Mohammed El-Kebir

J. Comput. Biol., January, 2024

Enforcing Temporal Consistency in Migration History Inference.

[BibT_eX]

[DOI]

Mrinmoy Saha Roddur

Sagi Snir

J. Comput. Biol., 2024

DERNA Enables Pareto Optimal RNA Design.

[BibT_eX]

[DOI]

Xinyu Gu

J. Comput. Biol., 2024

Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees.

[BibT_eX]

[DOI]

Proceedings of the 24th International Workshop on Algorithms in Bioinformatics, 2024

TRIBAL: Tree Inference of B Cell Clonal Lineages.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.

[BibT_eX]

[DOI]

PLoS Comput. Biol., October, 2023

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.

[BibT_eX]

[DOI]

Svetlana Gelpi-Dominguez

J. Comput. Aided Mol. Des., August, 2023

Inferring Temporally Consistent Migration Histories.

[BibT_eX]

[DOI]

Mrinmoy Saha Roddur

Sagi Snir

Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design.

[BibT_eX]

[DOI]

Xinyu Gu

Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

2022

CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data.

[BibT_eX]

[DOI]

PLoS Comput. Biol., October, 2022

Parsimonious Clone Tree Integration in cancer.

[BibT_eX]

[DOI]

Simone Zaccaria

Algorithms Mol. Biol., 2022

CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses.

[BibT_eX]

[DOI]

Chuanyi Zhang

Proceedings of the Research in Computational Molecular Biology, 2022

2021

doubletD: detecting doublets in single-cell DNA sequencing data.

[BibT_eX]

[DOI]

Leah L. Weber

Bioinform., 2021

Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors.

[BibT_eX]

[DOI]

Leah L. Weber

Algorithms Mol. Biol., 2021

Parsimonious Clone Tree Reconciliation in Cancer.

[BibT_eX]

[DOI]

Simone Zaccaria

Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

2020

PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2020

ClonArch: visualizing the spatial clonal architecture of tumors.

[BibT_eX]

[DOI]

Jiaqi Wu

Bioinform., 2020

Sampling and summarizing transmission trees with multi-strain infections.

[BibT_eX]

[DOI]

Bioinform., 2020

Detecting evolutionary patterns of cancers using consensus trees.

[BibT_eX]

[DOI]

Bioinform., 2020

Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors.

[BibT_eX]

[DOI]

Leah L. Weber

Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

PhySigs: Phylogenetic Inference of Mutational Signature Dynamics.

[BibT_eX]

[DOI]

Sarah A. Christensen

Mark D. M. Leiserson

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

2019

Summarizing the solution space in tumor phylogeny inference by multiple consensus trees.

[BibT_eX]

[DOI]

Nuraini Aguse

Bioinform., 2019

2018

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

[BibT_eX]

[DOI]

J. Comput. Biol., 2018

eXamine: Visualizing annotated networks in Cytoscape.

[BibT_eX]

[DOI]

F1000Research, 2018

SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error.

[BibT_eX]

[DOI]

Bioinform., 2018

Parsimonious Migration History Problem: Complexity and Algorithms.

[BibT_eX]

[DOI]

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem.

[BibT_eX]

[DOI]

Dikshant Pradhan

Proceedings of the Comparative Genomics - 16th International Conference, 2018

2017

Complexity and algorithms for copy-number evolution problems.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2017

The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2017

2016

metaModules identifies key functional subnetworks in microbiome-related disease.

[BibT_eX]

[DOI]

Bioinform., 2016

Copy-Number Evolution Problems: Complexity and Algorithms.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

[BibT_eX]

[DOI]

Lodewyk F. A. Wessels

Bioinform., 2015

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data.

[BibT_eX]

[DOI]

Bioinform., 2015

Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment.

[BibT_eX]

[DOI]

Jaap Heringa

Algorithms, 2015

2014

Solving the Maximum-Weight Connected Subgraph Problem to Optimality.

[BibT_eX]

[DOI]

CoRR, 2014

A web server for protein-protein interaction network querying.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2014

eXamine: Exploring annotated modules in networks.

[BibT_eX]

[DOI]

BMC Bioinform., 2014

2013

Charge Group Partitioning in Biomolecular Simulation.

[BibT_eX]

[DOI]

J. Comput. Biol., 2013

eXamine: a Cytoscape app for exploring annotated modules in networks.

[BibT_eX]

[DOI]

CoRR, 2013

Mapping proteins in the presence of paralogs using units of coevolution.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

2012

Charge Group Partitioning in Biomolecular Simulation.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2012

2011

A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding.

[BibT_eX]

[DOI]

Stefan Canzar

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Lagrangian Relaxation Applied to Sparse Global Network Alignment.

[BibT_eX]

[DOI]

Jaap Heringa