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Items: 1 to 50 of 211

1.

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.

Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW.

Nat Biotechnol. 2019 Aug 12. doi: 10.1038/s41587-019-0217-9. [Epub ahead of print]

PMID:
31406327
2.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Myer PR, Ghurye J, Pop M, Weimer PJ, Phillippy AM, Smith TPL.

Genome Biol. 2019 Aug 2;20(1):153. doi: 10.1186/s13059-019-1760-x.

3.

Proteomic Techniques to Examine Neuronal Translational Dynamics.

Koren SA, Gillett DA, D'Alton SV, Hamm MJ, Abisambra JF.

Int J Mol Sci. 2019 Jul 18;20(14). pii: E3524. doi: 10.3390/ijms20143524. Review.

4.

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.

Dilthey AT, Jain C, Koren S, Phillippy AM.

Nat Commun. 2019 Jul 11;10(1):3066. doi: 10.1038/s41467-019-10934-2.

5.

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.

Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM; NISC Comparative Sequencing Program, Mullikin JC, Burgess SM.

Sci Adv. 2019 Jun 26;5(6):eaav0547. doi: 10.1126/sciadv.aav0547. eCollection 2019 Jun.

6.

A chromosome-scale assembly of the major African malaria vector Anopheles funestus.

Ghurye J, Koren S, Small ST, Redmond S, Howell P, Phillippy AM, Besansky NJ.

Gigascience. 2019 Jun 1;8(6). pii: giz063. doi: 10.1093/gigascience/giz063.

7.

HLA*LA - HLA typing from linearly projected graph alignments.

Dilthey AT, Mentzer AJ, Carapito R, Cutland C, Cereb N, Madhi SA, Rhie A, Koren S, Bahram S, McVean G, Phillippy AM.

Bioinformatics. 2019 Apr 3. pii: btz235. doi: 10.1093/bioinformatics/btz235. [Epub ahead of print]

PMID:
30942877
8.

Self-reported influence of monetary grants in the choice of a medical residency in remote or under-served areas.

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

Isr J Health Policy Res. 2019 Feb 15;8(1):1. doi: 10.1186/s13584-018-0272-6.

9.

Tau drives translational selectivity by interacting with ribosomal proteins.

Koren SA, Hamm MJ, Meier SE, Weiss BE, Nation GK, Chishti EA, Arango JP, Chen J, Zhu H, Blalock EM, Abisambra JF.

Acta Neuropathol. 2019 Apr;137(4):571-583. doi: 10.1007/s00401-019-01970-9. Epub 2019 Feb 13.

10.

Quality of life following salvage surgery for squamous cell carcinoma of the anus.

Pedersen TB, Juvik AF, Koren SF, Gocht-Jensen P, Klein MF.

Eur J Surg Oncol. 2019 Jun;45(6):995-998. doi: 10.1016/j.ejso.2019.01.181. Epub 2019 Feb 1.

PMID:
30744945
11.

Reply to 'Errors in long-read assemblies can critically affect protein prediction'.

Koren S, Phillippy AM, Simpson JT, Loman NJ, Loose M.

Nat Biotechnol. 2019 Feb;37(2):127-128. doi: 10.1038/s41587-018-0005-y. No abstract available.

PMID:
30670797
12.

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.

13.

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. 2019 Apr;35(4):328-331. doi: 10.1080/09513590.2018.1525701. Epub 2018 Dec 31.

PMID:
30595073
14.

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.

15.

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.

16.

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.

17.

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.

18.

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. 2019 Jan;25(1):55-61. doi: 10.4158/EP-2018-0386. Epub 2018 Nov 1.

PMID:
30383500
19.

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.

20.

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]

21.

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
22.

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.

23.

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.

24.

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
25.

[NEW TREATMENTS IN DIABETES MELLITUS - AN UPDATE].

Koren S, Rapoport MJ.

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

PMID:
29804338
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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
32.

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.

33.

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.

34.

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.

35.

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
36.

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
37.

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.

38.

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.

39.

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
40.

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
41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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
50.

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.

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