary.

Bay RA, Bielawski JP.

J Mol Evol. 2013 Apr;76(4):205-15. doi: 10.1007/s00239-013-9549-0. Epub 2013 Feb 27.

PMID:
23443835
21.

Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices.

Dunn KA, Jiang W, Field C, Bielawski JP.

PLoS One. 2013;8(1):e55816. doi: 10.1371/journal.pone.0055816. Epub 2013 Jan 31.

22.

Detecting the signatures of adaptive evolution in protein-coding genes.

Bielawski JP.

Curr Protoc Mol Biol. 2013 Jan;Chapter 19:Unit 19.1.. doi: 10.1002/0471142727.mb1901s101.

PMID:
23288462
23.

Recombination detection under evolutionary scenarios relevant to functional divergence.

Bay RA, Bielawski JP.

J Mol Evol. 2011 Dec;73(5-6):273-86. doi: 10.1007/s00239-011-9473-0. Epub 2012 Jan 1.

PMID:
22210457
24.

Positive Darwinian selection in the piston that powers proton pumps in complex I of the mitochondria of Pacific salmon.

Garvin MR, Bielawski JP, Gharrett AJ.

PLoS One. 2011;6(9):e24127. doi: 10.1371/journal.pone.0024127. Epub 2011 Sep 28. Erratum in: PLoS One. 2012;7(8). doi: 10.1371/annotation/8a7e2019-c039-4a54-b797-e9adb2ce4efc.

25.

Reconciling ecological and genomic divergence among lineages of listeria under an "extended mosaic genome concept".

Dunn KA, Bielawski JP, Ward TJ, Urquhart C, Gu H.

Mol Biol Evol. 2009 Nov;26(11):2605-15. doi: 10.1093/molbev/msp176. Epub 2009 Aug 10.

PMID:
19666992
26.

Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth.

Morine MJ, Gu H, Myers RA, Bielawski JP.

J Mol Evol. 2009 May;68(5):506-15. doi: 10.1007/s00239-009-9226-5. Epub 2009 Apr 14.

PMID:
19365645
27.

Multilocus genotyping assays for single nucleotide polymorphism-based subtyping of Listeria monocytogenes isolates.

Ward TJ, Ducey TF, Usgaard T, Dunn KA, Bielawski JP.

Appl Environ Microbiol. 2008 Dec;74(24):7629-42. doi: 10.1128/AEM.01127-08. Epub 2008 Oct 17.

28.

Portal protein diversity and phage ecology.

Sullivan MB, Coleman ML, Quinlivan V, Rosenkrantz JE, Defrancesco AS, Tan G, Fu R, Lee JA, Waterbury JB, Bielawski JP, Chisholm SW.

Environ Microbiol. 2008 Oct;10(10):2810-23. doi: 10.1111/j.1462-2920.2008.01702.x. Epub 2008 Jul 31. Erratum in: Environ Microbiol. 2011 Oct;13(10):2832.

29.

Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of evolution.

Bao L, Gu H, Dunn KA, Bielawski JP.

Mol Biol Evol. 2008 Sep;25(9):1995-2007. doi: 10.1093/molbev/msn145. Epub 2008 Jun 26.

PMID:
18586695
30.
31.

Proposed standard nomenclature for the alpha- and beta-globin gene families.

Aguileta G, Bielawski JP, Yang Z.

Genes Genet Syst. 2006 Oct;81(5):367-71.

32.

Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events.

Aguileta G, Bielawski JP, Yang Z.

Gene. 2006 Sep 15;380(1):21-9. Epub 2006 May 4.

PMID:
16843621
33.

Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts.

Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW.

PLoS Biol. 2006 Jul;4(8):e234.

34.

Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation.

Aris-Brosou S, Bielawski JP.

Gene. 2006 Aug 15;378:58-64. Epub 2006 May 22.

PMID:
16797879
35.

Adaptive evolution of multicolored fluorescent proteins in reef-building corals.

Field SF, Bulina MY, Kelmanson IV, Bielawski JP, Matz MV.

J Mol Evol. 2006 Mar;62(3):332-9. Epub 2006 Feb 10.

PMID:
16474984
36.

Evolutionary rates and expression level in Chlamydomonas.

Popescu CE, Borza T, Bielawski JP, Lee RW.

Genetics. 2006 Mar;172(3):1567-76. Epub 2005 Dec 15.

37.

Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates.

Zeidner G, Bielawski JP, Shmoish M, Scanlan DJ, Sabehi G, Béjà O.

Environ Microbiol. 2005 Oct;7(10):1505-13.

PMID:
16156724
38.

Adaptive diversification of vomeronasal receptor 1 genes in rodents.

Shi P, Bielawski JP, Yang H, Zhang YP.

J Mol Evol. 2005 May;60(5):566-76.

PMID:
15983866
39.

Gene conversion and functional divergence in the beta-globin gene family.

Aguileta G, Bielawski JP, Yang Z.

J Mol Evol. 2004 Aug;59(2):177-89.

PMID:
15486692
40.

Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment.

Bielawski JP, Dunn KA, Sabehi G, Béjà O.

Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14824-9. Epub 2004 Oct 4.

42.

The origin and evolution of geminivirus-related DNA sequences in Nicotiana.

Murad L, Bielawski JP, Matyasek R, Kovarík A, Nichols RA, Leitch AR, Lichtenstein CP.

Heredity (Edinb). 2004 Apr;92(4):352-8.

43.

Widespread adaptive evolution in the human immunodeficiency virus type 1 genome.

Yang W, Bielawski JP, Yang Z.

J Mol Evol. 2003 Aug;57(2):212-21.

PMID:
14562964
44.

Novel Proteorhodopsin variants from the Mediterranean and Red Seas.

Sabehi G, Massana R, Bielawski JP, Rosenberg M, Delong EF, Béjà O.

Environ Microbiol. 2003 Oct;5(10):842-9.

PMID:
14510837
45.

Maximum likelihood methods for detecting adaptive evolution after gene duplication.

Bielawski JP, Yang Z.

J Struct Funct Genomics. 2003;3(1-4):201-12. Review.

PMID:
12836699
46.
47.

Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium.

Ward TJ, Bielawski JP, Kistler HC, Sullivan E, O'Donnell K.

Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9278-83. Epub 2002 Jun 21.

48.

Accuracy and power of bayes prediction of amino acid sites under positive selection.

Anisimova M, Bielawski JP, Yang Z.

Mol Biol Evol. 2002 Jun;19(6):950-8.

PMID:
12032251
49.

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.

Anisimova M, Bielawski JP, Yang Z.

Mol Biol Evol. 2001 Aug;18(8):1585-92.

PMID:
11470850
50.

Positive and negative selection in the DAZ gene family.

Bielawski JP, Yang Z.

Mol Biol Evol. 2001 Apr;18(4):523-9.

PMID:
11264403

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