A Linear Regression and Deep Learning Approach for Detecting Reliable Genetic Alterations in Cancer Using DNA Methylation and Gene Expression Data

MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors

(2020) Guimin Qin et al.   Scientific Reports

Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours

(2020) Saurav Mallik et al.   Epigenetics

Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data

(2019) Saurav Mallik et al.   BRIEFINGS IN BIOINFORMATICS

BioMethyl: an R package for biological interpretation of DNA methylation data

(2019) Yue Wang et al.   BIOINFORMATICS

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Quercetin modulates signaling pathways and induces apoptosis in cervical cancer cells

(2019) Madhumitha Kedhari Sundaram et al.   BIOSCIENCE REPORTS

An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays

(2018) Saurav Mallik et al.   BRIEFINGS IN BIOINFORMATICS

Exploration of methylation-driven genes for monitoring and prognosis of patients with lung adenocarcinoma

(2018) Chundi Gao et al.   Cancer Cell International

MicroRNA expression profiles and networks in placentas complicated with selective intrauterine growth restriction

(2017) Hong Wen et al.   Molecular Medicine Reports

The VPS4 component of the ESCRT machinery plays an essential role in HPV infectious entry and capsid disassembly

(2017) Justyna Broniarczyk et al.   Scientific Reports

Stochastic epigenetic outliers can define field defects in cancer

(2016) Andrew E. Teschendorff et al.   BMC BIOINFORMATICS

GRWD1 negatively regulates p53 via the RPL11–MDM2 pathway and promotes tumorigenesis

(2016) Kota Kayama et al.   EMBO REPORTS

RANWAR: Rank-Based Weighted Association Rule Mining From Gene Expression and Methylation Data

(2015) Saurav Mallik et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip

(2015) Zongli Xu et al.   NUCLEIC ACIDS RESEARCH

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

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

DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

(2014) Martin A Rijlaarsdam et al.   BMC BIOINFORMATICS

A Survey and Comparative Study of Statistical Tests for Identifying Differential Expression from Microarray Data

(2014) Sanghamitra Bandyopadhyay et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Simultaneous Characterization of Somatic Events and HPV-18 Integration in a Metastatic Cervical Carcinoma Patient Using DNA and RNA Sequencing

(2014) Winnie S. Liang et al.   INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types

(2012) Jung H Kim et al.   BMC GENOMICS

Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation

(2012) Andrew E Teschendorff et al.   Genome Medicine

Correction: The Dynamics and Prognostic Potential of DNA Methylation Changes at Stem Cell Gene Loci in Women's Cancer

(2012) Joanna Zhuang et al.   PLoS Genetics

DNA Methylation Array Analysis Identifies Profiles of Blood-Derived DNA Methylation Associated With Bladder Cancer

(2011) Carmen J. Marsit et al.   JOURNAL OF CLINICAL ONCOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY