A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products
Raphael Reher
Hyun Woo Kim
Chen Zhang
Huanru Henry Mao
Mingxun Wang
Louis-Félix Nothias
Andres Mauricio Caraballo-Rodriguez
Evgenia Glukhov
Bahar Teke
Tiago Leao
Kelsey L. Alexander
Brendan M. Duggan
Ezra L. Van Everbroeck
Pieter C. Dorrestein
Garrison W. Cottrell
William H. Gerwick
Journal of the American Chemical Society, 2020-2-11
Raphael Reher
Reher Raphael
ORCID: 0000-0002-5858-1173
A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria
10.3390/md19010020
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
10.1038/s41587-020-0740-8
Heterologous Expression of Cryptomaldamide in a Cyanobacterial Host
10.1021/acssynbio.0c00431
Cell‐permeable high‐affinity tracers for G
q
proteins provide structural insights, reveal distinct binding kinetics and identify small molecule inhibitors
10.1111/bph.14960
A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products
10.1021/jacs.9b13786
A community resource for paired genomic and metabolomic data mining
10.1038/s41589-020-00724-z
Design of Gallinamide A Analogs as Potent Inhibitors of the Cysteine Proteases Human Cathepsin L and Trypanosoma cruzi Cruzain
10.1021/acs.jmedchem.9b00294
Structural and Dynamical Basis of G Protein Inhibition by YM-254890 and FR900359: An Inhibitor in Action
10.1021/acs.jcim.9b00433
Direct targeting of Gαq and Gα11 oncoproteins in cancer cells
10.1126/scisignal.aau5948
Rational design of a heterotrimeric G protein α subunit with artificial inhibitor sensitivity
10.1074/jbc.ra118.007250
Heterologous Expression, Biosynthetic Studies, and Ecological Function of the Selective Gq‐Signaling Inhibitor FR900359
10.1002/anie.201707996
Applying Molecular Networking for the Detection of Natural Sources and Analogues of the Selective Gq Protein Inhibitor FR900359
10.1021/acs.jnatprod.8b00222
Deciphering Specificity Determinants for FR900359-Derived Gqα Inhibitors Based on Computational and Structure-Activity Studies
10.1002/cmdc.201800304
Lack of beta-arrestin signaling in the absence of active G proteins
10.1038/s41467-017-02661-3
The genome analysis of C
andidatus
Burkholderia crenata reveals that secondary metabolism may be a key function of the A
rdisia crenata
leaf nodule symbiosis
10.1111/1462-2920.13184
Brendan Duggan
Duggan Brendan
/ Brendan M. Duggan
ORCID: 0000-0002-7034-8374
Divergent biosynthesis yields a cytotoxic aminomalonate-containing precolibactin
10.1038/nchembio.2157
Three-dimensional Structure in Solution of the Calcium Channel Blocker ω-Conotoxin
10.1006/jmbi.1993.1595
The Arginine-Rich RNA-Binding Motif of HIV-1 Rev Is Intrinsically Disordered and Folds upon RRE Binding
10.1016/j.bpj.2013.07.022
1H, 13C and 15N assignments of the holo-acyl carrier protein of Pseudomonas aeruginosa
10.1007/s12104-012-9415-9
Microbial metabolic exchange in 3D
10.1038/ismej.2012.155
NMR assignments of the N-terminal domain of Nephila clavipes spidroin 1
10.1007/s12104-010-9284-z
The Alga Ochromonas danica Produces Bromosulfolipids
10.1021/acs.orglett.6b00230
Bioactivity-Guided Genome Mining Reveals the Lomaiviticin Biosynthetic Gene Cluster in Salinispora tropica
10.1002/cbic.201300147
Synthesis and structural characterisation of analogues of the potassium channel blocker charybdotoxin
10.1016/0167-4838(95)00182-4
Catalytic detoxification of nerve agent and pesticide organophosphates by butyrylcholinesterase assisted with non-pyridinium oximes
10.1042/bj20121612
Efficient red light photo-uncaging of active molecules in water upon assembly into nanoparticles
10.1039/c5sc03717d
Inherent flexibility in a potent inhibitor of blood coagulation, recombinant nematode anticoagulant protein c2
10.1046/j.1432-1327.1999.00781.x
Ultra-high resolution band-selective HSQC for nanomole-scale identification of chlorine-substituted13C in natural products drug discovery
10.1002/mrc.4415
A Distal Mutation Perturbs Dynamic Amino Acid Networks in Dihydrofolate Reductase
10.1021/bi400563c
Detailed Analysis of (−)-Palmyrolide A and Some Synthetic Derivatives as Voltage-Gated Sodium Channel Antagonists
10.1021/np500644k
Conformational dynamics of thyroid hormones by variable temperature nuclear magnetic resonance: The role of side chain rotations and cisoid/transoid interconversions
10.1021/jm9606610
Contribution of increased length and intact capping sequences to the conformational preference for helix in a 31-residue peptide from the C terminus of myohemerythrin
