List of works - Michael M. Hoffman

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data

scientific article

AANT: the Amino Acid-Nucleotide Interaction Database

scientific article published on January 2004

An effective model for natural selection in promoters

scientific article

Aspirin, NSAIDs, and colorectal cancer: possible involvement in an insulin-related pathway

scientific article (publication date: April 2004)

Associations among IRS1, IRS2, IGF1, and IGFBP3 genetic polymorphisms and colorectal cancer.

scientific article published in July 2004

BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactions

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

scientific article

ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data

scientific article

Classification and interaction in random forests

scientific article published on 12 February 2018

Colorectal tumor molecular phenotype and miRNA: expression profiles and prognosis

scientific article published on 20 May 2016

Comparative analysis of metazoan chromatin organization

scientific article

DNAmod: the DNA modification database

article published in 2019

Determining the epigenome using DNA alone

Dietary calcium, vitamin D, VDR genotypes and colorectal cancer

scientific article published in September 2004

Estimating the neutral rate of nucleotide substitution using introns

scientific article published in February 2007

Exploratory analysis of genomic segmentations with Segtools

scientific article

Extending reference assembly models

scientific article

Functional annotation of human long noncoding RNAs via molecular phenotyping

scientific article published on 27 July 2020

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

Genome Informatics 2016.

scientific article published on 16 January 2017

Integrative annotation of chromatin elements from ENCODE data

scientific article

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

scientific article

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

scientific article published on 21 September 2018

MicroRNA profiles in colorectal carcinomas, adenomas and normal colonic mucosa: variations in miRNA expression and disease progression

scientific article published on 6 January 2016

MicroRNAs and colon and rectal cancer: Differential expression by tumor location and subtype ⬇️

scientific article published on December 16, 2010

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

scientific article published in 2024

Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers

scientific article published on 25 March 2018

Opportunities and obstacles for deep learning in biology and medicine.

scientific article published in April 2018

Reproducibility standards for machine learning in the life sciences

scientific article

Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns

scientific article published on 14 October 2021

Segway 2.0: Gaussian mixture models and minibatch training

Semi-automated genome annotation using epigenomic data and Segway

Sensitive tumour detection and classification using plasma cell-free DNA methylomes

scientific article published in Nature

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Site-specific associations between miRNA expression and survival in colorectal cancer cases

scientific article published on 10 August 2016

Statistical Inference, Learning and Models in Big Data

The Genomedata format for storing large-scale functional genomics data

scientific article

Transparency and reproducibility in artificial intelligence

scientific article published on 14 October 2020

Umap and Bismap: quantifying genome and methylome mappability

scientific article published in November 2018

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

scientific article published on 18 March 2012

List of works by Michael M. Hoffman

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data

AANT: the Amino Acid-Nucleotide Interaction Database

An effective model for natural selection in promoters

Aspirin, NSAIDs, and colorectal cancer: possible involvement in an insulin-related pathway

Associations among IRS1, IRS2, IGF1, and IGFBP3 genetic polymorphisms and colorectal cancer.

BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactions

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data

Classification and interaction in random forests

Colorectal tumor molecular phenotype and miRNA: expression profiles and prognosis

Comparative analysis of metazoan chromatin organization

DNAmod: the DNA modification database

DNAmod: the DNA modification database

Determining the epigenome using DNA alone

Dietary calcium, vitamin D, VDR genotypes and colorectal cancer

Estimating the neutral rate of nucleotide substitution using introns

Exploratory analysis of genomic segmentations with Segtools

Extending reference assembly models

Functional annotation of human long noncoding RNAs via molecular phenotyping

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Genome Informatics 2016.

Integrative annotation of chromatin elements from ENCODE data

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

MicroRNA profiles in colorectal carcinomas, adenomas and normal colonic mucosa: variations in miRNA expression and disease progression

MicroRNAs and colon and rectal cancer: Differential expression by tumor location and subtype ⬇️

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers

Opportunities and obstacles for deep learning in biology and medicine.

Reproducibility standards for machine learning in the life sciences

Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns

Segway 2.0: Gaussian mixture models and minibatch training

Semi-automated genome annotation using epigenomic data and Segway

Sensitive tumour detection and classification using plasma cell-free DNA methylomes

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Site-specific associations between miRNA expression and survival in colorectal cancer cases

Statistical Inference, Learning and Models in Big Data

The Genomedata format for storing large-scale functional genomics data

Top considerations for creating bioinformatics software documentation

Transparency and reproducibility in artificial intelligence

Umap and Bismap: quantifying genome and methylome mappability

Umap and Bismap: quantifying genome and methylome mappability

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Virtual ChIP-seq: Predicting transcription factor binding by learning from the transcriptome