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Items: 1 to 20 of 49


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.


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

Solomon B, Kingsford C.

J Comput Biol. 2018 Mar 12. doi: 10.1089/cmb.2017.0265. [Epub ahead of print]


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.


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.


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.


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.


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.


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.


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.


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.


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.


Diffusion archeology for diffusion progression history reconstruction.

Sefer E, Kingsford C.

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


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.


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.


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.


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.


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.


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.


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.


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.

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