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Carl Kingsford
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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
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