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Items: 20

1.

Defining α-synuclein species responsible for Parkinson disease phenotypes in mice.

Froula JM, Castellana-Cruz M, Anabtawi NM, Camino JD, Chen SW, Thrasher DR, Freire J, Yazdi AA, Fleming S, Dobson CM, Kumita JR, Cremades N, Volpicelli-Daley LA.

J Biol Chem. 2019 May 29. pii: jbc.RA119.007743. doi: 10.1074/jbc.RA119.007743. [Epub ahead of print]

2.

α-Synuclein fibril-induced paradoxical structural and functional defects in hippocampal neurons.

Froula JM, Henderson BW, Gonzalez JC, Vaden JH, Mclean JW, Wu Y, Banumurthy G, Overstreet-Wadiche L, Herskowitz JH, Volpicelli-Daley LA.

Acta Neuropathol Commun. 2018 May 1;6(1):35. doi: 10.1186/s40478-018-0537-x.

3.

Best Practices for Generating and Using Alpha-Synuclein Pre-Formed Fibrils to Model Parkinson's Disease in Rodents.

Polinski NK, Volpicelli-Daley LA, Sortwell CE, Luk KC, Cremades N, Gottler LM, Froula J, Duffy MF, Lee VMY, Martinez TN, Dave KD.

J Parkinsons Dis. 2018;8(2):303-322. doi: 10.3233/JPD-171248.

4.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

5.

Preparing Fosmid Mate-Paired Libraries Using Cre-LoxP Recombination.

Peng Z, Froula JL, Cheng JF.

Methods Mol Biol. 2017;1642:263-284. doi: 10.1007/978-1-4939-7169-5_17.

PMID:
28815506
6.

Preparing Mate-Paired Illumina Libraries Using Cre Recombinase.

Peng Z, Nath N, Zhao Z, Froula JL, Cheng JF, Chen F.

Methods Mol Biol. 2017;1642:247-261. doi: 10.1007/978-1-4939-7169-5_16.

PMID:
28815505
7.

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.

Kamke J, Soni P, Li Y, Ganesh S, Kelly WJ, Leahy SC, Shi W, Froula J, Rubin EM, Attwood GT.

BMC Res Notes. 2017 Aug 8;10(1):367. doi: 10.1186/s13104-017-2671-0.

8.

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation.

Kamke J, Kittelmann S, Soni P, Li Y, Tavendale M, Ganesh S, Janssen PH, Shi W, Froula J, Rubin EM, Attwood GT.

Microbiome. 2016 Oct 19;4(1):56.

9.

The Epigenomic Landscape of Prokaryotes.

Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ.

PLoS Genet. 2016 Feb 12;12(2):e1005854. doi: 10.1371/journal.pgen.1005854. eCollection 2016 Feb. Erratum in: PLoS Genet. 2016 May;12(5):e1006064.

10.

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.

Bendall ML, Stevens SL, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, Shade A, Newton RJ, McMahon KD, Malmstrom RR.

ISME J. 2016 Jul;10(7):1589-601. doi: 10.1038/ismej.2015.241. Epub 2016 Jan 8.

11.

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.

Kang DD, Froula J, Egan R, Wang Z.

PeerJ. 2015 Aug 27;3:e1165. doi: 10.7717/peerj.1165. eCollection 2015.

12.

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.

Shi W, Moon CD, Leahy SC, Kang D, Froula J, Kittelmann S, Fan C, Deutsch S, Gagic D, Seedorf H, Kelly WJ, Atua R, Sang C, Soni P, Li D, Pinares-Patiño CS, McEwan JC, Janssen PH, Chen F, Visel A, Wang Z, Attwood GT, Rubin EM.

Genome Res. 2014 Sep;24(9):1517-25. doi: 10.1101/gr.168245.113. Epub 2014 Jun 6.

13.

Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation.

Piao H, Froula J, Du C, Kim TW, Hawley ER, Bauer S, Wang Z, Ivanova N, Clark DS, Klenk HP, Hess M.

Biotechnol Bioeng. 2014 Aug;111(8):1550-65. doi: 10.1002/bit.25250. Epub 2014 May 28.

PMID:
24728961
14.

Generation of long insert pairs using a Cre-LoxP Inverse PCR approach.

Peng Z, Zhao Z, Nath N, Froula JL, Clum A, Zhang T, Cheng JF, Copeland AC, Pennacchio LA, Chen F.

PLoS One. 2012;7(1):e29437. doi: 10.1371/journal.pone.0029437. Epub 2012 Jan 9.

15.

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics.

He S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P.

Nat Methods. 2010 Oct;7(10):807-12. doi: 10.1038/nmeth.1507. Epub 2010 Sep 19.

PMID:
20852648
16.

Comparative metagenomics and population dynamics of the gut microbiota in mother and infant.

Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, Francino MP.

Genome Biol Evol. 2010 Jan 6;2:53-66. doi: 10.1093/gbe/evp057.

17.
18.

Positional cloning of ZNF217 and NABC1: genes amplified at 20q13.2 and overexpressed in breast carcinoma.

Collins C, Rommens JM, Kowbel D, Godfrey T, Tanner M, Hwang SI, Polikoff D, Nonet G, Cochran J, Myambo K, Jay KE, Froula J, Cloutier T, Kuo WL, Yaswen P, Dairkee S, Giovanola J, Hutchinson GB, Isola J, Kallioniemi OP, Palazzolo M, Martin C, Ericsson C, Pinkel D, Albertson D, Li WB, Gray JW.

Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8703-8.

19.

Quinolone antibiotics in therapy of experimental pneumococcal meningitis in rabbits.

Nau R, Schmidt T, Kaye K, Froula JL, Täuber MG.

Antimicrob Agents Chemother. 1995 Mar;39(3):593-7.

20.

Clarithromycin lacks bactericidal activity in cerebrospinal fluid in experimental pneumococcal meningitis.

Schmidt T, Froula J, Täuber MG.

J Antimicrob Chemother. 1993 Oct;32(4):627-32. No abstract available.

PMID:
8288505

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