Lista de obras -

3D chromosome modeling with semi-definite programming and Hi-C data

artículo científico publicado en 2013

AP-2γ regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription

Adjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification.

artículo científico publicado en 2010

Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree.

artículo científico publicado en 2016

An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees

scientific article published on 16 April 2019

An O(m log m)-Time Algorithm for Detecting Superbubbles

artículo científico publicado en 2015

An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping

artículo científico publicado en 2019

An intrinsic mechanism controls reactivation of neural stem cells by spindle matrix proteins.

artículo científico publicado en 2017

An oestrogen-receptor-α-bound human chromatin interactome

artículo científico publicado en 2009

BATVI: Fast, sensitive and accurate detection of virus integrations.

artículo científico publicado en 2017

BatAlign: an incremental method for accurate alignment of sequencing reads

artículo científico publicado en 2015

BatMis: a fast algorithm for k-mismatch mapping ⬇️

artículo científico publicado el 10 de junio de 2012

CENTDIST: discovery of co-associated factors by motif distribution ⬇️

artículo científico publicado el 20 de mayo de 2011

CWig: compressed representation of Wiggle/BedGraph format.

artículo científico publicado en 2014

Calling large indels in 1047 Arabidopsis with IndelEnsembler

artículo científico publicado en 2021

Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state.

artículo científico publicado en 2011

ChIA-PET analysis of transcriptional chromatin interactions.

artículo científico publicado en 2012

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations

artículo científico publicado en 2013

Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation

scientific article published on 13 August 2019

Comparison of microarray-predicted closest genomes to sequencing for poliovirus vaccine strain similarity and influenza A phylogeny

artículo científico publicado en 2015

Comprehensive analysis of transcriptome profiles in hepatocellular carcinoma

artículo científico publicado en 2019

Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets ⬇️

artículo científico publicado el 1 de julio de 2011

Constructing phylogenetic supernetworks based on simulated annealing ⬇️

artículo científico publicado el 3 de marzo de 2012

D-SLIMMER: Domain–SLiM Interaction Motifs Miner for Sequence Based Protein–Protein Interaction Data ⬇️

artículo científico publicado el 2 de diciembre de 2011

Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma.

artículo científico publicado en 2014

Determining the Consistency of Resolved Triplets and Fan Triplets

artículo científico publicado en 2018

Differential transcriptomic analyses revealed genes and signaling pathways involved in iono-osmoregulation and cellular remodeling in the gills of euryhaline Mozambique tilapia, Oreochromis mossambicus

artículo científico publicado en 2014

Do triplets have enough information to construct the multi-labeled phylogenetic tree?

artículo científico publicado en 2014

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation ⬇️

artículo científico publicado el 20 de enero de 2012

Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts.

artículo científico publicado en 2011

Guest Editorial for the International Conference on Genome Informatics (GIW 2013).

artículo científico publicado en 2014

Identifying Differential Histone Modification Sites from ChIP‐seq Data ⬇️

artículo científico publicado el 1 de enero de 2012

Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

artículo científico publicado en 2018

Integration of Regulatory Networks by NKX3-1 Promotes Androgen-Dependent Prostate Cancer Survival ⬇️

artículo científico publicado el 14 de noviembre de 2011

International Conference on Genome Informatics (GIW 2013) in Singapore: Introduction to the systems biology contributions

artículo científico publicado en 2013

Large-scale functional organization of long-range chromatin interaction networks

artículo científico publicado en 2012

Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

artículo científico publicado en 2012

Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line.

artículo científico publicado en 2017

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences ⬇️

artículo científico publicado el 19 de septiembre de 2011

PE-Assembler: de novo assembler using short paired-end reads ⬇️

artículo científico publicado el 12 de diciembre de 2010

Pan-omics analysis of biological data

artículo científico publicado en 2016

Platform comparison for evaluation of ALK protein immunohistochemical expression, genomic copy number and hotspot mutation status in neuroblastomas

artículo científico publicado en 2014

Polynomial-Time Algorithms for Building a Consensus MUL-Tree ⬇️

artículo científico publicado el 1 de septiembre de 2012

Publisher Correction: Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

scientific article published on 01 February 2019

Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity

artículo científico publicado en 2015

Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm.

