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Items: 1 to 50 of 68

1.

Anxiety and Depression among Pregnant Women and Mothers of Children Under one Year in Sindupalchowk District.

Aryal KK, Alvik A, Thapa N, Mehata S, Roka T, Thapa P, Pandey P, Pedersen BS.

J Nepal Health Res Counc. 2018 Jul 3;16(2):195-204.

PMID:
29983437
2.

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.

Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, Layer RM.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy064.

3.

hts-nim: scripting high-performance genomic analyses.

Pedersen BS, Quinlan AR.

Bioinformatics. 2018 Apr 30. doi: 10.1093/bioinformatics/bty358. [Epub ahead of print]

PMID:
29718142
4.

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.

5.

Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2018 Feb 5;9(1):572. doi: 10.1038/s41467-017-02383-6.

6.

Methylene-tetrahydrofolate reductase contributes to allergic airway disease.

Eyring KR, Pedersen BS, Maclean KN, Stabler SP, Yang IV, Schwartz DA.

PLoS One. 2018 Jan 12;13(1):e0190916. doi: 10.1371/journal.pone.0190916. eCollection 2018.

7.

GIGGLE: a search engine for large-scale integrated genome analysis.

Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR.

Nat Methods. 2018 Feb;15(2):123-126. doi: 10.1038/nmeth.4556. Epub 2018 Jan 8.

8.

Mosdepth: quick coverage calculation for genomes and exomes.

Pedersen BS, Quinlan AR.

Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699.

9.

Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3. Erratum in: Nat Commun. 2018 Feb 5;9(1):572.

10.

Indexcov: fast coverage quality control for whole-genome sequencing.

Pedersen BS, Collins RL, Talkowski ME, Quinlan AR.

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix090.

11.

Regulation of MUC5B Expression in Idiopathic Pulmonary Fibrosis.

Helling BA, Gerber AN, Kadiyala V, Sasse SK, Pedersen BS, Sparks L, Nakano Y, Okamoto T, Evans CM, Yang IV, Schwartz DA.

Am J Respir Cell Mol Biol. 2017 Jul;57(1):91-99. doi: 10.1165/rcmb.2017-0046OC.

12.

Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.

Pedersen BS, Quinlan AR.

Am J Hum Genet. 2017 Mar 2;100(3):406-413. doi: 10.1016/j.ajhg.2017.01.017. Epub 2017 Feb 9.

13.

cyvcf2: fast, flexible variant analysis with Python.

Pedersen BS, Quinlan AR.

Bioinformatics. 2017 Jun 15;33(12):1867-1869. doi: 10.1093/bioinformatics/btx057.

14.

The nasal methylome and childhood atopic asthma.

Yang IV, Pedersen BS, Liu AH, O'Connor GT, Pillai D, Kattan M, Misiak RT, Gruchalla R, Szefler SJ, Khurana Hershey GK, Kercsmar C, Richards A, Stevens AD, Kolakowski CA, Makhija M, Sorkness CA, Krouse RZ, Visness C, Davidson EJ, Hennessy CE, Martin RJ, Togias A, Busse WW, Schwartz DA.

J Allergy Clin Immunol. 2017 May;139(5):1478-1488. doi: 10.1016/j.jaci.2016.07.036. Epub 2016 Oct 13.

15.

Novel Innate Immune Genes Regulating the Macrophage Response to Gram Positive Bacteria.

Alper S, Warg LA, De Arras L, Flatley BR, Davidson EJ, Adams J, Smith K, Wohlford-Lenane CL, McCray PB Jr, Pedersen BS, Schwartz DA, Yang IV.

Genetics. 2016 Sep;204(1):327-36. doi: 10.1534/genetics.115.185314. Epub 2016 Jun 29.

16.

Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.

Fingerlin TE, Zhang W, Yang IV, Ainsworth HC, Russell PH, Blumhagen RZ, Schwarz MI, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch DA, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Murphy E, Smith K, McKean D, Pedersen BS, Talbert J, Powers J, Markin CR, Beckman KB, Lathrop M, Freed B, Langefeld CD, Schwartz DA.

BMC Genet. 2016 Jun 7;17(1):74. doi: 10.1186/s12863-016-0377-2.

17.

Vcfanno: fast, flexible annotation of genetic variants.

Pedersen BS, Layer RM, Quinlan AR.

Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5.

18.

DNA Methylation Changes in Nasal Epithelia Are Associated with Allergic Asthma in the Inner City.

Yang IV, Pedersen BS, Liu AH, O'Connor GT, Teach SJ, Kattan M, Misiak RT, Gruchalla R, Steinbach SF, Szefler SJ, Gill MA, Calatroni A, David G, Hennessy CE, Davidson EJ, Gergen P, Togias A, Busse WW, Schwartz DA.

Ann Am Thorac Soc. 2016 Mar;13 Suppl 1:S99-S100. doi: 10.1513/AnnalsATS.201510-657MG. No abstract available.

