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Items: 1 to 50 of 200

1.

Manganese-Enhanced Magnetic Resonance Imaging: Overview and Central Nervous System Applications With a Focus on Neurodegeneration.

Cloyd RA, Koren SA, Abisambra JF.

Front Aging Neurosci. 2018 Dec 13;10:403. doi: 10.3389/fnagi.2018.00403. eCollection 2018. Review.

2.

Effect of pre-gestational weight and gestational weight gain in women with gestational diabetes controlled with medication on pregnancy outcomes - is recommended weight gain too liberal?

Koren R, Hochman Y, Koren S, Ziv-Baran T, Wiener Y.

Gynecol Endocrinol. 2018 Dec 31:1-4. doi: 10.1080/09513590.2018.1525701. [Epub ahead of print]

PMID:
30595073
3.

Long-Term Outcome after Hemithyroidectomy for Papillary Thyroid Cancer: A Comparative Study and Review of the Literature.

Geron Y, Benbassat C, Shteinshneider M, Koren S, Or K, Markus E, Hirsch D, Muallem Kalmovich L.

Cancers (Basel). 2018 Dec 27;11(1). pii: E26. doi: 10.3390/cancers11010026.

4.

Short-term Adherence with Discharge Recommendation for Insulin Treatment among Patients with Type 2 Diabetes.

Koren S, Yoshpa M, Koren R, Cantrell D, Rapoport MJ.

Isr Med Assoc J. 2018 Nov;20(11):691-694.

5.

Improved reference genome of Aedes aegypti informs arbovirus vector control.

Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC 4th, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB.

Nature. 2018 Nov;563(7732):501-507. doi: 10.1038/s41586-018-0692-z. Epub 2018 Nov 14.

PMID:
30429615
6.

A fast adaptive algorithm for computing whole-genome homology maps.

Jain C, Koren S, Dilthey A, Phillippy AM, Aluru S.

Bioinformatics. 2018 Sep 1;34(17):i748-i756. doi: 10.1093/bioinformatics/bty597.

7.

A 2017 SURVEY OF THE CLINICAL PRACTICE PATTERNS IN THE MANAGEMENT OF RELAPSING GRAVES' DISEASE.

Koren S, Shteinshnaider M, Or K, Cantrell D, Benbassat CA, Koren R.

Endocr Pract. 2018 Nov 1. doi: 10.4158/EP-2018-0386. [Epub ahead of print]

PMID:
30383500
8.

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification.

Nasko DJ, Koren S, Phillippy AM, Treangen TJ.

Genome Biol. 2018 Oct 30;19(1):165. doi: 10.1186/s13059-018-1554-6.

9.

De novo assembly of haplotype-resolved genomes with trio binning.

Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM.

Nat Biotechnol. 2018 Oct 22. doi: 10.1038/nbt.4277. [Epub ahead of print]

PMID:
30346939
10.

Adherence to ATA 2015 guidelines in the management of unifocal non-invasive papillary thyroid cancer: a clinical survey among endocrinologists and surgeons.

Or K, Benbassat C, Koren S, Shteinshneider M, Koren R, Cantrell D, Kummer E, Muallem Kalmovich L.

Eur Arch Otorhinolaryngol. 2018 Nov;275(11):2851-2859. doi: 10.1007/s00405-018-5126-x. Epub 2018 Sep 18.

PMID:
30229453
11.

Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen.

Pishchany G, Mevers E, Ndousse-Fetter S, Horvath DJ Jr, Paludo CR, Silva-Junior EA, Koren S, Skaar EP, Clardy J, Kolter R.

Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):10124-10129. doi: 10.1073/pnas.1807613115. Epub 2018 Sep 18.

PMID:
30228116
12.

Identification of novel reassortant mammalian orthoreoviruses from bats in Slovenia.

Naglič T, Rihtarič D, Hostnik P, Toplak N, Koren S, Kuhar U, Jamnikar-Ciglenečki U, Kutnjak D, Steyer A.

BMC Vet Res. 2018 Sep 3;14(1):264. doi: 10.1186/s12917-018-1585-y.

