Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Discovery of two-level modular organization from matched genomic data via joint matrix tri-factorization

(2018) Jinyu Chen et al.   NUCLEIC ACIDS RESEARCH

Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks

(2016) Siqi Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

RUNX1, an androgen- and EZH2-regulated gene, has differential roles in AR-dependent and -independent prostate cancer

(2015) Ken-ichi Takayama et al.   Oncotarget

Identification of Distinct Basal and Luminal Subtypes of Muscle-Invasive Bladder Cancer with Different Sensitivities to Frontline Chemotherapy

(2014) Woonyoung Choi et al.   CANCER CELL

Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes

(2014) Anne Biton et al.   Cell Reports

Breast cancer adaptive resistance: HER2 and cancer stem cell repopulation in a heterogeneous tumor society

(2013) Nadire Duru et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Differential principal component analysis of ChIP-seq

(2013) H. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NeNMF: An Optimal Gradient Method for Nonnegative Matrix Factorization

(2012) Naiyang Guan et al.   IEEE TRANSACTIONS ON SIGNAL PROCESSING

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

(2012) Shihua Zhang et al.   NUCLEIC ACIDS RESEARCH

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules

(2011) Shihua Zhang et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Substrate and product specificities of SET domain methyltransferases

(2011) Paul A. Del Rizzo et al.   Epigenetics

Development of targeted therapy in uterine serous carcinoma, a biologically aggressive variant of endometrial cancer

(2011) Karim S El-Sahwi et al.   Expert Review of Anticancer Therapy

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

(2011) B.-K. Lee et al.   GENOME RESEARCH

High prevalence of retinoblastoma protein loss in triple-negative breast cancers and its association with a good prognosis in patients treated with adjuvant chemotherapy

(2009) D. Trere et al.   ANNALS OF ONCOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

GATA-3 Expression in Breast Cancer Has a Strong Association with Estrogen Receptor but Lacks Independent Prognostic Value

(2008) D. Voduc et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Differentiation of Embryonic Stem Cells to Clinically Relevant Populations: Lessons from Embryonic Development

(2008) Charles E. Murry et al.   CELL

Loss of Retinoblastoma Tumor Suppressor Protein Makes Human Breast Cancer Cells More Sensitive to Antimetabolite Exposure

(2008) M. Derenzini et al.   CLINICAL CANCER RESEARCH

Defining early lineage specification of human embryonic stem cells by the orchestrated balance of canonical Wnt/ -catenin, Activin/Nodal and BMP signaling

(2008) T. Sumi et al.   DEVELOPMENT

GATA-3 as a Marker of Hormone Response in Breast Cancer

(2008) Sandy H. Fang et al.   JOURNAL OF SURGICAL RESEARCH

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Differential Activation of Multiple Signalling Pathways Dictates eNOS Upregulation by FGF2 but not VEGF in Placental Artery Endothelial Cells

(2008) Eugenia Mata-Greenwood et al.   PLACENTA

TGFβ-induced EMT requires focal adhesion kinase (FAK) signaling

(2007) Carla Cicchini et al.   EXPERIMENTAL CELL RESEARCH