19.

Gestational Diabetes Mellitus - A Public Health Concern in Rural Communities of Nepal.

Thapa P, Shrestha S, Flora MS, Bhattarai MD, Thapa N, Mahat B, Pedersen BS.

J Nepal Health Res Counc. 2015 Sep-Dec;13(31):175-81.

PMID:
27005708
20.

Desmoplakin Variants Are Associated with Idiopathic Pulmonary Fibrosis.

Mathai SK, Pedersen BS, Smith K, Russell P, Schwarz MI, Brown KK, Steele MP, Loyd JE, Crapo JD, Silverman EK, Nickerson D, Fingerlin TE, Yang IV, Schwartz DA.

Am J Respir Crit Care Med. 2016 May 15;193(10):1151-60. doi: 10.1164/rccm.201509-1863OC.

21.

In Utero Cigarette Smoke Affects Allergic Airway Disease But Does Not Alter the Lung Methylome.

Eyring KR, Pedersen BS, Yang IV, Schwartz DA.

PLoS One. 2015 Dec 7;10(12):e0144087. doi: 10.1371/journal.pone.0144087. eCollection 2015.

22.

Unique DNA Methylation Patterns in Offspring of Hypertensive Pregnancy.

Julian CG, Pedersen BS, Salmon CS, Yang IV, Gonzales M, Vargas E, Moore LG, Schwartz DA.

Clin Transl Sci. 2015 Dec;8(6):740-5. doi: 10.1111/cts.12346. Epub 2015 Nov 6.

23.

Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.

Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S.

Nucleic Acids Res. 2015 Jun 23;43(11):5307-17. doi: 10.1093/nar/gkv419. Epub 2015 May 1.

24.

DNA methylation and childhood asthma in the inner city.

Yang IV, Pedersen BS, Liu A, O'Connor GT, Teach SJ, Kattan M, Misiak RT, Gruchalla R, Steinbach SF, Szefler SJ, Gill MA, Calatroni A, David G, Hennessy CE, Davidson EJ, Zhang W, Gergen P, Togias A, Busse WW, Schwartz DA.

J Allergy Clin Immunol. 2015 Jul;136(1):69-80. doi: 10.1016/j.jaci.2015.01.025. Epub 2015 Mar 11.

25.

Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis.

Yang IV, Pedersen BS, Rabinovich E, Hennessy CE, Davidson EJ, Murphy E, Guardela BJ, Tedrow JR, Zhang Y, Singh MK, Correll M, Schwarz MI, Geraci M, Sciurba FC, Quackenbush J, Spira A, Kaminski N, Schwartz DA.

Am J Respir Crit Care Med. 2014 Dec 1;190(11):1263-72. doi: 10.1164/rccm.201408-1452OC.

26.

Inhibition of peroxisome proliferator-activated receptor γ: a potential link between chronic maternal hypoxia and impaired fetal growth.

Julian CG, Yang IV, Browne VA, Vargas E, Rodriguez C, Pedersen BS, Moore LG, Schwartz DA.

FASEB J. 2014 Mar;28(3):1268-79. doi: 10.1096/fj.13-239749. Epub 2013 Dec 4.

27.

CruzDB: software for annotation of genomic intervals with UCSC genome-browser database.

Pedersen BS, Yang IV, De S.

Bioinformatics. 2013 Dec 1;29(23):3003-6. doi: 10.1093/bioinformatics/btt534. Epub 2013 Sep 12.

28.

The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.

De S, Pedersen BS, Kechris K.

Brief Bioinform. 2014 Nov;15(6):919-28. doi: 10.1093/bib/bbt053. Epub 2013 Aug 16.

29.

Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes.

Pedersen BS, De S.

Nucleic Acids Res. 2013 Sep;41(16):7615-24. doi: 10.1093/nar/gkt552. Epub 2013 Jun 22.

30.

Copy neutral loss of heterozygosity is more frequent in older ovarian cancer patients.

Pedersen BS, Konstantinopoulos PA, Spillman MA, De S.

Genes Chromosomes Cancer. 2013 Sep;52(9):794-801. doi: 10.1002/gcc.22075. Epub 2013 May 28.

31.

Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.

Fingerlin TE, Murphy E, Zhang W, Peljto AL, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch D, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Cogan JD, Mason WR, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Smith K, McKean D, Pedersen BS, Talbert J, Kidd RN, Markin CR, Beckman KB, Lathrop M, Schwarz MI, Schwartz DA.

Nat Genet. 2013 Jun;45(6):613-20. doi: 10.1038/ng.2609. Epub 2013 Apr 14. Erratum in: Nat Genet. 2013 Nov;45(11):1409.

32.

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.

Pedersen BS, Schwartz DA, Yang IV, Kechris KJ.

Bioinformatics. 2012 Nov 15;28(22):2986-8. doi: 10.1093/bioinformatics/bts545. Epub 2012 Sep 5.

33.

Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy.

Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC.

Genetics. 2012 Apr;190(4):1563-74. doi: 10.1534/genetics.111.137349. Epub 2012 Feb 2.

34.

BioStar: an online question & answer resource for the bioinformatics community.

Parnell LD, Lindenbaum P, Shameer K, Dall'Olio GM, Swan DC, Jensen LJ, Cockell SJ, Pedersen BS, Mangan ME, Miller CA, Albert I.

PLoS Comput Biol. 2011 Oct;7(10):e1002216. doi: 10.1371/journal.pcbi.1002216. Epub 2011 Oct 27. No abstract available.

35.

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.

Dale RK, Pedersen BS, Quinlan AR.

Bioinformatics. 2011 Dec 15;27(24):3423-4. doi: 10.1093/bioinformatics/btr539. Epub 2011 Sep 23.

36.

Fatal Pneumocystis jirovecii pneumonia following immunosuppressive therapy with rituximab and prednisolone for posterior scleritis.

Stilling-Vinther MK, Pedersen BS.

Acta Ophthalmol. 2012 Mar;90(2):e154-5. doi: 10.1111/j.1755-3768.2011.02127.x. Epub 2011 Jun 8. No abstract available.

37.

Participatory design for computerization of clinical practice guidelines.

Lyng KM, Pedersen BS.

J Biomed Inform. 2011 Oct;44(5):909-18. doi: 10.1016/j.jbi.2011.05.005. Epub 2011 May 27.

38.

Gobe: an interactive, web-based tool for comparative genomic visualization.

Pedersen BS, Tang H, Freeling M.

Bioinformatics. 2011 Apr 1;27(7):1015-6. doi: 10.1093/bioinformatics/btr056. Epub 2011 Feb 3.

PMID:
21296748
39.

Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses.

Schnable JC, Pedersen BS, Subramaniam S, Freeling M.

Front Plant Sci. 2011 Mar 10;2:2. doi: 10.3389/fpls.2011.00002. eCollection 2011.

40.

Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.

Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M.

PLoS Biol. 2010 Jun 29;8(6):e1000409. doi: 10.1371/journal.pbio.1000409.

41.

IT for advanced life support in hospitals.

Pedersen BS, Jeberg KA, Koerner C, Balslev C, Andersen PO, Jensen MK, Lyng KM.

Stud Health Technol Inform. 2009;143:429-34.

PMID:
19380972
42.

DNA extraction and PCR assays for detection of Toxoplasma gondii.

Edvinsson B, Jalal S, Nord CE, Pedersen BS, Evengård B; ECSMID Study Group on Toxoplasmosis.

APMIS. 2004 Jun;112(6):342-8.

PMID:
15511271
43.

[Treatment of irritable colon with the food additive Appital].

Pedersen BS, Helø OH, Jørgensen FB, Kromann-Andersen H.

Ugeskr Laeger. 1998 Dec 7;160(50):7259-62. Danish.

PMID:
9859725
44.

Weight gain during the first year of life in relation to maternal smoking and breast feeding in Norway.

Nafstad P, Jaakkola JJ, Hagen JA, Pedersen BS, Qvigstad E, Botten G, Kongerud J.

J Epidemiol Community Health. 1997 Jun;51(3):261-5.

45.

Fetal exposure to tobacco smoke products: a comparison between self-reported maternal smoking and concentrations of cotinine and thiocyanate in cord serum.

Nafstad P, Kongerud J, Botten G, Urdal P, Silsand T, Pedersen BS, Jaakkola JJ.

Acta Obstet Gynecol Scand. 1996 Nov;75(10):902-7.

PMID:
9003090
46.

[Surgical treatment of "mushroom poisoning"].

Christensen JK, Møller HP, Pedersen BS.

Ugeskr Laeger. 1995 Aug 7;157(32):4466. Danish. No abstract available.

PMID:
7483028
47.

Papillomavirus infection among abortion applicants and patients at a sexually transmitted disease clinic.

Csángó PA, Skuland J, Nilsen A, Pedersen BS, Jagars G.

Sex Transm Dis. 1992 May-Jun;19(3):149-53.

PMID:
1326130
48.

Creatine kinase isoenzymes in serum from children--especially focusing on CK-BB.

Jørgensen FB, Badskjaer J, Pedersen BS, Boysen K.

Scand J Clin Lab Invest. 1984 Sep;44(5):429-32.

PMID:
6484482
49.

[Letter: Danish Hospital Institute].

Pedersen BS.

Ugeskr Laeger. 1976 Jan 26;138(5):285-7. Danish. No abstract available.

PMID:
1251493
50.

[Shall patients only survive?].

Pedersen BS.

Ugeskr Laeger. 1974;10:631-3. Danish. No abstract available.

PMID:
4822016

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