13.

Assessment on marine litter ingested by fish in the Adriatic and NE Ionian Sea macro-region (Mediterranean).

Anastasopoulou A, Kovač Viršek M, Bojanić Varezić D, Digka N, Fortibuoni T, Koren Š, Mandić M, Mytilineou C, Pešić A, Ronchi F, Šiljić J, Torre M, Tsangaris C, Tutman P.

Mar Pollut Bull. 2018 Aug;133:841-851. doi: 10.1016/j.marpolbul.2018.06.050. Epub 2018 Jun 26.

PMID:
30041385
14.

[NEW TREATMENTS IN DIABETES MELLITUS - AN UPDATE].

Koren S, Rapoport MJ.

Harefuah. 2018 May;157(5):318-321. Review. Hebrew.

PMID:
29804338
15.

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.

Kim JH, Dilthey AT, Nagaraja R, Lee HS, Koren S, Dudekula D, Wood Iii WH, Piao Y, Ogurtsov AY, Utani K, Noskov VN, Shabalina SA, Schlessinger D, Phillippy AM, Larionov V.

Nucleic Acids Res. 2018 Jul 27;46(13):6712-6725. doi: 10.1093/nar/gky442.

16.

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.

Jain C, Dilthey A, Koren S, Aluru S, Phillippy AM.

J Comput Biol. 2018 Jul;25(7):766-779. doi: 10.1089/cmb.2018.0036. Epub 2018 Apr 30.

PMID:
29708767
17.

A draft genome sequence for the Ixodes scapularis cell line, ISE6.

Miller JR, Koren S, Dilley KA, Harkins DM, Stockwell TB, Shabman RS, Sutton GG.

F1000Res. 2018 Mar 8;7:297. doi: 10.12688/f1000research.13635.1. eCollection 2018.

18.

Humoral hypercalcemia of pregnancy treated with bisphosphonates.

Koren R, Neeman O, Koren S, Benbassat CA.

Arch Endocrinol Metab. 2018 Feb;62(1):125-128. doi: 10.20945/2359-3997000000016.

19.

Thyroid Disease in Pregnancy: A Clinical Survey among Endocrinologists, Gynecologists, and Obstetricians in Israel.

Koren R, Wiener Y, Or K, Benbassat CA, Koren S.

Isr Med Assoc J. 2018 Mar;20(3):167-171.

20.

De novo transcriptome of the pallial gland of the date mussel (Lithophaga lithophaga).

Sivka U, Toplak N, Koren S, Jakše J.

Comp Biochem Physiol Part D Genomics Proteomics. 2018 Jun;26:1-9. doi: 10.1016/j.cbd.2018.02.001. Epub 2018 Feb 6.

PMID:
29454291
21.

Nanopore sequencing and assembly of a human genome with ultra-long reads.

Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.

Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29.

22.

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation.

Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen B, Chen XG, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, Sutton GG, Phillippy AM, Piermarini PM, Shabman RS.

Gigascience. 2018 Mar 1;7(3):1-13. doi: 10.1093/gigascience/gix135.

23.

De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads.

Eccles D, Chandler J, Camberis M, Henrissat B, Koren S, Le Gros G, Ewbank JJ.

BMC Biol. 2018 Jan 11;16(1):6. doi: 10.1186/s12915-017-0473-4.

24.

Reassessment of Differentiated Thyroid Cancer Patients Using the Eighth TNM/AJCC Classification System: A Comparative Study.

Shteinshnaider M, Muallem Kalmovich L, Koren S, Or K, Cantrell D, Benbassat C.

Thyroid. 2018 Feb;28(2):201-209. doi: 10.1089/thy.2017.0265. Epub 2018 Jan 22.

PMID:
29256827
25.

Exposure to a specific time-varying electromagnetic field inhibits cell proliferation via cAMP and ERK signaling in cancer cells.

Buckner CA, Buckner AL, Koren SA, Persinger MA, Lafrenie RM.

Bioelectromagnetics. 2018 Apr;39(3):217-230. doi: 10.1002/bem.22096. Epub 2017 Nov 10.