artículo científico publicado en 2013

Structural variation detection using next-generation sequencing data: A comparative technical review.

artículo científico publicado en 2016

SurVIndel: improving CNV calling from high-throughput sequencing data through statistical testing

scientific article published on 15 April 2019

SurVirus: a repeat-aware virus integration caller

artículo científico publicado en 2021

Telomerase directly regulates NF-κB-dependent transcription.

artículo científico publicado en 2012

The Integrator Complex Prevents Dedifferentiation of Intermediate Neural Progenitors back into Neural Stem Cells

scientific article published on 01 April 2019

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma

scientific article published on 27 February 2017

TranSurVeyor: an improved database-free algorithm for finding non-reference transpositions in high-throughput sequencing data.

artículo científico publicado en 2018

Whole-genome reconstruction and mutational signatures in gastric cancer.

artículo científico publicado en 2012

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

artículo científico publicado en 2013

Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis

artículo científico publicado en 2015

Lista de obras de

3D chromosome modeling with semi-definite programming and Hi-C data

AP-2γ regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription

Adjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification.

Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree.

An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees

An O(m log m)-Time Algorithm for Detecting Superbubbles

An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping

An intrinsic mechanism controls reactivation of neural stem cells by spindle matrix proteins.

An oestrogen-receptor-α-bound human chromatin interactome

BATVI: Fast, sensitive and accurate detection of virus integrations.

BatAlign: an incremental method for accurate alignment of sequencing reads

BatMis: a fast algorithm for k-mismatch mapping ⬇️

CENTDIST: discovery of co-associated factors by motif distribution ⬇️

CWig: compressed representation of Wiggle/BedGraph format.

Calling large indels in 1047 Arabidopsis with IndelEnsembler

Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state.

ChIA-PET analysis of transcriptional chromatin interactions.

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations

Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation

Comparison of microarray-predicted closest genomes to sequencing for poliovirus vaccine strain similarity and influenza A phylogeny

Comprehensive analysis of transcriptome profiles in hepatocellular carcinoma

Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets ⬇️

Constructing phylogenetic supernetworks based on simulated annealing ⬇️

D-SLIMMER: Domain–SLiM Interaction Motifs Miner for Sequence Based Protein–Protein Interaction Data ⬇️

Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma.

Determining the Consistency of Resolved Triplets and Fan Triplets

Differential transcriptomic analyses revealed genes and signaling pathways involved in iono-osmoregulation and cellular remodeling in the gills of euryhaline Mozambique tilapia, Oreochromis mossambicus

Do triplets have enough information to construct the multi-labeled phylogenetic tree?

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation ⬇️

Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts.

Guest Editorial for the International Conference on Genome Informatics (GIW 2013).

Identifying Differential Histone Modification Sites from ChIP‐seq Data ⬇️

Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

Integration of Regulatory Networks by NKX3-1 Promotes Androgen-Dependent Prostate Cancer Survival ⬇️

International Conference on Genome Informatics (GIW 2013) in Singapore: Introduction to the systems biology contributions

Large-scale functional organization of long-range chromatin interaction networks

Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line.

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences ⬇️

PE-Assembler: de novo assembler using short paired-end reads ⬇️

Pan-omics analysis of biological data

Platform comparison for evaluation of ALK protein immunohistochemical expression, genomic copy number and hotspot mutation status in neuroblastomas

Polynomial-Time Algorithms for Building a Consensus MUL-Tree ⬇️

Publisher Correction: Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity

Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm.

Structural variation detection using next-generation sequencing data: A comparative technical review.

SurVIndel: improving CNV calling from high-throughput sequencing data through statistical testing

SurVirus: a repeat-aware virus integration caller

Telomerase directly regulates NF-κB-dependent transcription.

The Integrator Complex Prevents Dedifferentiation of Intermediate Neural Progenitors back into Neural Stem Cells

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma

TranSurVeyor: an improved database-free algorithm for finding non-reference transpositions in high-throughput sequencing data.

Whole-genome reconstruction and mutational signatures in gastric cancer.

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis