-
1
-
-
85038611077
-
The experiment data depot: A web-based software tool for biological experimental data storage, sharing, and visualization
-
PMID: 28826210
-
Morrell W, Birkel G, Forrer M, Lopez T, Backman T, Dussault M, et al. The Experiment Data Depot: a web-based software tool for biological experimental data storage, sharing, and visualization. ACS Synth Biol. 2017; 6 (12), 2248–2259. https://doi.org/10.1021/acssynbio.7b00204 PMID: 28826210
-
(2017)
ACS Synth Biol
, vol.6
, Issue.12
, pp. 2248-2259
-
-
Morrell, W.1
Birkel, G.2
Forrer, M.3
Lopez, T.4
Backman, T.5
Dussault, M.6
-
2
-
-
84920937371
-
Computational methods in metabolic engineering for strain design
-
PMID: 25576846
-
Long MR, Ong WK, Reed JL. Computational methods in metabolic engineering for strain design. Curr Opin Biotechnol. 2015; 34:135–41. https://doi.org/10.1016/j.copbio.2014.12.019 PMID: 25576846
-
(2015)
Curr Opin Biotechnol
, vol.34
, pp. 135-141
-
-
Long, M.R.1
Ong, W.K.2
Reed, J.L.3
-
3
-
-
84901306814
-
Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
-
Machado D, Herrgård M. Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism. PLoS Comput Biol. 2014; 10(4). e1003989.
-
(2014)
PLoS Comput Biol
, vol.10
, Issue.4
-
-
Machado, D.1
Herrgård, M.2
-
4
-
-
84961223765
-
Metabolic burden: Cornerstones in synthetic biology and metabolic engineering applications
-
PMID: 26996613
-
Wu G, Yan Q, Jones JA, Tang YJ, Fong SS, Koffas MAG. Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications. Trends in Biotechnology. 2016; 34 (8), 652–664. https://doi.org/10.1016/j.tibtech.2016.02.010 PMID: 26996613
-
(2016)
Trends in Biotechnology
, vol.34
, Issue.8
, pp. 652-664
-
-
Wu, G.1
Yan, Q.2
Jones, J.A.3
Tang, Y.J.4
Fong, S.S.5
Koffas, M.A.G.6
-
5
-
-
84928315635
-
An ancient Chinese wisdom for metabolic engineering: Yin-yang
-
Wu G, He L, Wang Q, Tang YJ. An ancient Chinese wisdom for metabolic engineering: Yin-Yang. Microb Cell Fact. 2015; 14(1):39.
-
(2015)
Microb Cell Fact
, vol.14
, Issue.1
, pp. 39
-
-
Wu, G.1
He, L.2
Wang, Q.3
Tang, Y.J.4
-
6
-
-
84980022857
-
Deep learning for computational biology
-
PMID: 27474269
-
Angermueller C, Pärnamaa T, Parts L, Oliver S. Deep Learning for Computational Biology. Mol Syst Biol. 2016;(12):878. https://doi.org/10.15252/msb.20156651 PMID: 27474269
-
(2016)
Mol Syst Biol
, vol.12
, pp. 878
-
-
Angermueller, C.1
Pärnamaa, T.2
Parts, L.3
Oliver, S.4
-
7
-
-
84960460639
-
Engineering cellular metabolism
-
PMID: 26967285
-
Nielsen J, Keasling JD. Engineering Cellular Metabolism. Cell. 2016; 164(6):1185–97. https://doi.org/10.1016/j.cell.2016.02.004 PMID: 26967285
-
(2016)
Cell
, vol.164
, Issue.6
, pp. 1185-1197
-
-
Nielsen, J.1
Keasling, J.D.2
-
8
-
-
84934927409
-
The LASER database: Formalizing design rules for metabolic engineering
-
Winkler JD, Halweg-Edwards AL, Gill RT. The LASER database: Formalizing design rules for metabolic engineering. Metab Eng Commun. 2015; 2:30–8.
-
(2015)
Metab Eng Commun
, vol.2
, pp. 30-38
-
-
Winkler, J.D.1
Halweg-Edwards, A.L.2
Gill, R.T.3
-
9
-
-
84964774521
-
Rapid prediction of bacterial heterotrophic fluxomics using machine learning and constraint programming
-
PMID: 27092947
-
Wu G, Wang Y, Jiang W, Oyetunde T, Yao R, Zhang X, et al. Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming. PLoS Comput Biol. 2016; 12(4), e1004838. https://doi.org/10.1371/journal.pcbi.1004838 PMID: 27092947
-
(2016)
PLoS Comput Biol
, vol.12
, Issue.4
-
-
Wu, G.1
Wang, Y.2
Jiang, W.3
Oyetunde, T.4
Yao, R.5
Zhang, X.6
-
10
-
-
85049776867
-
KBaSe: The United States department of energy systems biology knowledgebase
-
PMID: 29979655
-
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018; 36: 566–569. https://doi.org/10.1038/nbt.4163 PMID: 29979655
-
(2018)
Nature Biotechnology
, vol.36
, pp. 566-569
-
-
Arkin, A.P.1
Cottingham, R.W.2
Henry, C.S.3
Harris, N.L.4
Stevens, R.L.5
Maslov, S.6
-
11
-
-
84897668947
-
A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803
-
Maarleveld TR, Boele J, Bruggeman FJ, Teusink B. A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803. Plant Physiol. 2014;pp-113.
-
(2014)
Plant Physiol
, pp. 113
-
-
Maarleveld, T.R.1
Boele, J.2
Bruggeman, F.J.3
Teusink, B.4
-
12
-
-
84941279254
-
CecAFDB: A curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics
-
Zhang Z, Shen T, Rui B, Zhou W, Zhou X, Shang C, et al. CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics. Nucleic Acids Res. 2014; 43(D1):D549–57.