PMID:
29125193
26.

Lobular carcinoma in situ and invasive lobular breast cancer are characterized by enhanced expression of transcription factor AP-2β.

Raap M, Gronewold M, Christgen H, Glage S, Bentires-Alj M, Koren S, Derksen PW, Boelens M, Jonkers J, Lehmann U, Feuerhake F, Kuehnle E, Gluz O, Kates R, Nitz U, Harbeck N, Kreipe HH, Christgen M.

Lab Invest. 2018 Jan;98(1):117-129. doi: 10.1038/labinvest.2017.106. Epub 2017 Oct 16.

27.

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.

Schmidt MH, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B.

Plant Cell. 2017 Oct;29(10):2336-2348. doi: 10.1105/tpc.17.00521. Epub 2017 Oct 12.

28.

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M.

Brief Bioinform. 2017 Aug 7. doi: 10.1093/bib/bbx098. [Epub ahead of print]

PMID:
28968737
29.

Microplastics as a vector for the transport of the bacterial fish pathogen species Aeromonas salmonicida.

Viršek MK, Lovšin MN, Koren Š, Kržan A, Peterlin M.

Mar Pollut Bull. 2017 Dec 15;125(1-2):301-309. doi: 10.1016/j.marpolbul.2017.08.024. Epub 2017 Sep 7.

PMID:
28889914
30.

Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station.

Venkateswaran K, Checinska Sielaff A, Ratnayake S, Pope RK, Blank TE, Stepanov VG, Fox GE, van Tongeren SP, Torres C, Allen J, Jaing C, Pierson D, Perry J, Koren S, Phillippy A, Klubnik J, Treangen TJ, Rosovitz MJ, Bergman NH.

Genome Announc. 2017 Aug 10;5(32). pii: e00680-17. doi: 10.1128/genomeA.00680-17.

31.

Extraction of Organochlorine Pesticides from Plastic Pellets and Plastic Type Analysis.

Pflieger M, Makorič P, Kovač Viršek M, Koren Š.

J Vis Exp. 2017 Jul 1;(125). doi: 10.3791/55531.

PMID:
28715401
32.

Scaffolding of long read assemblies using long range contact information.

Ghurye J, Pop M, Koren S, Bickhart D, Chin CS.

BMC Genomics. 2017 Jul 12;18(1):527. doi: 10.1186/s12864-017-3879-z.

33.

Metformin Does Not Induce Hyperlactatemia in Patients Admitted to Internal Medicine Ward.

Koren S, Zilberman-Itskovich S, Koren R, Doenyas-Barak K, Golik A.

Isr Med Assoc J. 2017 May;19(5):300-3.

34.

Genomic exploration of individual giant ocean viruses.

Wilson WH, Gilg IC, Moniruzzaman M, Field EK, Koren S, LeCleir GR, Martínez Martínez J, Poulton NJ, Swan BK, Stepanauskas R, Wilhelm SW.

ISME J. 2017 Aug;11(8):1736-1745. doi: 10.1038/ismej.2017.61. Epub 2017 May 12.

35.

Tackling Resistance to PI3K Inhibition by Targeting the Epigenome.

Koren S, Bentires-Alj M.

Cancer Cell. 2017 May 8;31(5):616-618. doi: 10.1016/j.ccell.2017.04.010.

36.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM.

Genome Res. 2017 May;27(5):849-864. doi: 10.1101/gr.213611.116. Epub 2017 Apr 10.

37.

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM.

Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15.

38.

The role of direct single monetary grants in residents' choice of field of residency.

Wasserstrum Y, Magnezi R, Tamir O, Koren S, Lotan D, Afek A.

Med Teach. 2017 May;39(5):548-554. doi: 10.1080/0142159X.2017.1297891. Epub 2017 Mar 10.

PMID:
28281835
39.

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.

Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, Zhou Y, Sun J, Crisà A, Ponce de León FA, Schwartz JC, Hammond JA, Waldbieser GC, Schroeder SG, Liu GE, Dunham MJ, Shendure J, Sonstegard TS, Phillippy AM, Van Tassell CP, Smith TP.

