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Items: 1 to 50 of 305

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.

Testing adequacy for DNA substitution models.

Chen W, Kenney T, Bielawski J, Gu H.

BMC Bioinformatics. 2019 Jun 20;20(1):349. doi: 10.1186/s12859-019-2905-3.

6.

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
7.

Bioactive sphingolipid profile in a xenograft mouse model of head and neck squamous cell carcinoma.

Bai A, Liu X, Bielawski J, Hannun YA.

PLoS One. 2019 Apr 19;14(4):e0215770. doi: 10.1371/journal.pone.0215770. eCollection 2019.

8.
9.

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
10.

Dose dependent actions of LCL521 on acid ceramidase and key sphingolipid metabolites.

Bai A, Bielawska A, Rahmaniyan M, Kraveka JM, Bielawski J, Hannun YA.

Bioorg Med Chem. 2018 Dec 15;26(23-24):6067-6075. doi: 10.1016/j.bmc.2018.11.012. Epub 2018 Nov 10.

PMID:
30448190
11.

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
12.

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
13.

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.

14.

Functional antagonism of sphingosine-1-phosphate receptor 1 prevents cuprizone-induced demyelination.

Kim S, Bielawski J, Yang H, Kong Y, Zhou B, Li J.

Glia. 2018 Mar;66(3):654-669. doi: 10.1002/glia.23272. Epub 2017 Nov 29.

15.

Sphingosine kinase 1 expression enhances colon tumor growth.

Furuya H, Shimizu Y, Tamashiro PM, Iino K, Bielawski J, Chan OTM, Pagano I, Kawamori T.

J Transl Med. 2017 Jun 6;15(1):120. doi: 10.1186/s12967-017-1220-x.

16.

Inhibiting glucosylceramide synthase exacerbates cisplatin-induced acute kidney injury.

Dupre TV, Doll MA, Shah PP, Sharp CN, Siow D, Megyesi J, Shayman J, Bielawska A, Bielawski J, Beverly LJ, Hernandez-Corbacho M, Clarke CJ, Snider AJ, Schnellmann RG, Obeid LM, Hannun YA, Siskind LJ.

J Lipid Res. 2017 Jul;58(7):1439-1452. doi: 10.1194/jlr.M076745. Epub 2017 May 10.

17.

Altered Levels of Serum Ceramide, Sphingosine and Sphingomyelin Are Associated with Colorectal Cancer: A Retrospective Pilot Study.

Separovic D, Shields AF, Philip PA, Bielawski J, Bielawska A, Pierce JS, Tarca AL.

Anticancer Res. 2017 Mar;37(3):1213-1218.

18.

Fumonisin B1 Inhibits Endoplasmic Reticulum Stress Associated-apoptosis After FoscanPDT Combined with C6-Pyridinium Ceramide or Fenretinide.

Boppana NB, Kraveka JM, Rahmaniyan M, Li LI, Bielawska A, Bielawski J, Pierce JS, Delor JS, Zhang K, Korbelik M, Separovic D.

Anticancer Res. 2017 Feb;37(2):455-463.

19.

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
20.

Ceramide activates lysosomal cathepsin B and cathepsin D to attenuate autophagy and induces ER stress to suppress myeloid-derived suppressor cells.

Liu F, Li X, Lu C, Bai A, Bielawski J, Bielawska A, Marshall B, Schoenlein PV, Lebedyeva IO, Liu K.

Oncotarget. 2016 Dec 20;7(51):83907-83925. doi: 10.18632/oncotarget.13438.

21.

Sphingomyelinase-like phosphodiesterase 3b mediates radiation-induced damage of renal podocytes.

Ahmad A, Mitrofanova A, Bielawski J, Yang Y, Marples B, Fornoni A, Zeidan YH.

FASEB J. 2017 Feb;31(2):771-780. doi: 10.1096/fj.201600618R. Epub 2016 Nov 11.

22.

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
23.

Cytokine-induced release of ceramide-enriched exosomes as a mediator of cell death signaling in an oligodendroglioma cell line.

Podbielska M, Szulc ZM, Kurowska E, Hogan EL, Bielawski J, Bielawska A, Bhat NR.

J Lipid Res. 2016 Nov;57(11):2028-2039. Epub 2016 Sep 13.

24.

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
25.

Smoothed Bootstrap Aggregation for Assessing Selection Pressure at Amino Acid Sites.

Mingrone J, Susko E, Bielawski J.