-
(2014)
Nucleic Acids Res
, vol.43
, Issue.D1
, pp. D549-D557
-
-
Zhang, Z.1
Shen, T.2
Rui, B.3
Zhou, W.4
Zhou, X.5
Shang, C.6
-
13
-
-
84863393849
-
OMero: Flexible, model-driven data management for experimental biology
-
PMID: 22373911
-
Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, et al. OMERO: flexible, model-driven data management for experimental biology. Nat Methods. 2012; 9(3):245–53. https://doi.org/10.1038/nmeth.1896 PMID: 22373911
-
(2012)
Nat Methods
, vol.9
, Issue.3
, pp. 245-253
-
-
Allan, C.1
Burel, J.M.2
Moore, J.3
Blackburn, C.4
Linkert, M.5
Loynton, S.6
-
14
-
-
85056608533
-
Comment on “Predicting reaction performance in C–N cross-coupling using machine learning
-
Nov 16
-
Chuang KV, Keiser MJ. Comment on “Predicting reaction performance in C–N cross-coupling using machine learning.” Science. 2018 Nov 16; 362(6416).
-
(2018)
Science
, vol.362
, Issue.6416
-
-
Chuang, K.V.1
Keiser, M.J.2
-
15
-
-
85041912553
-
Facilitate collaborations among synthetic biology, metabolic engineering and machine learning
-
Wu SG, Shimizu K, Tang JKH, Tang YJ. Facilitate Collaborations among Synthetic Biology, Metabolic Engineering and Machine Learning. ChemBioEng Rev. 2016; 3(2):45–54.
-
(2016)
ChemBioEng Rev
, vol.3
, Issue.2
, pp. 45-54
-
-
Wu, S.G.1
Shimizu, K.2
Tang, J.K.H.3
Tang, Y.J.4
-
16
-
-
79952604817
-
Evaluating factors that influence microbial synthesis yields by linear regression with numerical and ordinal variables
-
PMID: 21404262
-
Colletti PF, Goyal Y, Varman AM, Feng X, Wu B, Tang YJ. Evaluating factors that influence microbial synthesis yields by linear regression with numerical and ordinal variables. Biotechnol Bioeng. 2011; 108 (4):893–901. https://doi.org/10.1002/bit.22996 PMID: 21404262
-
(2011)
Biotechnol Bioeng
, vol.108
, Issue.4
, pp. 893-901
-
-
Colletti, P.F.1
Goyal, Y.2
Varman, A.M.3
Feng, X.4
Wu, B.5
Tang, Y.J.6
-
17
-
-
46249120116
-
Multiple correspondence analysis
-
Abdi H, Valentin D. Multiple correspondence analysis. Encycl Meas Stat. 2007;651–7.
-
(2007)
Encycl Meas Stat
, pp. 651-657
-
-
Abdi, H.1
Valentin, D.2
-
18
-
-
67650510587
-
A tutorial on Principal Components Analysis Introduction
-
Smith LI. A tutorial on Principal Components Analysis Introduction. Statistics. www.cs.otago.ac.nz/cosc453/student_tutorials/principal_components.pdf, 2002; 51:52.
-
(2002)
Statistics
, vol.51
, pp. 52
-
-
Smith, L.I.1
-
19
-
-
79961084093
-
Redesigning Escherichia coli metabolism for anaerobic production of isobutanol
-
21642415
-
Trinh CT, Li J, Blanch HW, Clark DS. Redesigning Escherichia coli metabolism for anaerobic production of isobutanol. Appl Environ Microbiol. 2011; 77(14):4894–904. https://doi.org/10.1128/AEM.00382-11PMID: 21642415
-
(2011)
Appl Environ Microbiol
, vol.77
, Issue.14
, pp. 4894-4904
-
-
Trinh, C.T.1
Li, J.2
Blanch, H.W.3
Clark, D.S.4
-
20
-
-
85031310018
-
IML1515, a knowledgebase that computes Escherichia coli traits
-
PMID: 29020004
-
Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, et al. iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol. 2017; 35(10):904. https://doi.org/10.1038/nbt.3956 PMID: 29020004
-
(2017)
Nat Biotechnol
, vol.35
, Issue.10
, pp. 904
-
-
Monk, J.M.1
Lloyd, C.J.2
Brunk, E.3
Mih, N.4
Sastry, A.5
King, Z.6
-
22
-
-
80555140075
-
Scikit-learn: Machine learning in Python
-
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al. Scikit-learn: Machine learning in Python. J Mach Learn Res. 2011; 12:2825–30.
-
(2011)
J Mach Learn Res
, vol.12
, pp. 2825-2830
-
-
Pedregosa, F.1
Varoquaux, G.2
Gramfort, A.3
Michel, V.4
Thirion, B.5
Grisel, O.6
-
24
-
-
84978978745
-
Keras: Deep learning library for python. Convnets, recurrent neural networks, and more. Runs on theano and tensorflow
-
Chollet F. Keras: Deep learning library for python. convnets, recurrent neural networks, and more. runs on theano and tensorflow. GitHub Repos. https://github.com/keras-team/keras. 2015.
-
(2015)
GitHub Repos
-
-
Chollet, F.1
-
26
-
-
34247493236
-
Matplotlib: A 2D graphics environment
-
Hunter JD. Matplotlib: A 2D graphics environment. Comput Sci Eng. 2007; 9(3):90–5.
-
(2007)
Comput Sci Eng
, vol.9
, Issue.3
, pp. 90-95
-
-
Hunter, J.D.1
|