Nat Genet. 2017 Apr;49(4):643-650. doi: 10.1038/ng.3802. Epub 2017 Mar 6.

40.

The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation.

Schwartz JC, Gibson MS, Heimeier D, Koren S, Phillippy AM, Bickhart DM, Smith TP, Medrano JF, Hammond JA.

Immunogenetics. 2017 Apr;69(4):255-269. doi: 10.1007/s00251-017-0973-y. Epub 2017 Feb 9.

41.

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.

Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL.

Genome Res. 2017 May;27(5):787-792. doi: 10.1101/gr.213405.116. Epub 2017 Jan 27.

42.

The Hippo kinases LATS1 and 2 control human breast cell fate via crosstalk with ERα.

Britschgi A, Duss S, Kim S, Couto JP, Brinkhaus H, Koren S, De Silva D, Mertz KD, Kaup D, Varga Z, Voshol H, Vissieres A, Leroy C, Roloff T, Stadler MB, Scheel CH, Miraglia LJ, Orth AP, Bonamy GM, Reddy VA, Bentires-Alj M.

Nature. 2017 Jan 26;541(7638):541-545. doi: 10.1038/nature20829. Epub 2017 Jan 9.

PMID:
28068668
43.

Protocol for Microplastics Sampling on the Sea Surface and Sample Analysis.

Kovač Viršek M, Palatinus A, Koren Š, Peterlin M, Horvat P, Kržan A.

J Vis Exp. 2016 Dec 16;(118). doi: 10.3791/55161.

44.

GLIOMA CELL PROLIFERATION MEDIATED BY COENZYME Q10 AT SERUM DEPRIVATION IN VITRO.

Krylova NG, Kulahova TA, Koren SV, Semenkova GN.

Tsitologiia. 2017;59(2):109-16. English, Russian.

PMID:
30199158
45.

The effects of electromagnetic fields on B16-BL6 cells are dependent on their spatial and temporal character.

Buckner CA, Buckner AL, Koren SA, Persinger MA, Lafrenie RM.

Bioelectromagnetics. 2017 Apr;38(3):165-174. doi: 10.1002/bem.22031. Epub 2016 Dec 27.

PMID:
28026051
46.

Complete Genome Sequence of a Bovine Viral Diarrhea Virus Subgenotype 1e Strain, SLO/2407/2006, Isolated in Slovenia.

Toplak I, Kuhar U, Kušar D, Papić B, Koren S, Toplak N.

Genome Announc. 2016 Nov 17;4(6). pii: e01310-16. doi: 10.1128/genomeA.01310-16.

47.

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.

Davison M, Treangen TJ, Koren S, Pop M, Bhaya D.

PLoS One. 2016 Sep 9;11(9):e0160574. doi: 10.1371/journal.pone.0160574. eCollection 2016.

48.

Mash: fast genome and metagenome distance estimation using MinHash.

Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM.

Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x.

49.

The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.

Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, Koren S, Jiang Y, Zimin A, Xu P, Phillippy AM, Geng X, Song L, Sun F, Li C, Wang X, Chen A, Jin Y, Yuan Z, Yang Y, Tan S, Peatman E, Lu J, Qin Z, Dunham R, Li Z, Sonstegard T, Feng J, Danzmann RG, Schroeder S, Scheffler B, Duke MV, Ballard L, Kucuktas H, Kaltenboeck L, Liu H, Armbruster J, Xie Y, Kirby ML, Tian Y, Flanagan ME, Mu W, Waldbieser GC.

Nat Commun. 2016 Jun 2;7:11757. doi: 10.1038/ncomms11757.

50.

Complete Genome Sequence of the Porcine Epidemic Diarrhea Virus Strain SLO/JH-11/2015.

Toplak I, Ipavec M, Kuhar U, Kušar D, Papić B, Koren S, Toplak N.

Genome Announc. 2016 Apr 7;4(2). pii: e01725-15. doi: 10.1128/genomeA.01725-15.

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