yusuke1997/dblp-id-title huggingface dataset:
Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape
Finding Maximum Likelihood Indel Scenarios
Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression
Rearrangements in Genomes with Centromeres Part I: Translocations
Faster genome annotation of non-coding RNA families without loss of accuracy
Speciation and Rate Variation in a Birth-and-Death Account of WGD and Fractionation; the Case of Solanaceae
Monte Carlo sequence alignment
PaccMann RL : Designing Anticancer Drugs From Transcriptomic Data via Reinforcement Learning
An Interactive Map of Regulatory Networks of Pseudomonas aeruginosa Genome
Comparative analysis of organelle genomes, a biologist's view of computational challenges (abstract only)
Nonparametric Combinatorial Sequence Models
Probability models for genome rearrangement and linear invariants for phylogenetic inference
An Adaptive and Memory Efficient Algorithm for Genotype Imputation
Approximation of protein structure for fast similarity measures
A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme
Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps
Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets
Motif Discovery Through Predictive Modeling of Gene Regulation
A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast
MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows
Biological and computational annotation of the Drosophila Genome Sequence
Framework for Identifying Common Aberrations in DNA Copy Number Data
ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation
A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract)
Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments
Algorithms for computing and integrating physical maps using unique probes
GRep: Gene Set Representation via Gaussian Embedding
Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs
Variations on a theme of Lander and Waterman (abstract)
Research in Computational Molecular Biology - 23rd Annual International Conference, RECOMB 2019, Washington, DC, USA, May 5-8, 2019, Proceedings
A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes
Subnetwork State Functions Define Dysregulated Subnetworks in Cancer
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast
Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings
Alignments without low-scoring regions
Domain Architecture in Homolog Identification
An Integrative Network Approach to Map the Transcriptome to the Phenome
MethCP: Differentially Methylated Region Detection with Change Point Models
Detecting Highways of Horizontal Gene Transfer
Finding motifs for insufficient number of sequences with strong binding to transcription facto
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets
Algorithmic determination of core positions in the V L and V H domains of immunoglobulin molecules
The application of Markov chain Monte Carlo methods to radiation hybrid mapping
Finding recurrent sources in sequences
Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils
A more efficient approximation scheme for tree alignment
RNA biology and the genome (abstract only)
NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks
Unified Integration of Spatial Transcriptomics Across Platforms
Protein structure prediction and potential energy landscape analysis using continuous global minimization
Estimators of Translocations and Inversions in Comparative Maps
Gap Filling as Exact Path Length Problem
Identifying Causal Variants by Fine Mapping Across Multiple Studies
Family-based homology detection via pairwise sequence comparison
Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions
Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition
Superbubbles, Ultrabubbles and Cacti
An Exact and Fast SAT Formulation for the DCJ Distance
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation
Evolution of metabolisms: a new method for the comparison of metabolic pathways
DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors
Cactus Graphs for Genome Comparisons
On the Representation of de Bruijn Graphs
Yeast Cells as a Discovery Platform for Neurodegenerative Disease
Recognition of remote protein homologies using three-dimensional information to generate a position specific scoring matrix in the program 3D-PSSM
Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach
An Efficient Nonlinear Regression Approach for Genome-Wide Detection of Marginal and Interacting Genetic Variations
A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data
GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly
metaSPAdes: A New Versatile de novo Metagenomics Assembler
Accurate Sub-population Detection and Mapping Across Single Cell Experiments with PopCorn
Comparison of minisatellites
Research in Computational Molecular Biology, 11th Annual International Conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007, Proceedings
Challenges of biomolecular structure prediction (abstract)
Optimal amnesic probabilistic automata or how to learn and classify proteins in linear time and space
Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks
Proceedings of the Fifth Annual International Conference on Computational Biology, RECOMB 2001, Montréal, Québec, Canada, April 22-25, 2001
New flexible approaches for multiple sequence alignment
Accurate Detection of Tandem Repeats from Error-Prone Sequences with EquiRep
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data
Immunoglobulin Classification Using the Colored Antibody Graph
Improvement of Computing Times in Boolean Networks Using Chi-square Tests
Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele
Limitations of Pseudogenes in Identifying Gene Losses
Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography
Determining the Consistency of Resolved Triplets and Fan Triplets
A General Framework for Genome Rearrangement with Biological Constraints
Compressing Genomic Sequence Fragments Using SlimGene
Enhancements in sequence analysis with DNA arrays (abstract)
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
NetMix2: Unifying Network Propagation and Altered Subnetworks
The theoretical limits of DNA sequence discrimination of polyamides
An Efficient and Accurate Graph-Based Approach to Detect Population Substructure
The Problem of Chromosome Reincorporation in DCJ Sorting and Halving
An Optimization-Based Sampling Scheme for Phylogenetic Trees
The ordinal quartet method
Clustering Short Gene Expression Profiles
Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data
Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations
mcRigor: A Statistical Method to Enhance the Rigor of Metacell Partitioning in Single-Cell RNA-seq and ATAC-seq Data Analysis
Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models
Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs
Winnowing sequences from a database search
An Adversarial Scheme for Integrating Multi-modal Data on Protein Function
Designing RNA Secondary Structures Is Hard
Identification of Deletion Polymorphisms from Haplotypes
Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples
Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data
An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, RECOMB 1998, New York, NY, USA, March 22-25, 1998
Fast Estimation of Genetic Correlation for Biobank-Scale Data
Gene Set Priorization Guided by Regulatory Networks with p-values through Kernel Mixed Model
Hunger for new technologies, metrics, and spatiotemporal models in functional genomic (abstract only)
Algorithms for Computing the Family-Free Genomic Similarity Under DCJ
Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning
Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes Using Pseudo-Boolean Optimization
Translation Rate Prediction and Regulatory Motif Discovery with Multi-task Learning
Efficient Computation of Approximate Gene Clusters Based on Reference Occurrences
Computational identification of evolutionarily conserved exons
On the Relationship between DNA Periodicity and Local Chromatin Structure
A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data
The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems
PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning
Analysis techniques for microarray time-series data
Rapid significance estimation in local sequence alignment with gaps
Fast Flux Module Detection Using Matroid Theory
Towards a Post-clustering Test for Differential Expression
Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments
On Genome Evolution with Accumulated Change and Innovation
The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data
Beyond mutation matrices: physical-chemistry based evolutionary models
Protein structure determination using protein threading and sparse NMR data (extended abstract)
MTGL-ADMET: A Novel Multi-task Graph Learning Framework for ADMET Prediction Enhanced by Status-Theory and Maximum Flow
Network Legos: Building Blocks of Cellular Wiring Diagrams
Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing
Imposing specificity by regulated localization (abstract only)
An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers
AdaFDR: A Fast, Powerful and Covariate-Adaptive Approach to Multiple Hypothesis Testing
The Statistical Power of Phylogenetic Motif Models
Metabolic Network Analysis Demystified
Conservation Patterns in cis -Elements Reveal Compensatory Mutations
Comparative Genomics, RECOMB 2004 International Workshop, RCG 2004, Bertinoro, Italy, October 16-19, 2004, Revised Selected Papers
Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions (Extended Abstract)
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition
Tractable and Expressive Generative Models of Genetic Variation Data
Comprehensive statistical method for protein fold recognition
BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data
Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
Fast detection of common geometric substructure in proteins
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs
Multi-break Rearrangements: From Circular to Linear Genomes
An algorithm for haplotype analysis
TreeShrink: Efficient Detection of Outlier Tree Leaves
Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data
Percolate: An Exponential Family JIVE Model to Design DNA-Based Predictors of Drug Response
A Guided Network Propagation Approach to Identify Disease Genes that Combines Prior and New Information
Optimization of Combinatorial Mutagenesis
Optimally Orienting Physical Networks
Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences
Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes
Toward a proteome atlas for C. Elegans
Low-level analyses of microarray data
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels
Discovering temporal relations in molecular pathways using protein-protein interactions
Reconstructing the Topology of Protein Complexes
A Parsimony Approach to Genome-Wide Ortholog Assignment
Notung: dating gene duplications using gene family trees
Limited Lifespan of Fragile Regions in Mammalian Evolution
Changepoint Analysis for Efficient Variant Calling
Hapsembler: An Assembler for Highly Polymorphic Genomes
Computation of Median Gene Clusters
A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles
AllSome Sequence Bloom Trees
A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery
BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract)
Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA
Gene functional classification from heterogeneous data
Biological Sequence Modeling with Convolutional Kernel Networks
Research in Computational Molecular Biology, 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings
Fast Bayesian Inference of Copy Number Variants Using Hidden Markov Models with Wavelet Compression
ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly
Fast and Optimal Sequence-to-Graph Alignment Guided by Seeds
DNA probe arrays - accessing the genome (abstract)
Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization
Edit distance between two RNA structures
Partitioning K clones: hardness results and practical algorithms for the K-populations problem
Picking alignments from (steiner) trees
Computational structural proteomics and virtual ligand screening
Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning
Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut
Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics
On Sorting by Translocations
ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching
Single-Cell Multi-omic Velocity Infers Dynamic and Decoupled Gene Regulation
Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-Higashi
Locating a Tree in a Reticulation-Visible Network in Cubic Time
EPR-Dictionaries: A Practical and Fast Data Structure for Constant Time Searches in Unidirectional and Bidirectional FM Indices
Building a Pangenome Reference for a Population
