Works by Bilmes, Jeff

Results: 19

Author Correction: ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.

Published in:

2025

By:

Gao, Vianne R.;
Yang, Rui;
Das, Arnav;
Luo, Renhe;
Luo, Hanzhi;
McNally, Dylan R.;
Karagiannidis, Ioannis;
Rivas, Martin A.;
Wang, Zhong-Min;
Barisic, Darko;
Karbalayghareh, Alireza;
Wong, Wilfred;
Zhan, Yingqian A.;
Chin, Christopher R.;
Noble, William S.;
Bilmes, Jeff A.;
Apostolou, Effie;
Kharas, Michael G.;
Béguelin, Wendy;
Viny, Aaron D.

Publication type:

Correction Notice

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53628-0

By:

Gao, Vianne R.;
Yang, Rui;
Das, Arnav;
Luo, Renhe;
Luo, Hanzhi;
McNally, Dylan R.;
Karagiannidis, Ioannis;
Rivas, Martin A.;
Wang, Zhong-Min;
Barisic, Darko;
Karbalayghareh, Alireza;
Wong, Wilfred;
Zhan, Yingqian A.;
Chin, Christopher R.;
Noble, William S.;
Bilmes, Jeff A.;
Apostolou, Effie;
Kharas, Michael G.;
Béguelin, Wendy;
Viny, Aaron D.

Publication type:

Article

DIAmeter: matching peptides to data-independent acquisition mass spectrometry data.

Published in:

Bioinformatics, 2021, v. 37, p. i434, doi. 10.1093/bioinformatics/btab284

By:

Lu, Yang Young;
Bilmes, Jeff;
Rodriguez-Mias, Ricard A;
Villén, Judit

Publication type:

Article

Constrained robust submodular sensor selection with application to multistatic sonar arrays.

Published in:

IET Radar, Sonar & Navigation (Wiley-Blackwell), 2017, v. 11, n. 12, p. 1776, doi. 10.1049/iet-rsn.2017.0075

By:

Powers, Thomas;
Krout, David W.;
Bilmes, Jeff;
Atlas, Les

Publication type:

Article

Constrained robust submodular sensor selection with application to multistatic sonar arrays.

Published in:

IET Radar, Sonar & Navigation (Wiley-Blackwell), 2017, v. 11, n. 12, p. 1776, doi. 10.1049/iet-rsn.2017.0075

By:

Powers, Thomas;
Krout, David W.;
Bilmes, Jeff;
Atlas, Les

Publication type:

Article

Graph cuts with interacting edge weights: examples, approximations, and algorithms.

Published in:

Mathematical Programming, 2017, v. 162, n. 1/2, p. 241, doi. 10.1007/s10107-016-1038-y

By:

Jegelka, Stefanie;
Bilmes, Jeff

Publication type:

Article

Faster and more accurate graphical model identification of tandem mass spectra using trellises.

Published in:

Bioinformatics, 2016, v. 32, n. 12, p. i322, doi. 10.1093/bioinformatics/btw269

By:

Shengjie Wang;
Halloran, John T.;
Bilmes, Jeff A.;
Noble, William S.

Publication type:

Article

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

Published in:

Bioinformatics, 2010, v. 26, n. 12, p. i334, doi. 10.1093/bioinformatics/btq175

By:

Chen, Xiaoyu;
Hoffman, Michael M.;
Bilmes, Jeff A.;
Hesselberth, Jay R.;
Noble, William S.

Publication type:

Article

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification.

Published in:

Bioinformatics, 2008, v. 24, n. 13, p. i348, doi. 10.1093/bioinformatics/btn189

By:

Aaron A. Klammer;
Sheila M. Reynolds;
Jeff A. Bilmes;
Michael J. MacCoss;
William Stafford Noble

Publication type:

Article

STATISTICAL MODELS FOR EMPIRICAL SEARCH-BASED PERFORMANCE TUNING.

Published in:

International Journal of High Performance Computing Applications, 2004, v. 18, n. 1, p. 65, doi. 10.1177/1094342004041293

By:

Vuduc, Richard;
Demmel, James W.;
Bilmes, Jeff A.

Publication type:

Article

Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure.

Published in:

BMC Bioinformatics, 2011, v. 12, n. 1, p. 154, doi. 10.1186/1471-2105-12-154

By:

Aydin, Zafer;
Singh, Ajit;
Bilmes, Jeff;
Noble, William S.

Publication type:

Article

Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 7, p. 1, doi. 10.1371/journal.pcbi.1000834

By:

Reynolds, Sheila M.;
Bilmes, Jeff A.;
Noble, William Stafford

Publication type:

Article

Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 11, p. 1, doi. 10.1371/journal.pcbi.1000213

By:

Reynolds, Sheila M.;
Käll, Lukas;
Riffle, Michael E.;
Bilmes, Jeff A.;
Noble, William Stafford

Publication type:

Article

Creating non-minimal triangulations for use in inference in mixed stochastic/deterministic graphical models.

Published in:

Machine Learning, 2011, v. 84, n. 3, p. 249, doi. 10.1007/s10994-010-5233-4

By:

Bartels, Chris;
Bilmes, Jeff

Publication type:

Article

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03635-9

By:

Durham, Timothy J.;
Libbrecht, Maxwell W.;
Howbert, J. Jeffry;
Noble, William Stafford;
Bilmes, Jeff

Publication type:

Article

Unsupervised pattern discovery in human chromatin structure through genomic segmentation.

Published in:

Nature Methods, 2012, v. 9, n. 5, p. 473, doi. 10.1038/nmeth.1937

By:

Hoffman, Michael M;
Buske, Orion J;
Wang, Jie;
Weng, Zhiping;
Bilmes, Jeff A;
Noble, William Stafford

Publication type:

Article

Semi-Supervised Learning with Measure Propagation.

Published in:

Journal of Machine Learning Research, 2011, v. 12, n. 11, p. 3311

By:

Subramanya, Amarnag;
Bilmes, Jeff

Publication type:

Article

Efficient Heuristics for Discriminative Structure Learning of Bayesian Network Classifiers.

Published in:

Journal of Machine Learning Research, 2010, v. 11, n. 8, p. 2323

By:

Pernkopf, Franz;
Bilmes, Jeff A.

Publication type:

Article

The Vocal Joystick: Evaluation of voice-based cursor control techniques for assistive technology.

Published in:

Disability & Rehabilitation: Assistive Technology, 2008, v. 3, n. 1/2, p. 22, doi. 10.1080/17483100701352963

By:

Harada, Susumu;
Landay, James A.;
Malkin, Jonathan;
Li, Xiao;
Bilmes, Jeff A.

Publication type:

Article