Search details
1.
Understanding metric-related pitfalls in image analysis validation.
Nat Methods
; 21(2): 182-194, 2024 Feb.
Article
in English
| MEDLINE | ID: mdl-38347140
2.
Metrics reloaded: recommendations for image analysis validation.
Nat Methods
; 21(2): 195-212, 2024 Feb.
Article
in English
| MEDLINE | ID: mdl-38347141
3.
Community consensus on core open science practices to monitor in biomedicine.
PLoS Biol
; 21(1): e3001949, 2023 01.
Article
in English
| MEDLINE | ID: mdl-36693044
4.
Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma.
Nucleic Acids Res
; 51(19): 10109-10131, 2023 10 27.
Article
in English
| MEDLINE | ID: mdl-37738673
5.
Sensitive tumour detection and classification using plasma cell-free DNA methylomes.
Nature
; 563(7732): 579-583, 2018 11.
Article
in English
| MEDLINE | ID: mdl-30429608
6.
Assessing and assuring interoperability of a genomics file format.
Bioinformatics
; 38(13): 3327-3336, 2022 06 27.
Article
in English
| MEDLINE | ID: mdl-35575355
7.
Exploring the merits of research performance measures that comply with the San Francisco Declaration on Research Assessment and strategies to overcome barriers of adoption: qualitative interviews with administrators and researchers.
Health Res Policy Syst
; 21(1): 43, 2023 Jun 05.
Article
in English
| MEDLINE | ID: mdl-37277824
8.
Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.
PLoS Comput Biol
; 17(10): e1009423, 2021 10.
Article
in English
| MEDLINE | ID: mdl-34648491
9.
Transparency and reproducibility in artificial intelligence.
Nature
; 586(7829): E14-E16, 2020 10.
Article
in English
| MEDLINE | ID: mdl-33057217
10.
Top considerations for creating bioinformatics software documentation.
Brief Bioinform
; 19(4): 693-699, 2018 07 20.
Article
in English
| MEDLINE | ID: mdl-28088754
11.
Comparative analysis of metazoan chromatin organization.
Nature
; 512(7515): 449-52, 2014 Aug 28.
Article
in English
| MEDLINE | ID: mdl-25164756
12.
Umap and Bismap: quantifying genome and methylome mappability.
Nucleic Acids Res
; 46(20): e120, 2018 11 16.
Article
in English
| MEDLINE | ID: mdl-30169659
13.
Reproducibility standards for machine learning in the life sciences.
Nat Methods
; 18(10): 1132-1135, 2021 10.
Article
in English
| MEDLINE | ID: mdl-34462593
14.
Segway 2.0: Gaussian mixture models and minibatch training.
Bioinformatics
; 34(4): 669-671, 2018 02 15.
Article
in English
| MEDLINE | ID: mdl-29028889
15.
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.
Inf Fusion
; 50: 71-91, 2019 Oct.
Article
in English
| MEDLINE | ID: mdl-30467459
16.
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.
Genome Res
; 25(4): 544-57, 2015 Apr.
Article
in English
| MEDLINE | ID: mdl-25677182
17.
Classification and interaction in random forests.
Proc Natl Acad Sci U S A
; 115(8): 1690-1692, 2018 02 20.
Article
in English
| MEDLINE | ID: mdl-29440440
18.
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Genome Res
; 22(9): 1813-31, 2012 Sep.
Article
in English
| MEDLINE | ID: mdl-22955991
19.
Unsupervised pattern discovery in human chromatin structure through genomic segmentation.
Nat Methods
; 9(5): 473-6, 2012 Mar 18.
Article
in English
| MEDLINE | ID: mdl-22426492
20.
Integrative annotation of chromatin elements from ENCODE data.
Nucleic Acids Res
; 41(2): 827-41, 2013 Jan.
Article
in English
| MEDLINE | ID: mdl-23221638