Author details

Full Name

Jeff A Bilmes

Affiliation

ORCID

Career Start Year

2008

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37546906	ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.		2023
37280678	Epiphany: predicting Hi-C contact maps from 1D epigenomic signals.		2023
36702456	MS1Connect: a mass spectrometry run similarity measure.		2023
36124797	Linking cells across single-cell modalities by synergistic matching of neighborhood structure.		2022
34479627	Author Correction: Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome.		2021
34252924	DIAmeter: matching peptides to data-independent acquisition mass spectrometry data.	Bioinformatics	2021
32966546	Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputedÂ data.		2021
33213499	A pitfall for machine learning methods aiming to predict across cell types.		2020
32228713	Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples.		2020
31462275	A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.	Genome Biol	2019
30362768	Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra.	Journal of Proteome Research	2019
29993658	Submodular Generalized Matching for Peptide Identification in Tandem Mass Spectrometry.	IEEE/ACM Transactions on Computational Biology and Bioinformatics	2019
30705579	Submodular Maximization via Gradient Ascent: The Case of Deep Submodular Functions.	Advances in Neural Information Processing Systems	2018
29028889	Segway 2.0: Gaussian mixture models and minibatch training.	Bioinformatics	2018
29345009	Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization.	Proteins: Structure, Function and Bioinformatics	2018
29643364	PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition.	Nature Communications	2018
29208983	Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies.	Sci Rep	2017
27846892	Choosing panels of genomics assays using submodular optimization.		2016
27397138	Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.	Journal of Proteome Research	2016
27307634	Faster and more accurate graphical model identification of tandem mass spectra using trellises.		2016
25677182	Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.	Genome Res	2015
25298752	Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry.		2014
23221638	Integrative annotation of chromatin elements from ENCODE data.	Nucleic Acids Res	2013
22426492	Unsupervised pattern discovery in human chromatin structure through genomic segmentation.	Nat Methods	2012
25383048	Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra.		2012
21569525	Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure.	BMC Bioinformatics	2011
20628623	Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.	PLoS Comput Biol	2010
20529925	A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.	Bioinformatics	2010
18586734	Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification.	Bioinformatics	2008
18416516	The Vocal Joystick: evaluation of voice-based cursor control techniques for assistive technology.	Disability and Rehabilitation: Assistive Technology	2008
18989393	Transmembrane topology and signal peptide prediction using dynamic bayesian networks.	PLoS Comput Biol	2008