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Items: 1 to 50 of 54

1.

Semi-nonparametric modeling of topological domain formation from epigenetic data.

Sefer E, Kingsford C.

Algorithms Mol Biol. 2019 Mar 5;14:4. doi: 10.1186/s13015-019-0142-y. eCollection 2019.

2.

Theory and A Heuristic for the Minimum Path Flow Decomposition Problem.

Shao M, Kingsford C.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Dec 4. doi: 10.1109/TCBB.2017.2779509. [Epub ahead of print]

PMID:
29990201
3.

Asymptotically optimal minimizers schemes.

Marçais G, DeBlasio D, Kingsford C.

Bioinformatics. 2018 Jul 1;34(13):i13-i22. doi: 10.1093/bioinformatics/bty258.

4.

Quantifying the similarity of topological domains across normal and cancer human cell types.

Sauerwald N, Kingsford C.

Bioinformatics. 2018 Jul 1;34(13):i475-i483. doi: 10.1093/bioinformatics/bty265.

5.

Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami.

Lee H, Kingsford C.

Methods Mol Biol. 2018;1802:235-247. doi: 10.1007/978-1-4939-8546-3_17.

PMID:
29858814
6.

SQUID: transcriptomic structural variation detection from RNA-seq.

Ma C, Shao M, Kingsford C.

Genome Biol. 2018 Apr 12;19(1):52. doi: 10.1186/s13059-018-1421-5.

7.

Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.

Solomon B, Kingsford C.

J Comput Biol. 2018 Jul;25(7):755-765. doi: 10.1089/cmb.2017.0265. Epub 2018 Mar 12.

PMID:
29641248
8.

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery.

Lee H, Kingsford C.

Genome Biol. 2018 Feb 7;19(1):16. doi: 10.1186/s13059-018-1388-2.

9.

Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data.

Wang H, Kingsford C, McManus CJ.

Methods. 2018 Mar 15;137:67-70. doi: 10.1016/j.ymeth.2018.01.002. Epub 2018 Jan 9.

10.

Accurate assembly of transcripts through phase-preserving graph decomposition.

Shao M, Kingsford C.

Nat Biotechnol. 2017 Dec;35(12):1167-1169. doi: 10.1038/nbt.4020. Epub 2017 Nov 13.

11.

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.

Orenstein Y, Pellow D, Marçais G, Shamir R, Kingsford C.

PLoS Comput Biol. 2017 Oct 2;13(10):e1005777. doi: 10.1371/journal.pcbi.1005777. eCollection 2017 Oct.

12.

Improving the performance of minimizers and winnowing schemes.

Marçais G, Pellow D, Bork D, Orenstein Y, Shamir R, Kingsford C.

Bioinformatics. 2017 Jul 15;33(14):i110-i117. doi: 10.1093/bioinformatics/btx235.

13.

Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings.

Sauerwald N, Zhang S, Kingsford C, Bahar I.

Nucleic Acids Res. 2017 Apr 20;45(7):3663-3673. doi: 10.1093/nar/gkx172.

14.

Salmon provides fast and bias-aware quantification of transcript expression.

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C.

Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6.

15.

A pathway-centric view of spatial proximity in the 3D nucleome across cell lines.

Karathia H, Kingsford C, Girvan M, Hannenhalli S.

Sci Rep. 2016 Dec 15;6:39279. doi: 10.1038/srep39279.

16.

Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters.

Pellow D, Filippova D, Kingsford C.

J Comput Biol. 2017 Jun;24(6):547-557. doi: 10.1089/cmb.2016.0155. Epub 2016 Nov 9.

17.

Diffusion archeology for diffusion progression history reconstruction.

Sefer E, Kingsford C.

Knowl Inf Syst. 2016 Nov;49(2):403-427. Epub 2015 Dec 11.

18.

Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast.

Wang H, McManus J, Kingsford C.

J Comput Biol. 2017 Jun;24(6):486-500. doi: 10.1089/cmb.2016.0147. Epub 2016 Oct 11.

19.

Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations.

Sefer E, Duggal G, Kingsford C.

J Comput Biol. 2016 Jun;23(6):425-38. doi: 10.1089/cmb.2015.0210.

20.

Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.

Wang H, McManus J, Kingsford C.

Bioinformatics. 2016 Jun 15;32(12):1880-2. doi: 10.1093/bioinformatics/btw085. Epub 2016 Feb 15.

21.

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.

Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C.

BMC Bioinformatics. 2016 Apr 8;17:155. doi: 10.1186/s12859-016-1008-7.

22.

Fast search of thousands of short-read sequencing experiments.

Solomon B, Kingsford C.

Nat Biotechnol. 2016 Mar;34(3):300-2. doi: 10.1038/nbt.3442. Epub 2016 Feb 8.

23.

Optimal seed solver: optimizing seed selection in read mapping.

Xin H, Nahar S, Zhu R, Emmons J, Pekhimenko G, Kingsford C, Alkan C, Mutlu O.

Bioinformatics. 2016 Jun 1;32(11):1632-42. doi: 10.1093/bioinformatics/btv670. Epub 2015 Nov 14.

24.

Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling.

Spealman P, Wang H, May G, Kingsford C, McManus CJ.

Methods Mol Biol. 2016;1358:71-97. doi: 10.1007/978-1-4939-3067-8_5.

PMID:
26463378
25.

Data-dependent bucketing improves reference-free compression of sequencing reads.

Patro R, Kingsford C.

Bioinformatics. 2015 Sep 1;31(17):2770-7. doi: 10.1093/bioinformatics/btv248. Epub 2015 Apr 24.

26.

Reference-based compression of short-read sequences using path encoding.

Kingsford C, Patro R.

Bioinformatics. 2015 Jun 15;31(12):1920-8. doi: 10.1093/bioinformatics/btv071. Epub 2015 Feb 2.

27.

Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.

Xin H, Greth J, Emmons J, Pekhimenko G, Kingsford C, Alkan C, Mutlu O.

Bioinformatics. 2015 May 15;31(10):1553-60. doi: 10.1093/bioinformatics/btu856. Epub 2015 Jan 10.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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
41.

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.

42.

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.

43.

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
44.

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.

45.

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.

46.

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.

47.

Exploring biological network dynamics with ensembles of graph partitions.

Navlakha S, Kingsford C.

Pac Symp Biocomput. 2010:166-77.

48.

2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates.

Kingsford C, Nagarajan N, Salzberg SL.

PLoS One. 2009 Jul 28;4(7):e6402. doi: 10.1371/journal.pone.0006402.

49.

Revealing biological modules via graph summarization.

Navlakha S, Schatz MC, Kingsford C.

J Comput Biol. 2009 Feb;16(2):253-64. doi: 10.1089/cmb.2008.11TT.

PMID:
19183002
50.

What are decision trees?

Kingsford C, Salzberg SL.

Nat Biotechnol. 2008 Sep;26(9):1011-3. doi: 10.1038/nbt0908-1011. Review.

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