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Items: 1 to 50 of 422

1.

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification.

Breitwieser FP, Salzberg SL.

Bioinformatics. 2019 Sep 25. pii: btz715. doi: 10.1093/bioinformatics/btz715. [Epub ahead of print]

PMID:
31553437
2.

Corrigendum to "Loving-kindness meditation slows biological aging in novices: Evidence from a 12-week randomized controlled trial" [Psychoneuroendocrinology 108 (2019) (October) 20-27].

Le Nguyen KD, Lin J, Algoe SB, Brantley MM, Kim SL, Brantley J, Salzberg S, Fredrickson BL.

Psychoneuroendocrinology. 2019 Sep 13:104440. doi: 10.1016/j.psyneuen.2019.104440. [Epub ahead of print] No abstract available.

PMID:
31526525
3.

Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations.

Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, Acevedo N, Araujo MI, Avila PC, Belbin G, Bleecker E, Bustamante C, Caraballo L, Cruz A, Dunston GM, Eng C, Faruque MU, Ferguson TS, Figueiredo C, Ford JG, Gan W, Gourraud PA, Hansel NN, Hernandez RD, Herrera-Paz EF, Jiménez S, Kenny EE, Knight-Madden J, Kumar R, Lange LA, Lange EM, Lizee A, Maul P, Maul T, Mayorga A, Meyers D, Nicolae DL, O'Connor TD, Oliveira RR, Olopade CO, Olopade O, Qin ZS, Rotimi C, Vince N, Watson H, Wilks RJ, Wilson JG, Salzberg S, Ober C, Burchard EG, Williams LK, Beaty TH, Taub MA, Ruczinski I, Mathias RA, Barnes KC; CAAPA.

Nat Commun. 2019 Sep 4;10(1):4082. doi: 10.1038/s41467-019-12158-w.

4.

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL.

Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2.

PMID:
31375807
5.

Cross-cultural adaptation and validation of the Argentine "American Shoulder and elbow surgeons, patient self-report section" questionnaire.

Policastro PO, Pierobon A, Pérez J, Novoa GA, Calvo Delfino M, Sajfar ME, Salzberg S, Carmody C, Dorado JH, Raguzzi I, Soliño S, Pérez Calvo EC.

Musculoskelet Sci Pract. 2019 Oct;43:37-44. doi: 10.1016/j.msksp.2019.05.010. Epub 2019 Jun 4.

PMID:
31220777
6.

Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities.

Saitta ET, Liang R, Lau MC, Brown CM, Longrich NR, Kaye TG, Novak BJ, Salzberg SL, Norell MA, Abbott GD, Dickinson MR, Vinther J, Bull ID, Brooker RA, Martin P, Donohoe P, Knowles TD, Penkman KE, Onstott T.

Elife. 2019 Jun 18;8. pii: e46205. doi: 10.7554/eLife.46205.

7.

Loving-kindness meditation slows biological aging in novices: Evidence from a 12-week randomized controlled trial.

Le Nguyen KD, Lin J, Algoe SB, Brantley MM, Kim SL, Brantley J, Salzberg S, Fredrickson BL.

Psychoneuroendocrinology. 2019 Oct;108:20-27. doi: 10.1016/j.psyneuen.2019.05.020. Epub 2019 May 20. Erratum in: Psychoneuroendocrinology. 2019 Sep 13;:104440.

PMID:
31185369
8.

"AF HeartTeam" Guided Indication for Stand-alone Thoracoscopic Left Atrial Ablation and Left Atrial Appendage Closure.

Salzberg SP, van Boven WJ, Wyss C, Hürlimann D, Reho I, Zerm T, Noll G, Emmert MY, Corti R, Grünenfelder J.

J Atr Fibrillation. 2019 Feb 28;11(5):2039. doi: 10.4022/jafib.2039. eCollection 2019 Feb-Mar.

9.

Next-generation genome annotation: we still struggle to get it right.

Salzberg SL.

Genome Biol. 2019 May 16;20(1):92. doi: 10.1186/s13059-019-1715-2.

10.

Human contamination in bacterial genomes has created thousands of spurious proteins.

Breitwieser FP, Pertea M, Zimin AV, Salzberg SL.

Genome Res. 2019 Jun;29(6):954-960. doi: 10.1101/gr.245373.118. Epub 2019 May 7.

PMID:
31064768
11.

Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations.

Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, Acevedo N, Araujo MI, Avila PC, Belbin G, Bleecker E, Bustamante C, Caraballo L, Cruz A, Dunston GM, Eng C, Faruque MU, Ferguson TS, Figueiredo C, Ford JG, Gan W, Gourraud PA, Hansel NN, Hernandez RD, Herrera-Paz EF, Jiménez S, Kenny EE, Knight-Madden J, Kumar R, Lange LA, Lange EM, Lizee A, Maul P, Maul T, Mayorga A, Meyers D, Nicolae DL, O'Connor TD, Oliveira RR, Olopade CO, Olopade O, Qin ZS, Rotimi C, Vince N, Watson H, Wilks RJ, Wilson JG, Salzberg S, Ober C, Burchard EG, Williams LK, Beaty TH, Taub MA, Ruczinski I, Mathias RA, Barnes KC; CAAPA.

Nat Commun. 2019 Feb 20;10(1):880. doi: 10.1038/s41467-019-08469-7. Erratum in: Nat Commun. 2019 Sep 4;10(1):4082.

12.

Author Correction: Assembly of a pan-genome from deep sequencing of 910 humans of African descent.

Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, Levin AM, Eng C, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Williams LK, Watson H, Ware LB, Olopade CO, Olopade O, Oliveira RR, Ober C, Nicolae DL, Meyers DA, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker ER, Araujo MI, Herrera-Paz EF, Campbell M, Foster C, Taub MA, Beaty TH, Ruczinski I, Mathias RA, Barnes KC, Salzberg SL.

Nat Genet. 2019 Feb;51(2):364. doi: 10.1038/s41588-018-0335-1.

PMID:
30647471
13.

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.

Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL.

Genome Biol. 2018 Nov 28;19(1):208. doi: 10.1186/s13059-018-1590-2.

14.

Assembly of a pan-genome from deep sequencing of 910 humans of African descent.

Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, Levin AM, Eng C, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Williams LK, Watson H, Ware LB, Olopade CO, Olopade O, Oliveira RR, Ober C, Nicolae DL, Meyers DA, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker ER, Araujo MI, Herrera-Paz EF, Campbell M, Foster C, Taub MA, Beaty TH, Ruczinski I, Mathias RA, Barnes KC, Salzberg SL.

Nat Genet. 2019 Jan;51(1):30-35. doi: 10.1038/s41588-018-0273-y. Epub 2018 Nov 19. Erratum in: Nat Genet. 2019 Feb;51(2):364.

15.

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.

Breitwieser FP, Baker DN, Salzberg SL.

Genome Biol. 2018 Nov 16;19(1):198. doi: 10.1186/s13059-018-1568-0.

16.

Genomic architecture of complex traits in loblolly pine.

De La Torre AR, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB.

New Phytol. 2019 Mar;221(4):1789-1801. doi: 10.1111/nph.15535. Epub 2018 Nov 9.

PMID:
30318590
17.

Epicardial Left Atrial Appendage Exclusion Reduces Blood Pressure in Patients With Atrial Fibrillation and Hypertension.

Turagam MK, Vuddanda V, Verberkmoes N, Ohtsuka T, Akca F, Atkins D, Bommana S, Emmert MY, Gopinathannair R, Dunnington G, Rasekh A, Cheng J, Salzberg S, Natale A, Cox J, Lakkireddy DR.

J Am Coll Cardiol. 2018 Sep 18;72(12):1346-1353. doi: 10.1016/j.jacc.2018.06.066.

18.

Open questions: How many genes do we have?

Salzberg SL.

BMC Biol. 2018 Aug 20;16(1):94. doi: 10.1186/s12915-018-0564-x.

19.

Postoperative rehabilitation of simultaneous rupture of anterior cruciate ligament and patellar ligament: A case report.

Pérez J, Novoa GA, Pierobon A, Soliño S, Calvo Delfino M, Sajfar ME, Carmody C, Vuoto T, Dorado JH, Salzberg S.

Physiother Res Int. 2018 Oct;23(4):e1735. doi: 10.1002/pri.1735. Epub 2018 Jul 29.

PMID:
30058203
20.

The Terabase Search Engine: a large-scale relational database of short-read sequences.

Wilton R, Wheelan SJ, Szalay AS, Salzberg SL.

Bioinformatics. 2019 Feb 15;35(4):665-670. doi: 10.1093/bioinformatics/bty657.

