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Results: 1 to 20 of 27

1.

Identification of alternative topological domains in chromatin.

Filippova D, Patro R, Duggal G, Kingsford C.

Algorithms Mol Biol. 2014 May 3;9:14. doi: 10.1186/1748-7188-9-14. eCollection 2014.

PMID:
24868242
[PubMed]
Free PMC Article
2.

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.

Patro R, Mount SM, Kingsford C.

Nat Biotechnol. 2014 May;32(5):462-4. doi: 10.1038/nbt.2862. Epub 2014 Apr 20.

PMID:
24752080
[PubMed - in process]
3.

Higher-order chromatin domains link eQTLs with the expression of far-away genes.

Duggal G, Wang H, Kingsford C.

Nucleic Acids Res. 2014 Jan;42(1):87-96. doi: 10.1093/nar/gkt857. Epub 2013 Oct 1.

PMID:
24089144
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Predicting protein interactions via parsimonious network history inference.

Patro R, Kingsford C.

Bioinformatics. 2013 Jul 1;29(13):i237-46. doi: 10.1093/bioinformatics/btt224.

PMID:
23812989
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Resolving spatial inconsistencies in chromosome conformation measurements.

Duggal G, Patro R, Sefer E, Wang H, Filippova D, Khuller S, Kingsford C.

Algorithms Mol Biol. 2013 Mar 9;8(1):8. doi: 10.1186/1748-7188-8-8.

PMID:
23497444
[PubMed]
Free PMC Article
6.

Coral: an integrated suite of visualizations for comparing clusterings.

Filippova D, Gadani A, Kingsford C.

BMC Bioinformatics. 2012 Oct 29;13:276. doi: 10.1186/1471-2105-13-276.

PMID:
23102108
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Global network alignment using multiscale spectral signatures.

Patro R, Kingsford C.

Bioinformatics. 2012 Dec 1;28(23):3105-14. doi: 10.1093/bioinformatics/bts592. Epub 2012 Oct 9.

PMID:
23047556
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Graph rigidity reveals well-constrained regions of chromosome conformation embeddings.

Duggal G, Kingsford C.

BMC Bioinformatics. 2012 Sep 21;13:241. doi: 10.1186/1471-2105-13-241.

PMID:
22998471
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Parsimonious reconstruction of network evolution.

Patro R, Sefer E, Malin J, Marçais G, Navlakha S, Kingsford C.

Algorithms Mol Biol. 2012 Sep 19;7(1):25. doi: 10.1186/1748-7188-7-25.

PMID:
22992218
[PubMed]
Free PMC Article
10.

A cost-aggregating integer linear program for motif finding.

Kingsford C, Zaslavsky E, Singh M.

J Discrete Algorithms (Amst). 2011 Dec 1;9(4):326-334.

PMID:
22081765
[PubMed]
Free PMC Article
11.

Network archaeology: uncovering ancient networks from present-day interactions.

Navlakha S, Kingsford C.

PLoS Comput Biol. 2011 Apr;7(4):e1001119. doi: 10.1371/journal.pcbi.1001119. Epub 2011 Apr 14.

PMID:
21533211
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies.

Wetzel J, Kingsford C, Pop M.

BMC Bioinformatics. 2011 Apr 13;12:95. doi: 10.1186/1471-2105-12-95.

PMID:
21486487
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Extracting between-pathway models from E-MAP interactions using expected graph compression.

Kelley DR, Kingsford C.

J Comput Biol. 2011 Mar;18(3):379-90. doi: 10.1089/cmb.2010.0268.

PMID:
21385041
[PubMed - indexed for MEDLINE]
14.

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.

Marçais G, Kingsford C.

Bioinformatics. 2011 Mar 15;27(6):764-70. doi: 10.1093/bioinformatics/btr011. Epub 2011 Jan 7.

PMID:
21217122
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

GiRaF: robust, computational identification of influenza reassortments via graph mining.

Nagarajan N, Kingsford C.

Nucleic Acids Res. 2011 Mar;39(6):e34. doi: 10.1093/nar/gkq1232. Epub 2010 Dec 21.

PMID:
21177643
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information.

Navlakha S, White J, Nagarajan N, Pop M, Kingsford C.

J Comput Biol. 2010 Mar;17(3):503-16. doi: 10.1089/cmb.2009.0173.

PMID:
20377460
[PubMed - indexed for MEDLINE]
17.

Alignment and clustering of phylogenetic markers--implications for microbial diversity studies.

White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M.

BMC Bioinformatics. 2010 Mar 24;11:152. doi: 10.1186/1471-2105-11-152.

PMID:
20334679
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The power of protein interaction networks for associating genes with diseases.

Navlakha S, Kingsford C.

Bioinformatics. 2010 Apr 15;26(8):1057-63. doi: 10.1093/bioinformatics/btq076. Epub 2010 Feb 24.

PMID:
20185403
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Assembly complexity of prokaryotic genomes using short reads.

Kingsford C, Schatz MC, Pop M.

BMC Bioinformatics. 2010 Jan 12;11:21. doi: 10.1186/1471-2105-11-21.

PMID:
20064276
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Exploring biological network dynamics with ensembles of graph partitions.

Navlakha S, Kingsford C.

Pac Symp Biocomput. 2010:166-77.

PMID:
19908369
[PubMed - indexed for MEDLINE]
Free Article

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