-
1
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
2
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015).
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
-
3
-
-
84875448918
-
Integrative annotation of chromatin elements from ENCODE data
-
Hoffman, M. M. et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 41, 827-841 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 827-841
-
-
Hoffman, M.M.1
-
4
-
-
79955583542
-
Systematic analysis of chromatin state dynamics in nine human cell types
-
Ernst, J. et al. Systematic analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
-
5
-
-
84866361701
-
Circuitry and dynamics of human transcription factor regulatory networks
-
Neph, S. et al. Circuitry and dynamics of human transcription factor regulatory networks. Cell 150, 1274-1286 (2012).
-
(2012)
Cell
, vol.150
, pp. 1274-1286
-
-
Neph, S.1
-
6
-
-
84998590108
-
Choosing panels of genomics assays using submodular optimization
-
Wei, K., Libbrecht, M. W., Bilmes, J. A. & Noble, W. S. Choosing panels of genomics assays using submodular optimization. Genome Biol. 17, 229 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 229
-
-
Wei, K.1
Libbrecht, M.W.2
Bilmes, J.A.3
Noble, W.S.4
-
7
-
-
84926632357
-
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
-
Ernst, J. & Kellis, M. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nat. Biotechnol. 33, 364-376 (2015).
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 364-376
-
-
Ernst, J.1
Kellis, M.2
-
8
-
-
0002740437
-
Foundations of the PARAFAC procedure: Models and conditions for an "explanatory" multi-modal factor analysis
-
Harshman, R. A. Foundations of the PARAFAC procedure: models and conditions for an "explanatory" multi-modal factor analysis. UCLA Working Papers in Phonetics 16, 1-84 (1970).
-
(1970)
UCLA Working Papers in Phonetics
, vol.16
, pp. 1-84
-
-
Harshman, R.A.1
-
9
-
-
34250499792
-
Analysis of individual differences in multidimensional scaling via an n-way generalization of eckart-young decomposition
-
Carroll, J. D. & Chang, J.-J. Analysis of individual differences in multidimensional scaling via an n-way generalization of Eckart-Young decomposition. Psychometrika 35, 283-319 (1970).
-
(1970)
Psychometrika
, vol.35
, pp. 283-319
-
-
Carroll, J.D.1
Chang, J.-J.2
-
10
-
-
84887496761
-
Many human accelerated regions are developmental enhancers
-
Capra, J. A., Erwin, G. D., McKinsey, G., Rubenstein, J. L. R. & Pollard, K. S. Many human accelerated regions are developmental enhancers. Philos. Trans. R Soc. Lond. B Biol. Sci. 368, 20130025-20130025 (2013).
-
(2013)
Philos. Trans. R Soc. Lond. B Biol. Sci.
, vol.368
, pp. 20130025
-
-
Capra, J.A.1
Erwin, G.D.2
McKinsey, G.3
Rubenstein, J.L.R.4
Pollard, K.S.5
-
11
-
-
84865760395
-
GENCODE: The reference human genome annotation for the ENCODE project
-
Harrow, J. et al. GENCODE: the reference human genome annotation for the ENCODE Project. Genome Res. 22, 1760-1774 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
-
12
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009).
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
-
13
-
-
84906496320
-
Exploring the genesis and functions of human accelerated regions sheds light on their role in human evolution
-
Hubisz, M. J. & Pollard, K. S. Exploring the genesis and functions of human accelerated regions sheds light on their role in human evolution. Curr. Opin. Genet. Dev. 29, 15-21 (2014).
-
(2014)
Curr. Opin. Genet. Dev.
, vol.29
, pp. 15-21
-
-
Hubisz, M.J.1
Pollard, K.S.2
-
14
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King, M.-C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107-116 (1975).
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.-C.1
Wilson, A.C.2
-
15
-
-
51149097366
-
Human-specific gain of function in a developmental enhancer
-
Prabhakar, S. et al. Human-specific gain of function in a developmental enhancer. Science 321, 1346-1350 (2008).
-
(2008)
Science
, vol.321
, pp. 1346-1350
-
-
Prabhakar, S.1
-
16
-
-
84876520556
-
The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome
-
Kamm, G. B., Pisciottano, F., Kliger, R. & Franchini, L. F. The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome. Mol. Biol. Evol. 30, 1088-1102 (2013).
