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Items: 1 to 50 of 117

1.

Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations.

Harel N, Meir M, Gophna U, Stern A.

Nucleic Acids Res. 2019 Oct 30. pii: gkz907. doi: 10.1093/nar/gkz907. [Epub ahead of print]

PMID:
31665473
2.

Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.

Dubinsky V, Reshef L, Bar N, Keizer D, Golan N, Rabinowitz K, Godny L, Yadgar K, Zonensain K, Tulchinsky H, Gophna U, Dotan I.

Gastroenterology. 2019 Oct 9. pii: S0016-5085(19)41416-9. doi: 10.1053/j.gastro.2019.10.001. [Epub ahead of print]

PMID:
31605691
3.

An electrode-assisted anaerobic digestion process for the production of high-quality biogas.

Yanuka-Golub K, Baransi-Karkaby K, Szczupak A, Reshef L, Rishpon J, Shechter R, Gophna U, Sabbah I.

Water Sci Technol. 2019 Jun;79(11):2145-2155. doi: 10.2166/wst.2019.214.

PMID:
31318352
4.

Fruit Consumption is Associated with Alterations in Microbial Composition and Lower Rates of Pouchitis.

Godny L, Maharshak N, Reshef L, Goren I, Yahav L, Fliss-Isakov N, Gophna U, Tulchinsky H, Dotan I.

J Crohns Colitis. 2019 Sep 27;13(10):1265-1272. doi: 10.1093/ecco-jcc/jjz053.

PMID:
30828722
5.

The Effect of Density-Dependent Phase on the Locust Gut Bacterial Composition.

Lavy O, Gophna U, Gefen E, Ayali A.

Front Microbiol. 2019 Jan 18;9:3020. doi: 10.3389/fmicb.2018.03020. eCollection 2018.

6.

Starch Consumption May Modify Antiglycan Antibodies and Fecal Fungal Composition in Patients With Ileo-Anal Pouch.

Goren I, Godny L, Reshef L, Yanai H, Gophna U, Tulchinsky H, Dotan I.

Inflamm Bowel Dis. 2019 Mar 14;25(4):742-749. doi: 10.1093/ibd/izy370.

PMID:
30535148
7.

Coordinated change at the colony level in fruit bat fur microbiomes through time.

Kolodny O, Weinberg M, Reshef L, Harten L, Hefetz A, Gophna U, Feldman MW, Yovel Y.

Nat Ecol Evol. 2019 Jan;3(1):116-124. doi: 10.1038/s41559-018-0731-z. Epub 2018 Dec 10.

PMID:
30532043
8.

Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation.

Turgeman-Grott I, Joseph S, Marton S, Eizenshtein K, Naor A, Soucy SM, Stachler AE, Shalev Y, Zarkor M, Reshef L, Altman-Price N, Marchfelder A, Gophna U.

Nat Microbiol. 2019 Jan;4(1):177-186. doi: 10.1038/s41564-018-0302-8. Epub 2018 Nov 26.

9.

The unbearable ease of expression-how avoidance of spurious transcription can shape G+C content in bacterial genomes.

Gophna U.

FEMS Microbiol Lett. 2018 Dec 1;365(23). doi: 10.1093/femsle/fny267. No abstract available.

PMID:
30423131
10.

Pandemic Bacteremic Escherichia Coli Strains: Evolution and Emergence of Drug-Resistant Pathogens.

Yair Y, Gophna U.

Curr Top Microbiol Immunol. 2018;416:163-180. doi: 10.1007/82_2018_109. Review.

PMID:
30046983
11.

The Escherichia coli Type III Secretion System 2 Has a Global Effect on Cell Surface.

Shulman A, Yair Y, Biran D, Sura T, Otto A, Gophna U, Becher D, Hecker M, Ron EZ.

MBio. 2018 Jul 3;9(4). pii: e01070-18. doi: 10.1128/mBio.01070-18.

12.

Repeat modularity as a beneficial property of multiple CRISPR-Cas systems.

Yair Y, Gophna U.