Mol Biol Evol. 2016 Nov;33(11):2976-2989. Epub 2016 Aug 2.

PMID:
27486222
26.

Increased Plasma Levels of Select Deoxy-ceramide and Ceramide Species are Associated with Increased Odds of Diabetic Neuropathy in Type 1 Diabetes: A Pilot Study.

Hammad SM, Baker NL, El Abiad JM, Spassieva SD, Pierce JS, Rembiesa B, Bielawski J, Lopes-Virella MF, Klein RL; DCCT/EDIC Group of Investigators.

Neuromolecular Med. 2017 Mar;19(1):46-56. doi: 10.1007/s12017-016-8423-9. Epub 2016 Jul 7.

27.

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
28.

Ectopic expression of ceramide synthase 2 in neurons suppresses neurodegeneration induced by ceramide synthase 1 deficiency.

Spassieva SD, Ji X, Liu Y, Gable K, Bielawski J, Dunn TM, Bieberich E, Zhao L.

Proc Natl Acad Sci U S A. 2016 May 24;113(21):5928-33. doi: 10.1073/pnas.1522071113. Epub 2016 May 9.

29.

Endothelial Nogo-B regulates sphingolipid biosynthesis to promote pathological cardiac hypertrophy during chronic pressure overload.

Zhang Y, Huang Y, Cantalupo A, Azevedo PS, Siragusa M, Bielawski J, Giordano FJ, Di Lorenzo A.

JCI Insight. 2016 Apr 21;1(5). pii: e85484.

30.

Enhanced apoptotic cancer cell killing after Foscan photodynamic therapy combined with fenretinide via de novo sphingolipid biosynthesis pathway.

Boppana NB, DeLor JS, Van Buren E, Bielawska A, Bielawski J, Pierce JS, Korbelik M, Separovic D.

J Photochem Photobiol B. 2016 Jun;159:191-5. doi: 10.1016/j.jphotobiol.2016.02.040. Epub 2016 Mar 16.

31.

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.

32.

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
33.

Regulation of cellular sphingosine-1-phosphate by sphingosine kinase 1 and sphingosine-1-phopshate lyase determines chemotherapy resistance in gastroesophageal cancer.

Matula K, Collie-Duguid E, Murray G, Parikh K, Grabsch H, Tan P, Lalwani S, Garau R, Ong Y, Bain G, Smith AD, Urquhart G, Bielawski J, Finnegan M, Petty R.

BMC Cancer. 2015 Oct 22;15:762. doi: 10.1186/s12885-015-1718-7.

34.

Regulation of Chlamydomonas flagella and ependymal cell motile cilia by ceramide-mediated translocation of GSK3.

Kong JN, Hardin K, Dinkins M, Wang G, He Q, Mujadzic T, Zhu G, Bielawski J, Spassieva S, Bieberich E.

Mol Biol Cell. 2015 Dec 1;26(24):4451-65. doi: 10.1091/mbc.E15-06-0371. Epub 2015 Oct 7.

35.

Elevation of 20-carbon long chain bases due to a mutation in serine palmitoyltransferase small subunit b results in neurodegeneration.

Zhao L, Spassieva S, Gable K, Gupta SD, Shi LY, Wang J, Bielawski J, Hicks WL, Krebs MP, Naggert J, Hannun YA, Dunn TM, Nishina PM.

Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):12962-7. doi: 10.1073/pnas.1516733112. Epub 2015 Oct 5.

36.

Ceramides promote apoptosis for virus-infected lymphoma cells through induction of ceramide synthases and viral lytic gene expression.

Dai L, Trillo-Tinoco J, Bai A, Chen Y, Bielawski J, Del Valle L, Smith CD, Ochoa AC, Qin Z, Parsons C.

Oncotarget. 2015 Sep 15;6(27):24246-60.

37.

Neurotoxic 1-deoxysphingolipids and paclitaxel-induced peripheral neuropathy.

Kramer R, Bielawski J, Kistner-Griffin E, Othman A, Alecu I, Ernst D, Kornhauser D, Hornemann T, Spassieva S.

FASEB J. 2015 Nov;29(11):4461-72. doi: 10.1096/fj.15-272567. Epub 2015 Jul 21.

38.

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.

39.

Enhanced killing of SCC17B human head and neck squamous cell carcinoma cells after photodynamic therapy plus fenretinide via the de novo sphingolipid biosynthesis pathway and apoptosis.

Boppana NB, Stochaj U, Kodiha M, Bielawska A, Bielawski J, Pierce JS, Korbelik M, Separovic D.