PMID:
30052772
21.

Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics.

Simner PJ, Miller HB, Breitwieser FP, Pinilla Monsalve G, Pardo CA, Salzberg SL, Sears CL, Thomas DL, Eberhart CG, Carroll KC.

J Clin Microbiol. 2018 Aug 27;56(9). pii: e00472-18. doi: 10.1128/JCM.00472-18. Print 2018 Sep.

22.

Removing contaminants from databases of draft genomes.

Lu J, Salzberg SL.

PLoS Comput Biol. 2018 Jun 25;14(6):e1006277. doi: 10.1371/journal.pcbi.1006277. eCollection 2018 Jun.

23.

Genomic Variation Among and Within Six Juglans Species.

Stevens KA, Woeste K, Chakraborty S, Crepeau MW, Leslie CA, Martínez-García PJ, Puiu D, Romero-Severson J, Coggeshall M, Dandekar AM, Kluepfel D, Neale DB, Salzberg SL, Langley CH.

G3 (Bethesda). 2018 Jul 2;8(7):2153-2165. doi: 10.1534/g3.118.200030.

24.

Closure of Large Percutaneous Femoral Venous Access Using a Modified "Figure-of-Eight" Suture.

Wyss CA, Anliker O, Gämperli O, Sürder D, Biaggi P, Buhler I, Salzberg SP, Grünenfelder J, Corti R.

Innovations (Phila). 2018 Mar/Apr;13(2):147-151. doi: 10.1097/IMI.0000000000000488.

PMID:
29688942
25.

Surgical epicardial left atrial appendage closure:A true alternative.

Salzberg S, Emmert M.

J Atr Fibrillation. 2017 Dec 31;10(4):1655. doi: 10.4022/jafib.1655. eCollection 2017 Dec.

26.

Surgical device-enabled epicardial LAA closure to achieve safe, complete, and durable LAA occlusion.

Caliskan E, Cox JL, Falk V, Salzberg SP, Emmert MY.

Nat Rev Cardiol. 2018 Feb 13;15(3):191. doi: 10.1038/nrcardio.2018.8. No abstract available.

PMID:
29434359
27.

MUMmer4: A fast and versatile genome alignment system.

Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A.

PLoS Comput Biol. 2018 Jan 26;14(1):e1005944. doi: 10.1371/journal.pcbi.1005944. eCollection 2018 Jan.

28.

Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.

Li Z, Breitwieser FP, Lu J, Jun AS, Asnaghi L, Salzberg SL, Eberhart CG.

Invest Ophthalmol Vis Sci. 2018 Jan 1;59(1):280-288. doi: 10.1167/iovs.17-21617.

29.

Positive Emotion Correlates of Meditation Practice: A Comparison of Mindfulness Meditation and Loving-kindness Meditation.

Fredrickson BL, Boulton AJ, Firestine AM, Van Cappellen P, Algoe SB, Brantley MM, Kim SL, Brantley J, Salzberg S.

Mindfulness (N Y). 2017 Dec;8(6):1623-1633. doi: 10.1007/s12671-017-0735-9. Epub 2017 May 29.

30.

Surgical techniques for left atrial appendage exclusion.

Salzberg SP, Emmert MY, Caliskan E.

Herzschrittmacherther Elektrophysiol. 2017 Dec;28(4):360-365. doi: 10.1007/s00399-017-0532-0. Epub 2017 Nov 17. Review.

PMID:
29150698
31.

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J.

Nature. 2017 Nov 23;551(7681):498-502. doi: 10.1038/nature24486. Epub 2017 Nov 15.

PMID:
29143815
32.

Impact of Left Atrial Appendage Exclusion on Cardiovascular Outcomes in Patients With Atrial Fibrillation Undergoing Coronary Artery Bypass Grafting-The Surgeon's Comment.

Caliskan E, Salzberg SP, Emmert MY.

Am J Cardiol. 2018 Jan 1;121(1):142. doi: 10.1016/j.amjcard.2017.09.017. Epub 2017 Oct 12. No abstract available.

PMID:
29103602
33.

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.

Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL.

Gigascience. 2017 Nov 1;6(11):1-7. doi: 10.1093/gigascience/gix097.

34.

A review of methods and databases for metagenomic classification and assembly.

Breitwieser FP, Lu J, Salzberg SL.