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 1088-1102
-
-
Kamm, G.B.1
Pisciottano, F.2
Kliger, R.3
Franchini, L.F.4
-
17
-
-
84873506311
-
Function and regulation of AUTS2, a gene implicated in autism and human evolution
-
Oksenberg, N., Stevison, L., Wall, J. D. & Ahituv, N. Function and regulation of AUTS2, a gene implicated in autism and human evolution. PLoS Genet. 9, e1003221 (2013).
-
(2013)
PLoS Genet.
, vol.9
, pp. e1003221
-
-
Oksenberg, N.1
Stevison, L.2
Wall, J.D.3
Ahituv, N.4
-
18
-
-
84903388630
-
Integrating diverse datasets improves developmental enhancer prediction
-
Erwin, G. D. et al. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput. Biol. 10, e1003677 (2014).
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003677
-
-
Erwin, G.D.1
-
19
-
-
69249097024
-
Interacting haplotypes at the NPAS3 locus alter risk of schizophrenia and bipolar disorder
-
Pickard, B. S. et al. Interacting haplotypes at the NPAS3 locus alter risk of schizophrenia and bipolar disorder. Mol. Psychiatry 14, 874-884 (2008).
-
(2008)
Mol. Psychiatry
, vol.14
, pp. 874-884
-
-
Pickard, B.S.1
-
20
-
-
33846112470
-
VISTA enhancer browsera database of tissue-specific human enhancers
-
Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. A. VISTA Enhancer Browsera database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88-D92 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D88-D92
-
-
Visel, A.1
Minovitsky, S.2
Dubchak, I.3
Pennacchio, L.A.4
-
21
-
-
77952214662
-
GREAT improves functional interpretation of cisregulatory regions
-
McLean, C. Y. et al. GREAT improves functional interpretation of cisregulatory regions. Nat. Biotechnol. 28, 495-501 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 495-501
-
-
McLean, C.Y.1
-
22
-
-
0030813663
-
Tutorial and applications
-
PARAFAC
-
Bro, R. PARAFAC. Tutorial and applications. Chemom. Intell. Lab. Syst. 38, 149-171 (1997).
-
(1997)
Chemom. Intell. Lab. Syst.
, vol.38
, pp. 149-171
-
-
Bro, R.1
-
23
-
-
68649096448
-
Tensor decompositions and applications
-
Kolda, T. G. & Bader, B. W. Tensor decompositions and applications. SIAM Rev. 51, 455-500 (2009).
-
(2009)
SIAM Rev.
, vol.51
, pp. 455-500
-
-
Kolda, T.G.1
Bader, B.W.2
-
24
-
-
85020225755
-
Tensor factorization toward precision medicine
-
Luo, Y., Wang, F. & Szolovits, P. Tensor factorization toward precision medicine. Brief. Bioinform. 18, 511-514 (2017).
-
(2017)
Brief. Bioinform.
, vol.18
, pp. 511-514
-
-
Luo, Y.1
Wang, F.2
Szolovits, P.3
-
25
-
-
84960877099
-
Constructing 3d interaction maps from 1d epigenomes
-
Zhu, Y. et al. Constructing 3d interaction maps from 1d epigenomes. Nat. Commun. 7, 10812 (2016).
-
(2016)
Nat. Commun.
, vol.7
, pp. 10812
-
-
Zhu, Y.1
-
26
-
-
84980335767
-
Tensor decomposition for multiple-tissue gene expression experiments
-
Hore, V. et al. Tensor decomposition for multiple-tissue gene expression experiments. Nat. Genet. 48, 1094-1100 (2016).
-
(2016)
Nat. Genet.
, vol.48
, pp. 1094-1100
-
-
Hore, V.1
-
27
-
-
79952446596
-
Scalable tensor factorizations for incomplete data
-
Acar, E., Dunlavy, D. M., Kolda, T. G. & Mrup, M. Scalable tensor factorizations for incomplete data. Chemom. Intell. Lab. Syst. 106, 41-56 (2011).
-
(2011)
Chemom. Intell. Lab. Syst.
, vol.106
, pp. 41-56
-
-
Acar, E.1
Dunlavy, D.M.2
Kolda, T.G.3
Mrup, M.4
-
28
-
-
85008044987
-
Matrix factorization techniques for recommender systems
-
Koren, Y., Bell, R. & Volinsky, C. Matrix factorization techniques for recommender systems. IEEE Comput. 42, 30-37 (2009).
-
(2009)
IEEE Comput.