Int J Oncol. 2015 May;46(5):2003-10. doi: 10.3892/ijo.2015.2909. Epub 2015 Feb 26.

40.

C6-pyridinium ceramide sensitizes SCC17B human head and neck squamous cell carcinoma cells to photodynamic therapy.

Boppana NB, Stochaj U, Kodiha M, Bielawska A, Bielawski J, Pierce JS, Korbelik M, Separovic D.

J Photochem Photobiol B. 2015 Feb;143:163-8. doi: 10.1016/j.jphotobiol.2015.01.001. Epub 2015 Jan 10.

41.

Sphingolipid pathway regulates innate immune responses at the fetomaternal interface during pregnancy.

Mizugishi K, Inoue T, Hatayama H, Bielawski J, Pierce JS, Sato Y, Takaori-Kondo A, Konishi I, Yamashita K.

J Biol Chem. 2015 Jan 23;290(4):2053-68. doi: 10.1074/jbc.M114.628867. Epub 2014 Dec 11.

42.

Targeting (cellular) lysosomal acid ceramidase by B13: design, synthesis and evaluation of novel DMG-B13 ester prodrugs.

Bai A, Szulc ZM, Bielawski J, Pierce JS, Rembiesa B, Terzieva S, Mao C, Xu R, Wu B, Clarke CJ, Newcomb B, Liu X, Norris J, Hannun YA, Bielawska A.

Bioorg Med Chem. 2014 Dec 15;22(24):6933-44. doi: 10.1016/j.bmc.2014.10.025. Epub 2014 Oct 22.

43.

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.

44.

Ceramide synthase inhibitor fumonisin B1 inhibits apoptotic cell death in SCC17B human head and neck squamous carcinoma cells after Pc4 photosensitization.

Boppana NB, Kodiha M, Stochaj U, Lin HS, Haimovitz-Friedman A, Bielawska A, Bielawski J, Divine GW, Boyd JA, Korbelik M, Separovic D.

Photochem Photobiol Sci. 2014 Nov;13(11):1621-7. doi: 10.1039/c4pp00292j.

45.

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
46.

Ceramide modulates pre-mRNA splicing to restore the expression of wild-type tumor suppressor p53 in deletion-mutant cancer cells.

Patwardhan GA, Hosain SB, Liu DX, Khiste SK, Zhao Y, Bielawski J, Jazwinski SM, Liu YY.

Biochim Biophys Acta. 2014 Nov;1841(11):1571-80. doi: 10.1016/j.bbalip.2014.08.017. Epub 2014 Sep 6.

47.

Dietary glucosylceramides suppress tumor growth in a mouse xenograft model of head and neck squamous cell carcinoma by the inhibition of angiogenesis through an increase in ceramide.

Yazama H, Kitatani K, Fujiwara K, Kato M, Hashimoto-Nishimura M, Kawamoto K, Hasegawa K, Kitano H, Bielawska A, Bielawski J, Okazaki T.

Int J Clin Oncol. 2015 Jun;20(3):438-46. doi: 10.1007/s10147-014-0734-y. Epub 2014 Aug 1.

PMID:
25080062
48.

Impairment of ceramide synthesis causes a novel progressive myoclonus epilepsy.

Vanni N, Fruscione F, Ferlazzo E, Striano P, Robbiano A, Traverso M, Sander T, Falace A, Gazzerro E, Bramanti P, Bielawski J, Fassio A, Minetti C, Genton P, Zara F.

Ann Neurol. 2014 Aug;76(2):206-12. doi: 10.1002/ana.24170. Epub 2014 May 20.

PMID:
24782409
49.

Sphingosine kinase 1 regulates adipose proinflammatory responses and insulin resistance.

Wang J, Badeanlou L, Bielawski J, Ciaraldi TP, Samad F.

Am J Physiol Endocrinol Metab. 2014 Apr 1;306(7):E756-68. doi: 10.1152/ajpendo.00549.2013. Epub 2014 Jan 28.

50.

Ceramide targets xIAP and cIAP1 to sensitize metastatic colon and breast cancer cells to apoptosis induction to suppress tumor progression.

Paschall AV, Zimmerman MA, Torres CM, Yang D, Chen MR, Li X, Bieberich E, Bai A, Bielawski J, Bielawska A, Liu K.

BMC Cancer. 2014 Jan 15;14:24. doi: 10.1186/1471-2407-14-24.

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