Carl Kingsford

Latest

• DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes
• Constructing small genome graphs via string compression
• Practical selection of representative sets of RNA-seq samples using a hierarchical approach
• Sequence-specific minimizers via polar sets
• Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism
• Capturing the complexity of topologically associating domains through multi-feature optimization
• Probabilistic method corrects previously uncharacterized Hi-C artifact
• Cong Ma Completes Her Ph.D.
• Natalie Sauerwald Successfully Defends Her Ph.D.
• Exact Transcript Quantification Over Splice Graphs
• Optimizing Dynamic Structures with Bayesian Generative Search
• Harvestman: A framework for hierarchical feature learning and selection from whole genome sequencing data.
• Improved design and analysis of practical minimizers
• Lower density selection schemes via small universal hitting sets with short remaining path length
• VariantStore: A Large-Scale Genomic Variant Search Index
• Finding ranges of optimal transcript expression quantification in cases of non-identifiability
• Estimating mutual information under measurement error
• A statistical method for identifying consistently important features across samples
• Detecting, categorizing, and correcting coverage anomalies of RNA-seq quantification
• How much data is sufficient to learn high-performing algorithms?
• Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem
• Alignment and mapping methodology influence transcript abundance estimation
• Practical universal k-mer sets for minimizer schemes
• Context-Aware Seeds for Read Mapping
• Quantifying the Benefit Offered by Transcript Assembly on Single-Molecule Long Reads
• Collective Model Fusion for Multiple Black-Box Experts
• Sketching and Sublinear Data Structures in Genomics
• Maximum Likelihood Reconstruction of Ancestral Networks by Integer Linear Programming
• Analysis of the structural variability of topologically associated domains as revealed by Hi-C
• Identification of Microbiota-Induced Gene Expression Changes in the Drosophila melanogaster Head
• Locality sensitive hashing for the edit distance
• More accurate transcript assembly via parameter advising
• Topological data analysis reveals principles of chromosome structure throughout cellular differentiation
• Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami
• Asymptotically optimal minimizers schemes
• Improved search of large transcriptomic sequencing databases using split sequence bloom trees
• Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery
• Quantifying the similarity of topological domains across normal and cancer human cell types
• SQUID: transcriptomic structural variation detection from RNA-seq
• Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data
• Accurate assembly of transcripts through phase-preserving graph decomposition
• Accurate recovery of ribosome positions reveals slow translation of wobble-pairing codons in yeast
• Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings
• Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing
• Improved search of large transcriptomic sequencing databases using split sequence bloom trees
• Improving Bloom filter performance on sequence data using k-mer Bloom filters
• Improving the performance of minimizers and winnowing schemes
• Salmon provides fast and bias-aware quantification of transcript expression
• Theory and A Heuristic for the Minimum Path Flow Decomposition Problem
• A pathway-centric view of spatial proximity in the 3D nucleome across cell lines
• Compact universal k-mer hitting sets
• Deconvolution of ensemble chromatin interaction data reveals the latent mixing structures in cell subpopulations
• Diffusion archeology for diffusion progression history reconstruction
• Efficient index maintenance under dynamic genome modification
• Exploring ribosome positioning on translating transcripts with ribosome profiling
• Fast search of thousands of short-read sequencing experiments
• Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap
• Teaching Computation to Biologists (book review)
• The second decade of the international conference on research in computational molecular biology (RECOMB)
• Convex risk minimization to infer networks from probabilistic diffusion data at multiple scales
• Data-dependent bucketing improves reference-free compression of sequencing reads
• Optimal seed solver: optimizing seed selection in read mapping
• Rapid, separable compression enables fast analyses of sequence alignments
• Reference-based compression of short-read sequences using path encoding
• Semi-nonparametric modeling of topological domain formation from epigenetic data
• Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping
• Identification of alternative topological domains in chromatin
• Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
• Higher-order chromatin domains link eQTLs with the expression of far-away genes
• Multiscale identification of topological domains in chromatin
• Predicting protein interactions via parsimonious network history inference
• Resolving spatial inconsistencies in chromosome conformation measurements
• Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin
• Coral: an integrated suite of visualizations for comparing clusterings
• Dynamic exploration of recording sessions between jazz musicians over time
• Global network alignment using multiscale spectral signatures
• Graph rigidity reveals well-constrained regions of chromosome conformation embeddings
• Parsimonious reconstruction of network evolution
• Resolving spatial inconsistencies in chromosome conformation data
• The missing models: A data-driven approach for learning how networks grow
• A cost-aggregating integer linear program for motif finding
• A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
• Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
• Extracting between-pathway models from E-MAP interactions using expected graph compression
• Metric labeling and semi-metric embedding for protein annotation prediction
• Network archaeology: uncovering ancient networks from present-day interactions
• Alignment and clustering of phylogenetic markers-implications for microbial diversity studies
• Assembly complexity of prokaryotic genomes using short reads
• Exploring biological network dynamics with ensembles of graph partitions
• Extracting between-pathway models from E-MAP interactions using expected graph compression
• Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information
• GiRaF: robust, computational identification of influenza reassortments via graph mining
• Particle swarm optimization for multimodal combinatorial problems and its application to protein design
• The power of protein interaction networks for associating genes with diseases
• Uncovering many views of biological networks using ensembles of near-optimal partitions
• 2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates
• A cooperative combinatorial particle swarm optimization algorithm for side-chain packing
• A synthesis for exactly 3-edge-connected graphs
• Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information
• Revealing biological modules via graph summarization
• Vertices of degree k in edge-minimal, k-edge-connected graphs
• Uncovering genomic reassortments among influenza strains by enumerating maximal bicliques
• What are decision trees?
• A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes
• Genome analysis linking recent European and African influenza (H5N1) viruses
• A compact mathematical programming formulation for DNA motif finding
• A semidefinite programming approach to side chain positioning with new rounding strategies
• The inapproximability of side-chain positioning
• The side-chain positioning problem: a semidefinite programming formulation with new rounding schemes
• Experimental construction of very large scale DNA databases with associative search capability