Brief Bioinform. 2019 Jul 19;20(4):1125-1136. doi: 10.1093/bib/bbx120.

PMID:
29028872
35.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Oct 1;6(10):1. doi: 10.1093/gigascience/gix072.

36.

Epicardial left atrial appendage AtriClip occlusion reduces the incidence of stroke in patients with atrial fibrillation undergoing cardiac surgery.

Caliskan E, Sahin A, Yilmaz M, Seifert B, Hinzpeter R, Alkadhi H, Cox JL, Holubec T, Reser D, Falk V, Grünenfelder J, Genoni M, Maisano F, Salzberg SP, Emmert MY.

Europace. 2018 Jul 1;20(7):e105-e114. doi: 10.1093/europace/eux211.

PMID:
29016813
37.

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans).

Luo R, Zimin A, Workman R, Fan Y, Pertea G, Grossman N, Wear MP, Jia B, Miller H, Casadevall A, Timp W, Zhang SX, Salzberg SL.

G3 (Bethesda). 2017 Nov 6;7(11):3831-3836. doi: 10.1534/g3.117.300107.

38.

Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia.

Pallavajjala A, Kim D, Li T, Ghiaur G, Jones RJ, Burns KH, Salzberg SL, Ning Y.

Leuk Lymphoma. 2018 May;59(5):1231-1238. doi: 10.1080/10428194.2017.1372577. Epub 2017 Sep 7.

39.

Interventional and surgical occlusion of the left atrial appendage.

Caliskan E, Cox JL, Holmes DR Jr, Meier B, Lakkireddy DR, Falk V, Salzberg SP, Emmert MY.

Nat Rev Cardiol. 2017 Dec;14(12):727-743. doi: 10.1038/nrcardio.2017.107. Epub 2017 Aug 10. Review.

PMID:
28795688
40.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL.

G3 (Bethesda). 2017 Sep 7;7(9):3157-3167. doi: 10.1534/g3.117.300078.

41.

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model.

Luo R, Schatz MC, Salzberg SL.

Gigascience. 2017 Jul 1;6(7):1-4. doi: 10.1093/gigascience/gix045.

42.

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs.

Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A.

Ann Intern Med. 2017 Jul 4;167(1):1-7. doi: 10.7326/M17-0085. Epub 2017 Jun 6.

43.

Short Read Mapping: An Algorithmic Tour.

Canzar S, Salzberg SL.

Proc IEEE Inst Electr Electron Eng. 2017 Mar;105(3):436-458. doi: 10.1109/JPROC.2015.2455551. Epub 2015 Sep 7.

44.

Horizontal gene transfer is not a hallmark of the human genome.

Salzberg SL.

Genome Biol. 2017 May 8;18(1):85. doi: 10.1186/s13059-017-1214-2.

45.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Jan 1;6(1):1-4. doi: 10.1093/gigascience/giw016. Erratum in: Gigascience. 2017 Oct 1;6(10):1.

46.

Symptomatic, Inspiration-Induced Atrioventricular Block: Treated with Pacemaker Implant.

Hoffmann DA, Atamañuk AN, Ruiz GA, Chirife R, Tentori MC, Salzberg S.

Pacing Clin Electrophysiol. 2017 Jul;40(7):900-903. doi: 10.1111/pace.13035. Epub 2017 Mar 3.

PMID:
28155224
47.

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.

48.

The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus.

Sun Z, Ke X, Salzberg SL, Kim D, Antonescu V, Cheng Y, Huang B, Song JH, Abraham JM, Ibrahim S, Tian H, Meltzer SJ.

Cancer. 2017 May 1;123(9):1507-1515. doi: 10.1002/cncr.30510. Epub 2017 Jan 12.

49.

Effective orifice area and hemodynamic performance of the transcatheter Edwards Sapien 3 prosthesis: short-term and 1-year follow-up.

Külling M, Külling J, Wyss C, Hürlimann D, Reho I, Salzberg S, Bühler I, Noll G, Grünenfelder J, Corti R, Biaggi P.

Eur Heart J Cardiovasc Imaging. 2018 Jan 1;19(1):23-30. doi: 10.1093/ehjci/jew301.

PMID:
28065915
50.

Centrifuge: rapid and sensitive classification of metagenomic sequences.

Kim D, Song L, Breitwieser FP, Salzberg SL.

Genome Res. 2016 Dec;26(12):1721-1729. Epub 2016 Oct 17.

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