X. Yang

发表

Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia

Bin Wang, Luonan Chen, Jianjun Chen, 2015, BMC Bioinformatics.

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions

Lorenzo L. Pesce, Jason H. Moore, J. Denny, 2016, npj Genomic Medicine.

Identification of epigenetic modifications that contribute to pathogenesis in therapy-related AML: Effective integration of genome-wide histone modification with transcriptional profiles

J. Cunningham, X. Yang, Bin Wang, 2015, BMC Medical Genomics.

Curation-free biomodules mechanisms in prostate cancer predict recurrent disease

Y. Lussier, X. Yang, Haiquan Li, 2013, BMC Medical Genomics.

A common genetic variant within SCN10A modulates cardiac SCN5A expression.

J. Seidman, M. Nóbrega, C. Seidman, 2014, The Journal of clinical investigation.

Pitx2 modulates a Tbx5-dependent gene regulatory network to maintain atrial rhythm

Christopher R. Weber, M. Zhang, J. Seidman, 2016, Science Translational Medicine.

De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects

M. Hurles, E. Eichler, V. Sheffield, 2016, PLoS genetics.

Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers

Xiao Sun, X. Yang, 2007, BMC Bioinformatics.

Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors

J. Cunningham, X. Yang, I. Moskowitz, 2022, Nucleic acids research.

Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation

S. Vokes, A. McMahon, X. Yang, 2014, PLoS genetics.

Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages.

M. Kyba, Kohta Ikegami, X. Yang, 2022, Developmental cell.

Transcriptional Patterning of the Ventricular Cardiac Conduction System

M. Nóbrega, I. Efimov, Kohta Ikegami, 2020, Circulation research.

Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancer

Xiao Sun, Yves A. Lussier, Hong Fan, 2010, Chinese science bulletin = Kexue tongbao.

Comparability of gene expression in human blood, immune and carcinoma cells

Zuhong Lu, Xiao Sun, Xinan Yang, 2008, Appl. Math. Comput..

Tipping-point analysis uncovers critical transition signals from gene expression profiles

Zhezhen Wang, Fangming Tang, John M. Cunningham, 2019, bioRxiv.

Tipping-point analysis uncovers critical transition signals from gene expression profiles

J. Cunningham, X. Yang, Yuxi Sun, 2019, bioRxiv.

MicroRNA Expression Characterizes Oligometastasis(es)

R. Weichselbaum, Y. Lussier, X. Yang, 2011, PloS one.

Bridging Cancer Biology with the Clinic: Relative Expression of a GRHL2-Mediated Gene-Set Pair Predicts Breast Cancer Metastasis

Xinan Yang, John M. Cunningham, J. Cunningham, 2013, PloS one.

Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm

Christopher R. Weber, W. de Laat, X. Yang, 2017, eLife.

Hedgehog signaling activates a heterochronic gene regulatory network to control differentiation timing across lineages

M. Kyba, Kohta Ikegami, X. Yang, 2020, bioRxiv.

Adopting tipping-point theory to patient transcriptomes unravels gene regulatory network dynamics

Zhezhen Wang, Qier An, Fangming Tang, 2019 .

Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma

Xinan Yang, Fangming Tang, Jisu Shin, 2017, BMC Systems Biology.

A c-Myc-regulated stem cell-like signature in high-risk neuroblastoma: A systematic discovery (Target neuroblastoma ESC-like signature)

J. Cunningham, X. Yang, Fangming Tang, 2017, Scientific Reports.

Detecting Common Gene Expression Patterns in Multiple Cancer Outcome Entities

Rainer Spang, Xinan Yang, Stefan Bentink, 2005, Biomedical microdevices.

Correction: Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation

S. Vokes, A. McMahon, X. Yang, 2016, PLoS genetics.

Cilia gene mutations cause atrioventricular septal defects by multiple mechanisms.

J. Shendure, C. Maslen, X. Yang, 2016, Human molecular genetics.

Computational prognostic indicators for breast cancer

Xinan Yang, John M Cunningham, J. Cunningham, 2014, Cancer management and research.