RNA Biol. 2019 Apr;16(4):585-587. doi: 10.1080/15476286.2018.1474073. Epub 2018 Aug 10.

13.

The nuts and bolts of the Haloferax CRISPR-Cas system I-B.

Maier LK, Stachler AE, Brendel J, Stoll B, Fischer S, Haas KA, Schwarz TS, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Gophna U, Marchfelder A.

RNA Biol. 2019 Apr;16(4):469-480. doi: 10.1080/15476286.2018.1460994. Epub 2018 May 21.

14.

Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax.

Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U.

Genes (Basel). 2018 Mar 20;9(3). pii: E172. doi: 10.3390/genes9030172.

15.

Microbiome associated with denture malodour.

Yitzhaki S, Reshef L, Gophna U, Rosenberg M, Sterer N.

J Breath Res. 2018 Jan 17;12(2):027103. doi: 10.1088/1752-7163/aa95e0.

PMID:
29341956
16.

Microbiome associated with dentures malodour.

Yitzhaki S, Reshef L, Gophna U, Rosenberg M, Sterer N.

J Breath Res. 2017 Oct 25. doi: 10.1088/1752-7163/aa95e0. [Epub ahead of print]

PMID:
29068319
17.

Cell Surface Glycosylation Is Required for Efficient Mating of Haloferax volcanii.

Shalev Y, Turgeman-Grott I, Tamir A, Eichler J, Gophna U.

Front Microbiol. 2017 Jul 5;8:1253. doi: 10.3389/fmicb.2017.01253. eCollection 2017.

18.

Cis-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids.

Artieri CG, Naor A, Turgeman-Grott I, Zhou Y, York R, Gophna U, Fraser HB.

Sci Rep. 2017 Jun 21;7(1):3986. doi: 10.1038/s41598-017-04278-4.

19.

Finally, Archaea Get Their CRISPR-Cas Toolbox.

Gophna U, Allers T, Marchfelder A.

Trends Microbiol. 2017 Jun;25(6):430-432. doi: 10.1016/j.tim.2017.03.009. Epub 2017 Apr 6.

PMID:
28391963
20.

High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon.

Stachler AE, Turgeman-Grott I, Shtifman-Segal E, Allers T, Marchfelder A, Gophna U.

Nucleic Acids Res. 2017 May 19;45(9):5208-5216. doi: 10.1093/nar/gkx150.

21.

Oscillospira and related bacteria - From metagenomic species to metabolic features.

Gophna U, Konikoff T, Nielsen HB.

Environ Microbiol. 2017 Mar;19(3):835-841. doi: 10.1111/1462-2920.13658. Epub 2017 Feb 3.

PMID:
28028921
22.

Alterations of Enteric Microbiota in Patients with a Normal Ileal Pouch Are Predictive of Pouchitis.

Maharshak N, Cohen NA, Reshef L, Tulchinsky H, Gophna U, Dotan I.

J Crohns Colitis. 2017 Mar 1;11(3):314-320. doi: 10.1093/ecco-jcc/jjw157.

PMID:
27613294
23.

Impact of a homing intein on recombination frequency and organismal fitness.

Naor A, Altman-Price N, Soucy SM, Green AG, Mitiagin Y, Turgeman-Grott I, Davidovich N, Gogarten JP, Gophna U.

Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):E4654-61. doi: 10.1073/pnas.1606416113. Epub 2016 Jul 26.

24.

Reply.

Naftali T, Reshef L, Kovacs A, Porat R, Amir I, Konikoff FM, Gophna U.

Inflamm Bowel Dis. 2016 May;22(5):E15-6. doi: 10.1097/MIB.0000000000000782. No abstract available.

PMID:
27096566
25.

Community structure dynamics during startup in microbial fuel cells - The effect of phosphate concentrations.

Yanuka-Golub K, Reshef L, Rishpon J, Gophna U.

Bioresour Technol. 2016 Jul;212:151-159. doi: 10.1016/j.biortech.2016.04.016. Epub 2016 Apr 6.

PMID:
27092994
26.

Oscillospira: a Central, Enigmatic Component of the Human Gut Microbiota.

Konikoff T, Gophna U.

Trends Microbiol. 2016 Jul;24(7):523-524. doi: 10.1016/j.tim.2016.02.015. Epub 2016 Mar 17.

PMID:
26996766
27.

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.

Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R, Henry CS, Ben-Tal N, Dwyer DJ, Gophna U, Ruppin E.

PLoS Comput Biol. 2016 Jan 28;12(1):e1004705. doi: 10.1371/journal.pcbi.1004705. eCollection 2016 Jan.

28.

Distinct Microbiotas are Associated with Ileum-Restricted and Colon-Involving Crohn's Disease.

Naftali T, Reshef L, Kovacs A, Porat R, Amir I, Konikoff FM, Gophna U.

Inflamm Bowel Dis. 2016 Feb;22(2):293-302. doi: 10.1097/MIB.0000000000000662.

PMID:
26752462
29.

Harnessing the landscape of microbial culture media to predict new organism-media pairings.

Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk HP, Gophna U, Ruppin E.

Nat Commun. 2015 Oct 13;6:8493. doi: 10.1038/ncomms9493.

30.

Detecting Horizontal Gene Transfer between Closely Related Taxa.

Adato O, Ninyo N, Gophna U, Snir S.

PLoS Comput Biol. 2015 Oct 6;11(10):e1004408. doi: 10.1371/journal.pcbi.1004408. eCollection 2015 Oct.

31.

Interactions between the intestinal microbiota and bile acids in gallstones patients.

Keren N, Konikoff FM, Paitan Y, Gabay G, Reshef L, Naftali T, Gophna U.

Environ Microbiol Rep. 2015 Dec;7(6):874-80. doi: 10.1111/1758-2229.12319. Epub 2015 Aug 7.

PMID:
26149537
32.

The gill microbiota of invasive and indigenous Spondylus oysters from the Mediterranean Sea and northern Red Sea.

Roterman YR, Benayahu Y, Reshef L, Gophna U.

Environ Microbiol Rep. 2015 Dec;7(6):860-7. doi: 10.1111/1758-2229.12315. Epub 2015 Aug 7.

PMID:
26111733
33.

Archaea in and on the Human Body: Health Implications and Future Directions.

Lurie-Weinberger MN, Gophna U.

PLoS Pathog. 2015 Jun 11;11(6):e1004833. doi: 10.1371/journal.ppat.1004833. eCollection 2015 Jun. Review. No abstract available.

34.

Pouch Inflammation Is Associated With a Decrease in Specific Bacterial Taxa.

Reshef L, Kovacs A, Ofer A, Yahav L, Maharshak N, Keren N, Konikoff FM, Tulchinsky H, Gophna U, Dotan I.

Gastroenterology. 2015 Sep;149(3):718-27. doi: 10.1053/j.gastro.2015.05.041. Epub 2015 May 27.

PMID:
26026389
35.

Escherichia coli isolates from patients with bacteremic urinary tract infection are genetically distinct from those derived from sepsis following prostate transrectal biopsy.

Dan M, Yair Y, Samosav A, Gottesman T, Yossepowitch O, Harari-Schwartz O, Tsivian A, Schreiber R, Gophna U.

Int J Med Microbiol. 2015 Jun-Aug;305(4-5):464-8. doi: 10.1016/j.ijmm.2015.04.003. Epub 2015 Apr 25.

PMID:
25963574
36.

No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales.

Gophna U, Kristensen DM, Wolf YI, Popa O, Drevet C, Koonin EV.

ISME J. 2015 Sep;9(9):2021-7. doi: 10.1038/ismej.2015.20. Epub 2015 Feb 24.

37.

Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations.

Eilam O, Zarecki R, Oberhardt M, Ursell LK, Kupiec M, Knight R, Gophna U, Ruppin E.

MBio. 2014 Aug 12;5(4). pii: e01526-14. doi: 10.1128/mBio.01526-14.

