List of works - Alexander J Hartemink

A Bayesian approach to joint feature selection and classifier design

scientific article

A branching process model for flow cytometry and budding index measurements in cell synchrony experiments ⬇️

scientific article published on January 1, 2009

A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments ⬇️

scientific article published on July 1, 2011

A nucleosome-guided map of transcription factor binding sites in yeast

scientific article

A probabilistic model for cell cycle distributions in synchrony experiments

scientific article published on 12 February 2007

Advances to Bayesian network inference for generating causal networks from observational biological data

scientific article

An ensemble model of competitive multi-factor binding of the genome

scientific article published on 31 August 2009

Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program

scientific article published on 6 February 2013

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

scientific article

Characterization of dependencies between growth and division in budding yeast.

scientific article published in February 2017

Combining location and expression data for principled discovery of genetic regulatory network models

scientific article

Computational and experimental identification of novel human imprinted genes

scientific article

Computational inference of neural information flow networks

scientific article

Convergent transcriptional specializations in the brains of humans and song-learning birds

scientific article

Core and region-enriched networks of behaviorally regulated genes and the singing genome

scientific article

Distinguishing direct versus indirect transcription factor-DNA interactions

scientific article

Domain-oriented edge-based alignment of protein interaction networks

scientific article published on June 2009

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading

scientific article

Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

scientific article published on 27 October 2016

Evaluating functional network inference using simulations of complex biological systems

scientific article published in January 2002

Finding diagnostic biomarkers in proteomic spectra.

scientific article

Finding regulatory DNA motifs using alignment-free evolutionary conservation information

scientific article

Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly

scientific article

Genome-wide prediction of imprinted murine genes

scientific article

Global control of cell-cycle transcription by coupled CDK and network oscillators

scientific article

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing

scientific article published on 31 January 2011

Influence of network topology and data collection on network inference

scientific article

Informative priors based on transcription factor structural class improve de novo motif discovery

scientific article

Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data.

scientific article

Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors ⬇️

scientific article published on January 1, 2012

Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data

scientific article published in January 2004

Joint learning from multiple types of genomic data.

scientific article

Learning protein-DNA interaction landscapes by integrating experimental data through computational models

scientific article

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

scientific article

Mapping nucleosome positions using DNase-seq

scientific article published on 15 January 2016

Non-stationary dynamic Bayesian networks ⬇️

article by Joshua W. Robinson & Alexander J Hartemink published 2009 in Advances in Neural Information Processing Systems 21

On Semi-Supervised Classification ⬇️

scientific article published in January 2005

Reverse engineering gene regulatory networks

scientific article published in May 2005

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

scientific article

Sequence features of DNA binding sites reveal structural class of associated transcription factor

scientific article published on 2 November 2005

Sparse multinomial logistic regression: fast algorithms and generalization bounds

scientific article published in June 2005

Stability selection for regression-based models of transcription factor-DNA binding specificity.

scientific article published on July 2013

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

scientific article published on 3 February 2013

Theoretical and practical advances in genome halving

scientific article published on 28 October 2004

Using DNA duplex stability information for transcription factor binding site discovery.

scientific article published in January 2008

Using DNase digestion data to accurately identify transcription factor binding sites

scientific article

Verification of systems biology research in the age of collaborative competition

scientific article

List of works by Alexander J Hartemink

A Bayesian approach to joint feature selection and classifier design

A branching process model for flow cytometry and budding index measurements in cell synchrony experiments ⬇️

A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments ⬇️

A nucleosome-guided map of transcription factor binding sites in yeast

A probabilistic model for cell cycle distributions in synchrony experiments

Advances to Bayesian network inference for generating causal networks from observational biological data

An ensemble model of competitive multi-factor binding of the genome

Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program

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

Characterization of dependencies between growth and division in budding yeast.

Combining location and expression data for principled discovery of genetic regulatory network models

Computational and experimental identification of novel human imprinted genes

Computational inference of neural information flow networks

Convergent transcriptional specializations in the brains of humans and song-learning birds

Core and region-enriched networks of behaviorally regulated genes and the singing genome

Distinguishing direct versus indirect transcription factor-DNA interactions

Domain-oriented edge-based alignment of protein interaction networks

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading

Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

Evaluating functional network inference using simulations of complex biological systems

Finding diagnostic biomarkers in proteomic spectra.

Finding regulatory DNA motifs using alignment-free evolutionary conservation information

Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly

Genome-wide prediction of imprinted murine genes

Global control of cell-cycle transcription by coupled CDK and network oscillators

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing

Influence of network topology and data collection on network inference

Informative priors based on transcription factor structural class improve de novo motif discovery

Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data.

Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors ⬇️

Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data

Joint learning from multiple types of genomic data.

Learning protein-DNA interaction landscapes by integrating experimental data through computational models

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

Mapping nucleosome positions using DNase-seq

Non-stationary dynamic Bayesian networks ⬇️

On Semi-Supervised Classification ⬇️

Reverse engineering gene regulatory networks

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

Sequence features of DNA binding sites reveal structural class of associated transcription factor

Sparse multinomial logistic regression: fast algorithms and generalization bounds

Stability selection for regression-based models of transcription factor-DNA binding specificity.

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

Theoretical and practical advances in genome halving

Using DNA duplex stability information for transcription factor binding site discovery.

Using DNase digestion data to accurately identify transcription factor binding sites

Verification of systems biology research in the age of collaborative competition