Timothy J. Durham

Most-cited papers

1. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations

   S. Rath, Rohit Sharma, Rahul Gupta, Tslil Ast +28 more

   2020Nucleic Acids Res.1,625 citations Open access

   Semantic Scholar

   Save

2. A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

   B. Bernstein, C. Epstein, N. Shoresh, Jesse A. Ernst +13 more

   2011PLoS Biology1,039 citations Open access

   Semantic Scholar

   Save

3. MIT Open Access Articles Mapping and Analysis of Chromatin State Dynamics in Nine Human Cell Types

   J. Ernst, P. Kheradpour, T. Mikkelsen, N. Shoresh +10 more

   633 citations

   Semantic Scholar

   Save

4. Genome-wide chromatin state transitions associated with developmental and environmental cues

   Jiang Zhu, Mazhar Adli, J. Zou, Griet Verstappen +16 more

   2013Cell548 citations Open access

   Semantic Scholar

   Save

5. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

   Oren Ram, Alon Goren, I. Amit, N. Shoresh +12 more

   2011Cell359 citations Open access

   Semantic Scholar

   Save

6. The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors

   Michelle M. Kudron, Alec Victorsen, L. Gevirtzman, L. Hillier +28 more

   2017Genetics200 citations Open access

   Semantic Scholar

   Save

7. Inferring causal gene regulatory networks from coupled single cell expression dynamics using Scribe

   Xiao-Jie Qiu, Arman Rahimzamani, Li Wang, Bingcheng Ren +6 more

   2020Cell Systems158 citations Open access

   Semantic Scholar

   Save

8. Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome

   Jacob M. Schreiber, Timothy J. Durham, Jeff A. Bilmes, W. S. Noble

   2020Genome Biology97 citations Open access

   Semantic Scholar

   Save

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

   Timothy J. Durham, M. Libbrecht, J. Howbert, Jeff A. Bilmes +1 more

   2018Nature Communications64 citations Open access

   Semantic Scholar

   Save

10. Functional characterization of enhancer evolution in the primate lineage

    Jason C. Klein, Aidan Keith, V. Agarwal, Timothy J. Durham +1 more

    2018Genome Biology56 citations Open access

    Semantic Scholar

    Save

11. Hypoxia extends lifespan and neurological function in a mouse model of aging

    Robert S Rogers, Hong Wang, Timothy J. Durham, Jonathan A. Stefely +5 more

    2023PLoS Biology49 citations Open access

    Semantic Scholar

    Save

12. Systematic analysis of chromatin state dynamics in nine human cell types

    J. Ernst, P. Kheradpour, T. Mikkelsen, N. Shoresh +10 more

    2011Nature37 citations Open access

    Semantic Scholar

    Save

13. Towards inferring causal gene regulatory networks from single cell expression Measurements

    Xiao-Jie Qiu, Arman Rahimzamani, Li Wang, Qi Mao +5 more

    2018bioRxiv30 citations Open access

    Semantic Scholar

    Save

14. Multi-scale deep tensor factorization learns a latent representation of the human epigenome

    Jacob Schreiber, Timothy J. Durham, Jeff A. Bilmes, William Stafford Noble

    2018bioRxiv22 citations Open access

    Semantic Scholar

    Save

15. Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

    Timothy J. Durham, R. Daza, L. Gevirtzman, D. Cusanovich +4 more

    2020bioRxiv20 citations Open access

    Semantic Scholar

    Save

16. Minimal genomes, maximal productivity: comparative genomics of the photosystem and light-harvesting complexes in the marine cyanobacterium, Prochlorococcus

    Claire Ting, M. E. Ramsey, Yvette L. Wang, A. Frost +2 more

    2009Photosynthesis Research13 citations

    Semantic Scholar

    Save

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

    Timothy J. Durham, M. Libbrecht, J. Howbert, Jeff A. Bilmes +1 more

    2017bioRxiv7 citations Open access

    Semantic Scholar

    Save

18. Author Correction: Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome

    Jacob M. Schreiber, Timothy J. Durham, Jeff A. Bilmes, William Stafford Noble

    2021Genome Biology3 citations Open access

    Semantic Scholar

    Save

19. Matrix prior for data transfer between single cell data types in latent Dirichlet allocation

    Alan T. Min, Timothy J. Durham, L. Gevirtzman, William Stafford Noble

    2022bioRxiv2 citations Open access

    Semantic Scholar

    Save

20. Review response for: Matrix prior for data transfer between single cell data types in latent Dirichlet allocation

    Alan T. Min, Timothy J. Durham, L. Gevirtzman, W. S. Noble

    20230 citations

    Semantic Scholar

    Save

21. Avocado: Deep tensor factorization characterizes the human epigenome via imputation of tens of thousands of functional experiments

    Jacob M. Schreiber, Timothy J. Durham, William Stafford Noble, Jeff A. Bilmes

    2020ACM International Conference on Bioinformatics, Computational Biology and Biomedicine0 citations

    Semantic Scholar

    Save

22. Additional File 1: Hyperparameter selection

    Jacob M. Schreiber, Timothy J. Durham, Jeff A. Bilmes, W. S. Noble

    20190 citations

    Semantic Scholar

    Save

23. Additional File 6: Promoter-enhancer interaction data set

    Jacob M. Schreiber, Timothy J. Durham, Jeff A. Bilmes, William Stafford Noble

    20190 citations

    Semantic Scholar

    Save