38.

A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness.

Zarecki R, Oberhardt MA, Reshef L, Gophna U, Ruppin E.

PLoS Comput Biol. 2014 Jul 17;10(7):e1003726. doi: 10.1371/journal.pcbi.1003726. eCollection 2014 Jul.

39.

Ribosomal mutations affecting the translation of genes that use non-optimal codons.

Pelchovich G, Nadejda S, Dana A, Tuller T, Bravo IG, Gophna U.

FEBS J. 2014 Aug;281(16):3701-18. doi: 10.1111/febs.12892. Epub 2014 Aug 8.

40.

Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms.

Zarecki R, Oberhardt MA, Yizhak K, Wagner A, Shtifman Segal E, Freilich S, Henry CS, Gophna U, Ruppin E.

PLoS One. 2014 May 27;9(5):e98372. doi: 10.1371/journal.pone.0098372. eCollection 2014.

41.

DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival.

Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, Soppa J.

PLoS One. 2014 Apr 14;9(4):e94819. doi: 10.1371/journal.pone.0094819. eCollection 2014.

42.

Extracellular DNA metabolism in Haloferax volcanii.

Chimileski S, Dolas K, Naor A, Gophna U, Papke RT.

Front Microbiol. 2014 Feb 20;5:57. doi: 10.3389/fmicb.2014.00057. eCollection 2014.

43.

Investigating a lotic microbial community following a severe detergent spill.

Or A, Gophna U.

Arch Microbiol. 2014 Feb;196(2):119-24. doi: 10.1007/s00203-013-0948-9. Epub 2014 Jan 1.

PMID:
24379053
44.

Eisenbergiella tayi gen. nov., sp. nov., isolated from human blood.

Amir I, Bouvet P, Legeay C, Gophna U, Weinberger A.

Int J Syst Evol Microbiol. 2014 Mar;64(Pt 3):907-14. doi: 10.1099/ijs.0.057331-0. Epub 2013 Nov 26.

PMID:
24282142
45.

Phylo SI: a new genome-wide approach for prokaryotic phylogeny.

Shifman A, Ninyo N, Gophna U, Snir S.

Nucleic Acids Res. 2014 Feb;42(4):2391-404. doi: 10.1093/nar/gkt1138. Epub 2013 Nov 15.

46.

Menaquinone and iron are essential for complex colony development in Bacillus subtilis.

Pelchovich G, Omer-Bendori S, Gophna U.

PLoS One. 2013 Nov 4;8(11):e79488. doi: 10.1371/journal.pone.0079488. eCollection 2013.

47.

Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious.

Wagner A, Zarecki R, Reshef L, Gochev C, Sorek R, Gophna U, Ruppin E.

Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):19166-71. doi: 10.1073/pnas.1312361110. Epub 2013 Nov 6.

48.

Gastric microbiota is altered in oesophagitis and Barrett's oesophagus and further modified by proton pump inhibitors.

Amir I, Konikoff FM, Oppenheim M, Gophna U, Half EE.

Environ Microbiol. 2014 Sep;16(9):2905-14. doi: 10.1111/1462-2920.12285. Epub 2013 Oct 22.

PMID:
24112768
49.

In and out: an analysis of epibiotic vs periplasmic bacterial predators.

Pasternak Z, Njagi M, Shani Y, Chanyi R, Rotem O, Lurie-Weinberger MN, Koval S, Pietrokovski S, Gophna U, Jurkevitch E.

ISME J. 2014 Mar;8(3):625-35. doi: 10.1038/ismej.2013.164. Epub 2013 Oct 3.

50.

The correlation between Clostridium-difficile infection and human gut concentrations of Bacteroidetes phylum and clostridial species.

Goldberg E, Amir I, Zafran M, Gophna U, Samra Z, Pitlik S, Bishara J.

Eur J Clin Microbiol Infect Dis. 2014 Mar;33(3):377-83. doi: 10.1007/s10096-013-1966-x. Epub 2013 Sep 19.

PMID:
24048726

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