, vol.42
, pp. 30-37
-
-
Koren, Y.1
Bell, R.2
Volinsky, C.3
-
30
-
-
84945531855
-
Peak shape clustering reveals biological insights
-
Cremona, M. A. et al. Peak shape clustering reveals biological insights. BMC Bioinformatics 16, 349 (2015).
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 349
-
-
Cremona, M.A.1
-
31
-
-
84887880021
-
MMDiff: Quantitative testing for shape changes in ChIP-seq data sets
-
Schweikert, G., Cseke, B., Clouaire, T., Bird, A. & Sanguinetti, G. MMDiff: quantitative testing for shape changes in ChIP-Seq data sets. BMC Genomics 14, 826 (2013).
-
(2013)
BMC Genomics
, vol.14
, pp. 826
-
-
Schweikert, G.1
Cseke, B.2
Clouaire, T.3
Bird, A.4
Sanguinetti, G.5
-
32
-
-
84907221181
-
Transcription factor binding predicts histone modifications in human cell lines
-
Benveniste, D., Sonntag, H.-J., Sanguinetti, G. & Sproul, D. Transcription factor binding predicts histone modifications in human cell lines. Proc. Natl Acad. Sci. USA 111, 13367-13372 (2014).
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. 13367-13372
-
-
Benveniste, D.1
Sonntag, H.-J.2
Sanguinetti, G.3
Sproul, D.4
-
33
-
-
84923779988
-
Predicting the human epigenome from DNA motifs
-
Whitaker, J. W., Chen, Z. & Wang, W. Predicting the human epigenome from DNA motifs. Nat. Methods 12, 265-272 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 265-272
-
-
Whitaker, J.W.1
Chen, Z.2
Wang, W.3
-
34
-
-
84958257565
-
Predicting effects of noncoding variants with deep learning-based sequence model
-
Zhou, J. & Troyanskaya, O. G. Predicting effects of noncoding variants with deep learning-based sequence model. Nat. Methods 12, 931-934 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 931-934
-
-
Zhou, J.1
Troyanskaya, O.G.2
-
35
-
-
84862785201
-
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
-
Hoffman, M. M. et al. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods 9, 473-476 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 473-476
-
-
Hoffman, M.M.1
-
36
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
37
-
-
85161967549
-
Parallelized stochastic gradient descent
-
Zinkevich, M., Weimer, M., Li, L. & Smola, A. J. Parallelized stochastic gradient descent. Adv. Neural Inf. Process. Syst. 23, 2595-2603 (2010).
-
(2010)
Adv. Neural Inf. Process. Syst.
, vol.23
, pp. 2595-2603
-
-
Zinkevich, M.1
Weimer, M.2
Li, L.3
Smola, A.J.4
-
39
-
-
85012923563
-
-
Technical Report (Stanford University). Preprint at
-
Dozat, T. Incorporating Nesterov Momentum into Adam. Technical Report (Stanford University). Preprint at: http://cs229.stanford.edu/proj2015/054-report.pdf (2015).
-
(2015)
Incorporating Nesterov Momentum into Adam
-
-
Dozat, T.1
-
40
-
-
79952595565
-
The NumPy array: A structure for efficient numerical computation
-
Walt, S. van der, Colbert, S. C., Varoquaux, G. The NumPy array: a structure for efficient numerical computation. Computing in Science Engineering 13, 22-30 (2011).
-
(2011)
Computing in Science Engineering
, vol.13
, pp. 22-30
-
-
Van Der-Walt, S.1
Colbert, S.C.2
Varoquaux, G.3
-
41
-
-
84857855190
-
Random search for hyper-parameter optimization
-
Bergstra, J. & Bengio, Y. Random search for hyper-parameter optimization. J. Mach. Learn. Res. 13, 281-305 (2012).
-
(2012)
J. Mach. Learn. Res.
, vol.13
, pp. 281-305
-
-
Bergstra, J.1
Bengio, Y.2
-
44
-
-
84957453122
-
Python-ternary: Ternary plots in python
-
Harper, M. et al. python-ternary: ternary plots in Python. Zenodo. https://doi.org/10.5281/zenodo.594435 (2017)
-
(2017)
Zenodo
-
-
Harper, M.1
-
45
-
-
80555140075
-
Scikit-learn: Machine learning in python
-
Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825-2830 (2011).
-
(2011)
J. Mach. Learn. Res.
, vol.12
, pp. 2825-2830
-
-
Pedregosa, F.1
|