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Author Details

Louxin Zhang
National University of Singapore
1996
61
18
Nathan Sheffield (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37217252A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings.Genome Res2023
34529029How much can deep learning improve prediction of the responses to drugs in cancer cell lines?Brief Bioinform2022
36418585Two results about the Sackin and Colless indices for phylogenetic trees and their shapes.J Math Biol2022
35211690Detecting molecular subtypes from multi-omics datasets using SUMO.Cell Rep Methods2022
31927568A survey and systematic assessment of computational methods for drug response prediction.Brief Bioinform2021
34895112Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics.J Bioinform Comput Biol2021
34112201The Bourque distances for mutation trees of cancers.Algorithms Mol Biol2021
32568070Evidence for transmission of COVID-19 prior to symptom onset.Elife2020
33087126Stage-specific protein-domain mutational profile of invasive ductal breast cancer.BMC Med Genomics2020
30624954Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem.J Comput Biol2019
31842746Generating normal networks via leaf insertion and nearest neighbor interchange.BMC Bioinformatics2019
31888434ZDOG: zooming in on dominating genes with mutations in cancer pathways.BMC Bioinformatics2019
29762653RecPhyloXML: a format for reconciled gene trees.Bioinformatics2018
30423060S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks.Bioinformatics2018
28768489Improved anticancer drug response prediction in cell lines using matrix factorization with similarity regularization.BMC Cancer2017
28361712A program to compute the soft Robinson-Foulds distance between phylogenetic networks.BMC Genomics2017
26791325Predicting chemotherapeutic drug combinations through gene network profiling.Sci Rep2016
27587668A program for verification of phylogenetic network models.Bioinformatics2016
27228397On Tree-Based Phylogenetic Networks.J Comput Biol2016
25669599Fitness profiling links topoisomerase II regulation of centromeric integrity to doxorubicin resistance in fission yeast.Sci Rep2015
24988427Are the duplication cost and Robinson-Foulds distance equivalent?J Comput Biol2014
26356016Effect of Incomplete Lineage Sorting On Tree-Reconciliation-Based Inference of Gene Duplication.IEEE/ACM Trans Comput Biol Bioinform2014
25300490Profiling the transcription factor regulatory networks of human cell types.Nucleic Acids Res2014
23427990Motif discovery with data mining in 3D protein structure databases: discovery, validation and prediction of the U-shape zinc binding ("Huf-Zinc") motif.J Bioinform Comput Biol2013
24407300Maximum likelihood inference of the evolutionary history of a PPI network from the duplication history of its proteins.IEEE/ACM Trans Comput Biol Bioinform2013
23917172Counting motifs in the human interactome.Nat Commun2013
23457601Inverted expression profiles of sex-biased genes in response to toxicant perturbations and diseases.PLoS One2013
22454131Revealing mammalian evolutionary relationships by comparative analysis of gene clusters.Genome Biol Evol2012
23272195Toxicogenomic analysis suggests chemical-induced sexual dimorphism in the expression of metabolic genes in zebrafish liver.PLoS One2012
23282116Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry.BMC Syst Biol2012
21576759From gene trees to species trees II: species tree inference by minimizing deep coalescence events.IEEE/ACM Trans Comput Biol Bioinform2011
22140468Existence of inverted profile in chemically responsive molecular pathways in the zebrafish liver.PLoS One2011
22151151Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree.BMC Bioinformatics2011
21798034Conversion events in gene clusters.BMC Evol Biol2011
20087670Analyzing the fitch method for reconstructing ancestral states on ultrametric phylogenetic trees.Bull Math Biol2010
20874406CAGE: Combinatorial Analysis of Gene-cluster Evolution.J Comput Biol2010
20140213Greedy selection of species for ancestral state reconstruction on phylogenies: elimination is better than insertion.PLoS One2010
19159490Positive correlation between gene coexpression and positional clustering in the zebrafish genome.BMC Genomics2009
18709600More taxa are not necessarily better for the reconstruction of ancestral character states.Syst Biol2008
18774902DUPCAR: reconstructing contiguous ancestral regions with duplications.J Comput Biol2008
18831783A stable iterative method for refining discriminative gene clusters.BMC Genomics2008
19040365Run probabilities of seed-like patterns and identifying good transition seeds.J Comput Biol2008
18549302Spectrum-based de novo repeat detection in genomic sequences.J Comput Biol2008
17666759Reconstructing recombination network from sequence data: the small parsimony problem.IEEE/ACM Trans Comput Biol Bioinform2007
17708627Transcriptome analysis of cold syndrome using microarray.Am J Chin Med2007
17666769Superiority of spaced seeds for homology search.IEEE/ACM Trans Comput Biol Bioinform2007
16983148Reconstructing contiguous regions of an ancestral genome.Genome Res2006
15713729Divide-and-conquer approach for the exemplar breakpoint distance.Bioinformatics2005
16192568A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays.Nucleic Acids Res2005
16305325Quick, practical selection of effective seeds for homology search.J Comput Biol2005
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Collaborators

Webb Miller
Co-authored papers 5
Jian Ma
Co-authored papers 3
Choong Yong Ung
Co-authored papers 3
Aakrosh Ratan
Center for Public Health Genomics, University of Virginia
Co-authored papers 2
Eric D Green
National Human Genome Research Institute, National Institutes of Health
Co-authored papers 2
Wing-Kin Sung
Co-authored papers 2
Hu Li
Co-authored papers 2
David Haussler
Genomics Institute, University of California Santa Cruz
Co-authored papers 2
Bernard Suh
Center for Biomolecular Science and Engineering, University of California
Co-authored papers 2
Ross C Hardison
Co-authored papers 2
Nathan Sheffield (CM4AI)
University of Virginia
Co-authored papers 1
Christophe Dessimoz
University of Lausanne
Co-authored papers 1
William James Kent
Co-authored papers 1
Karolina Sienkiewicz
Center for Public Health Genomics, University of Virginia
Co-authored papers 1
John T Lawson
Center for Public Health Genomics, University of Virginia
Co-authored papers 1
Ajay Chatrath
University of Virginia
Co-authored papers 1
Jinyu Chen
National University of Singapore
Co-authored papers 1
Niko Beerenwinkel
ETH Zurich
Co-authored papers 1
Release 1.2