Up-regulation of a HOXA-PBX3 homeobox-gene signature following down-regulation of miR-181 is associated with adverse prognosis in patients with cytogenetically abnormal AML.

M. Caligiuri, C. Bloomfield, M. Radmacher, 2012, Blood.

Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis

Mark Gerstein, Yong Huang, Yves A. Lussier, 2010, PLoS Comput. Biol..

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data

Bin Wang, Xinan Yang, John M. Cunningham, 2015, Bioinform..

Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases

Yves A. Lussier, Jianrong Li, Haiquan Li, 2013, J. Am. Medical Informatics Assoc..

Identification of a 24-gene prognostic signature that improves the European LeukemiaNet risk classification of acute myeloid leukemia: an international collaborative study.

Ulrich Mansmann, Xinan Yang, Guido Marcucci, 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Evolutionarily conserved Tbx5–Wnt2/2b pathway orchestrates cardiopulmonary development

R. Ho, M. Kyba, F. Conlon, 2018, Proceedings of the National Academy of Sciences.

GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns

Yves A. Lussier, Jianrong Li, Younghee Lee, 2011, Bioinform..

The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation.

F. Conlon, I. Cristea, X. Yang, 2016, Developmental cell.

Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development

Kohta Ikegami, X. Yang, P. Chaturvedi, 2021, bioRxiv.

Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq

Xiangying Sun, Zhezhen Wang, Carlos Perez-Cervantes, 2019, bioRxiv.

Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer

Yong Huang, Yves A. Lussier, Jianrong Li, 2012, PLoS Comput. Biol..

Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia

Xiao Sun, Yong Huang, Yves A. Lussier, 2009, BMC Bioinformatics.

Genetic Interactions between Chromosomes 11 and 18 Contribute to Airway Hyperresponsiveness in Mice

Yves A. Lussier, Jianrong Li, Xinan Yang, 2012, PloS one.

OrderedList - a bioconductor package for detecting similarity in ordered gene lists

Rainer Spang, Claudio Lottaz, Xinan Yang, 2006, Bioinform..

Similarities of Ordered Gene Lists

Rainer Spang, Xinan Yang, Stefan Bentink, 2006, J. Bioinform. Comput. Biol..

R. Spang, C. Lottaz, X. Yang, 2006 .

Hedgehog signaling controls progenitor differentiation timing during heart development

M. Kyba, Kohta Ikegami, X. Yang, 2018 .

Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models

Yong Huang, Yves A. Lussier, James L. Chen, 2010, BMC Bioinformatics.

In Silico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment

Y. Lussier, V. Gardeux, X. Yang, 2014, BMC Medical Genomics.

Cancer Management and Research Dovepress Computational Prognostic Indicators for Breast Cancer

J. Cunningham, X. Yang, Holly Yang, 2022 .

Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers

Xiao Sun, X. Yang, 2007, BMC Bioinformatics.

Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions.

Xiao Sun, Zuhong Lu, Jianming Xie, 2008, Biophysical journal.

Identification of a 24-gene prognostic signature that improves the European LeukemiaNet risk classification of acute myeloid leukemia: an international collaborative study.

M. Caligiuri, C. Bloomfield, M. Radmacher, 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases

E. Gamazon, Y. Lussier, X. Yang, 2013, J. Am. Medical Informatics Assoc..

Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers

Xiao Sun, X. Yang, J. Phelps, 2007, BMC Bioinformatics.

CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs

Xinan Yang, Zhezhen Wang, John M. Cunningham, 2018, Bioinform..

Meta-analysis of cancer gene-profiling data.

Xiao Sun, Xinan Yang, Xiao Sun, 2010, Methods in molecular biology.

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data

Bin Wang, J. Cunningham, X. Yang, 2015, Bioinform..

Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data

Yong Huang, Yves A. Lussier, Jianrong Li, 2010, J. Biomed. Informatics.

Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases

E. Gamazon, Y. Lussier, X. Yang, 2013, J. Am. Medical Informatics Assoc..