Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 148

1.

HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization.

Paulsen J, Sandve GK, Gundersen S, Lien TG, Trengereid K, Hovig E.

Bioinformatics. 2014 Jun 1;30(11):1620-2. doi: 10.1093/bioinformatics/btu082.

2.

Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements.

Paulsen J, Lien TG, Sandve GK, Holden L, Borgan O, Glad IK, Hovig E.

Nucleic Acids Res. 2013 May 1;41(10):5164-74. doi: 10.1093/nar/gkt227.

3.

The 3DGD: a database of genome 3D structure.

Li C, Dong X, Fan H, Wang C, Ding G, Li Y.

Bioinformatics. 2014 Jun 1;30(11):1640-2. doi: 10.1093/bioinformatics/btu081.

PMID:
24526713
4.

The Hitchhiker's guide to Hi-C analysis: practical guidelines.

Lajoie BR, Dekker J, Kaplan N.

Methods. 2015 Jan 15;72:65-75. doi: 10.1016/j.ymeth.2014.10.031.

5.

A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions.

Paulsen J, Rødland EA, Holden L, Holden M, Hovig E.

Nucleic Acids Res. 2014 Oct;42(18):e143. doi: 10.1093/nar/gku738.

6.

The Genomic HyperBrowser: an analysis web server for genome-scale data.

Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W133-41. doi: 10.1093/nar/gkt342.

7.

SynTView - an interactive multi-view genome browser for next-generation comparative microorganism genomics.

Lechat P, Souche E, Moszer I.

BMC Bioinformatics. 2013 Sep 22;14:277. doi: 10.1186/1471-2105-14-277.

8.

NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

Merelli I, Liò P, Milanesi L.

PLoS One. 2013 Sep 19;8(9):e75146. doi: 10.1371/journal.pone.0075146.

9.

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.

Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK.

Genome Biol. 2010;11(2):R22. doi: 10.1186/gb-2010-11-2-r22.

10.

CrossMap: a versatile tool for coordinate conversion between genome assemblies.

Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L.

Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730.

11.

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY.

Bioinformatics. 2015 May 1;31(9):1469-71. doi: 10.1093/bioinformatics/btu828.

12.

iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.

Giurato G, De Filippo MR, Rinaldi A, Hashim A, Nassa G, Ravo M, Rizzo F, Tarallo R, Weisz A.

BMC Bioinformatics. 2013 Dec 13;14:362. doi: 10.1186/1471-2105-14-362.

13.

BigWig and BigBed: enabling browsing of large distributed datasets.

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D.

Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351.

14.

HTSeq--a Python framework to work with high-throughput sequencing data.

Anders S, Pyl PT, Huber W.

Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638.

15.

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions.

Stadhouders R, Kolovos P, Brouwer R, Zuin J, van den Heuvel A, Kockx C, Palstra RJ, Wendt KS, Grosveld F, van Ijcken W, Soler E.

Nat Protoc. 2013 Mar;8(3):509-24. doi: 10.1038/nprot.2013.018.

PMID:
23411633
16.

CanSNPer: a hierarchical genotype classifier of clonal pathogens.

Lärkeryd A, Myrtennäs K, Karlsson E, Dwibedi CK, Forsman M, Larsson P, Johansson A, Sjödin A.

Bioinformatics. 2014 Jun 15;30(12):1762-4. doi: 10.1093/bioinformatics/btu113.

PMID:
24574113
17.

ChIA-PET analysis of transcriptional chromatin interactions.

Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y.

Methods. 2012 Nov;58(3):289-99. doi: 10.1016/j.ymeth.2012.08.009.

PMID:
22926262
18.

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.

Boitard S, Kofler R, Françoise P, Robelin D, Schlötterer C, Futschik A.

Mol Ecol Resour. 2013 Mar;13(2):337-40. doi: 10.1111/1755-0998.12063.

19.

Quantitative analysis of genome-wide chromatin remodeling.

Baek S, Sung MH, Hager GL.

Methods Mol Biol. 2012;833:433-41. doi: 10.1007/978-1-61779-477-3_26.

PMID:
22183609
20.

Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.

Li W, Gong K, Li Q, Alber F, Zhou XJ.

Bioinformatics. 2015 Mar 15;31(6):960-2. doi: 10.1093/bioinformatics/btu747.

Supplemental Content

Support Center