10.1021/bi970038x
1 H and 13 C NMR Relaxation Studies of Molecular Dynamics of the Thyroid Hormones Thyroxine, 3,5,3‘-Triiodothyronine, and 3,5-Diiodothyronine †
10.1021/jm960231+
MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus
10.1038/ja.2013.99
Mollenynes B-E from the Marine Sponge Spirastrella mollis. Band-Selective Heteronuclear Single Quantum Coherence for Discrimination of Bromo-Chloro Regioisomerism in Natural Products
10.1021/jacs.5b07858
Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria
10.1021/acs.jnatprod.5b00301
Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research
10.1038/s41598-017-13923-x
Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules
10.1073/pnas.1315492110
Messenger RNAs under differential translational control in Ki-ras-transformed cells
10.1158/1541-7786.MCR-04-0187
SANE (Structure Assisted NOE Evaluation): An automated model-based approach for NOE assignment
10.1023/A:1011227824104
Potential bias in NMR relaxation data introduced by peak intensity analysis and curve fitting methods
10.1023/A:1011966718826
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides
10.1038/nmicrobiol.2016.197
MS/MS networking guided analysis of molecule and gene cluster families
10.1073/pnas.1303471110
Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae
10.7554/eLife.24214
Interkingdom metabolic transformations captured by microbial imaging mass spectrometry
10.1073/pnas.1206855109
Identification of a 3-alkylpyridinium compound from the red sea sponge Amphimedon chloros with in vitro inhibitory activity against the West Nile Virus NS3 protease
10.3390/molecules23061472
Toward Expanded Diversity of Host–Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives
10.1007/s10953-018-0769-1
Facile synthesis of a diverse library of mono-3-substituted β-cyclodextrin analogues
10.1080/10610278.2018.1562191
Lepadins I–K, 3-O-(3′-Methylthio)acryloyloxy-decahydroquinoline Esters from a Bahamian Ascidian Didemnum sp. Assignment of Absolute Stereostructures
10.1021/acs.joc.8b01609
Editorial to the Special Issue—“Technology for Natural Products Research”
10.3390/molecules25020327
The Pierced Lasso Topology Leptin has a Bolt on Dynamic Domain Composed by the Disordered Loops I and III
10.1016/j.jmb.2020.01.035
Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research
10.1038/s41598-020-60108-0
Commensal Oral Rothia mucilaginosa Produces Enterobactin, a Metal-Chelating Siderophore
10.1128/mSystems.00161-20
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides
10.1038/nmicrobiol.2017.10
Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds
10.1007/s10822-020-00350-w
A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products
10.1021/jacs.9b13786
Tutuilamides A-C: Vinyl-Chloride-Containing Cyclodepsipeptides from Marine Cyanobacteria with Potent Elastase Inhibitory Properties
10.1021/acschembio.9b00992
Searching for Small Molecules with an Atomic Sort
10.1002/anie.201911862
Searching for Small Molecules with an Atomic Sort
10.1002/anie.202000826
Synthesis, Pharmacological Characterization, and Structure-Activity Relationships of Noncanonical Selective Agonists for α7 nAChRs
10.1021/acs.jmedchem.9b01467
Chen Zhang
Zhang Chen
ORCID: 0000-0003-4805-0392
Laucysteinamide A, a Hybrid PKS/NRPS Metabolite from a Saipan Cyanobacterium, cf. Caldora penicillata
10.3390/md15040121
Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research
10.1038/s41598-017-13923-x
Dual-Functionalized Theranostic Nanocarriers
10.1021/acsami.6b02761
Synthesis of nano-bowls with a Janus template
10.1039/c4nr05153j
Magnetically-responsive silica-gold nanobowls for targeted delivery and SERS-based sensing
10.1039/c6nr02445a
Bastimolide A, a Potent Antimalarial Polyhydroxy Macrolide from the Marine Cyanobacterium Okeania hirsuta
10.1021/acs.joc.5b01264
Designing hollow nano gold golf balls
10.1021/am502519x
Carboxylated nanodiamonds inhibit γ-irradiation damage of human red blood cells
10.1039/c5nr06789h
Energetically biased DNA motor containing a thermodynamically stable partial strand displacement state
10.1021/la503711g
Asymmetric Colloidal Janus Particle Formation Is Core-Size-Dependent
10.1021/acs.langmuir.5b01499
The Samholides, Swinholide Related Metabolites from a Marine Cyanobacterium cf. Phormidium sp.
