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Bioinformatics (Oxford, England)|November 2, 2020
Maximum likelihood reconstruction of ancestral networks by integer linear programmingVaibhav Rajan, Ziqi Zhang, Carl Kingsford, et al.
Molecular Biology and Evolution|July 24, 2007
A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genesCarl Kingsford, Arthur L Delcher, Steven L Salzberg
Bioinformatics (Oxford, England)|May 11, 2026
CodonMoE: DNA Language Models for Codon-Dependent mRNA PredictionShiyi Du, Litian Liang, Jiayi Li, et al.
Scientific Reports|December 16, 2016
A pathway-centric view of spatial proximity in the 3D nucleome across cell linesHiren Karathia, Carl Kingsford, Michelle Girvan, et al.
Nucleic Acids Research|March 24, 2017
Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplingsNatalie Sauerwald, She Zhang, Carl Kingsford, et al.
Algorithms for Molecular Biology : AMB|May 29, 2014
Identification of alternative topological domains in chromatinDarya Filippova, Rob Patro, Geet Duggal, et al.
Bioinformatics (Oxford, England)|September 13, 2019
Locality-sensitive hashing for the edit distanceGuillaume Marçais, Dan DeBlasio, Prashant Pandey, et al.
Algorithms for Molecular Biology : AMB|May 30, 2020
Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements ProblemYutong Qiu, Cong Ma, Han Xie, et al.
Biorxiv : the Preprint Server for Biology|January 23, 2024
Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning frameworkHaotian Teng, Marcus Stoiber, Ziv Bar-Joseph, et al.
Genome Research|October 15, 2024
Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning frameworkHaotian Teng, Marcus Stoiber, Ziv Bar-Joseph, et al.
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