Regulatory Genomics, RECOMB 2004 International Workshop, RRG 2004, San Diego, CA, USA, March 26-27, 2004, Revised Selected Papers
Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast
A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters
E Pluribus Unum: United States of Single Cells
SNPing in the human genome
An algorithm to enumerate all sorting reversals
Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors
Variable Selection through Correlation Sifting
An anytime algorithm for gapped block protein threading with pair interactions
The deferred path heuristic for the generalized tree alignment problem
Improved Recombination Lower Bounds for Haplotype Data
Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models
Rapid Protein Side-Chain Packing via Tree Decomposition
Sequencing the human genome
SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation
An iterative method for improved protein structural motif recognition
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data
From promoter sequence to expression: a probabilistic framework
Graph-Based Genome Inference from Hi-C Data
A branch-and-cut algorithm for multiple sequence alignment
WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads
Whole-Genome Analysis of Gene Conversion Events
Mapping Cell Fate Transition in Space and Time
Exact Pattern Matching for RNA Structure Ensembles
BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment
An Interaction-Dependent Model for Transcription Factor Binding
Haplotype Inference and Its Application in Linkage Disequilibrium Mapping
Deciphering Signaling Specificity with Deep Neural Networks
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data
Algorithms for identifying protein cross-links via tandem mass spectrometry
Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction
On approximation algorithms for local multiple alignment
Applications of generalized pair hidden Markov models to alignment and gene finding problems
The past, present and future of protein structure prediction (abstract)
Provably sensitive Indexing strategies for biosequence similarity search
Overcoming Observation Bias for Cancer Progression Modeling
An algorithm for clustering cDNAs for gene expression analysis
Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways
Multiple Genome Alignment by Clustering Pairwise Matches
Significance testing for genomic mismatch scanning
Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions
OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional Disorders
Research in Computational Molecular Biology, 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 2-5, 2006, Proceedings
Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps
A Multi-species Functional Embedding Integrating Sequence and Network Structure
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks
Discovering local structure in gene expression data: the order-preserving submatrix problem
Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics Platforms
QNet: A Tool for Querying Protein Interaction Networks
The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem
DNA segmentation as a model selection process
Gene-Gene Interactions Detection Using a Two-Stage Model
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives
Separtating repeats in DNA sequence assembly
The Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data
A new approach to fragment assembly in DNA sequencing
From four-taxon trees to phylogenies (preliminary report): the case of mammalian evolution
Assessing inhomogeneities in bacterial long genomic sequences
RIBRA-An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem
Chimeric alignment by dynamic programming: algorithm and biological uses
Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast
Assembly of Long Error-Prone Reads Using de Bruijn Graphs
Reconstruction of Gene Regulatory Networks by Integrating Biological Model and a Recommendation System
Poetry and prose of the sequences
Tree Inference for Single-Cell Data
Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics
Algorithms for optical mapping
IPED: Inheritance Path Based Pedigree Reconstruction Algorithm Using Genotype Data
Sorting Signed Permutations by Inversions in O(nlogn) Time
Beyond Galled Trees - Decomposition and Computation of Galled Networks
Research in Computational Molecular Biology, 12th Annual International Conference, RECOMB 2008, Singapore, March 30 - April 2, 2008. Proceedings
Structure-Guided Deimmunization of Therapeutic Proteins
Sequencing by hybridization using direct and reverse cooperating spectra
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-rotamer-like Efficiency
Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function
Algorithms for Detecting Significantly Mutated Pathways in Cancer
Somatic evolution of cancer
Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, RECOMB 1997, Santa Fe, NM, USA, January 20-23, 1997
Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions
Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsimony over Distributions
Combining pairwise sequence similarity and support vector machines for remote protein homology detection
Non-parametric and Semi-parametric Support Estimation Using SEquential RESampling Random Walks on Biomolecular Sequences
Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction
An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test
Longitudinal Genotype-Phenotype Association Study via Temporal Structure Auto-learning Predictive Model
Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport
Microarrays: how many do you need?
The Statistical Significance of Max-Gap Clusters
Discovery and Annotation of Genetic Modules
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
Variational Upper Bounds for Probabilistic Phylogenetic Models
Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data - (Extended Abstract)
QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data
An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments
Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations
T-Cell Receptor Optimization with Reinforcement Learning and Mutation Polices for Precision Immunotherapy
Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution
De Novo Sequencing of Nonribosomal Peptides
Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT)
Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Hong Kong, China, May 3-7, 2017, Proceedings
Orientation-Aware Networks for Protein Structure Representation Learning