10.1021/acs.joc.8b00028
Pagoamide A, a Cyclic Depsipeptide Isolated from a Cultured Marine Chlorophyte, Derbesia sp., Using MS/MS-Based Molecular Networking
10.1021/acs.jnatprod.9b01019
A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products
10.1021/jacs.9b13786
Author Correction: Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research
10.1038/s41598-020-60108-0
Total Synthesis of Laucysteinamide A, a Monomeric Congener of Somocystinamide A
10.1021/acs.jnatprod.0c01317
Garrison Cottrell
Cottrell Garrison
ORCID: 0000-0001-7538-1715
Interhemispheric connectivity endures across species: An allometric exposé on the corpus callosum
10.1101/2021.01.10.426155
Lexical ambiguity resolution: Perspective from psycholinguistics, neuropsychology and artificial intelligence
10.1016/B978-0-08-051013-2.50022
A model of lexical access of ambiguous words
10.1016/B978-0-08-051013-2.50011-2
Neurocomputational Models of Face Processing
10.1093/oxfordhb/9780199559053.013.0021
Modeling Perceptual Expertise
10.1093/acprof:oso/9780195309607.003.0008
Churchland on connectionism
10.1017/CBO9781139165280.006
SUN: A Bayesian framework for saliency using natural statistics
10.1167/8.7.32
Autofocus layer for semantic segmentation
10.1007/978-3-030-00931-1_69
Hierarchical Cellular Automata for Visual Saliency
10.1007/s11263-017-1062-2
Parallel Dog Processing: Explorations in the Nanostructure of Dognition
10.1080/09540098908915636
Substructure vibration NARX neural network approach for statistical damage inference
10.1061/(ASCE)EM.1943-7889.0000363
Connectionist models of face processing: A survey
10.1016/0031-3203(94)90006-X
Speech recognition and multi-speaker diarization of long conversations
10.21437/Interspeech.2020-3039
Predicting an observer's task using multi-fixation pattern analysis
10.1145/2578153.2578208
Hemispheric asymmetry in perception: A differential encoding account
10.1162/jocn_a_00377
Learning Simple Arithmetic Procedures
10.1080/09540099308915684
NPClassifier: A deep neural network-based structural classification tool for natural products
10.26434/chemrxiv.12885494.v1
Acquiring the Mapping from Meaning to Sounds
10.1080/09540099408915731
Early lateralization and orientation tuning for face, word, and object processing in the visual cortex
10.1016/j.neuroimage.2003.07.010
Latent Semantic Indexing is an optimal special case of multidimensional scaling
10.1145/133160.133191
End-to-End Incomplete Time-Series Modeling from Linear Memory of Latent Variables
10.1109/TCYB.2019.2906426
Color constancy algorithms for object and face recognition
10.1007/978-3-642-17289-2_20
Event-specific image importance
10.1109/CVPR.2016.520
User lenses - achieving 100% precision on frequently asked questions
10.1007/978-3-7091-2490-1_9
Modeling the Sequential Behavior of the Dog: The Second Naïve Dog Physics Manifesto
10.1080/09540099308915695
The roles of visual expertise and visual input in the face inversion effect: Behavioral and neurocomputational evidence
10.1016/j.visres.2007.11.025
Bikers are like tobacco shops, formal dressers are like suits: Recognizing urban tribes with caffe
10.1109/WACV.2015.121
Fusion via a linear combination of scores
10.1023/A:1009980820262
Humour: Approaches to the Inverse Dogmatics Problem: Time for a Return to Localist Networks?
10.1080/09540099308915687
From PDP to NDP through LFG:. The naive dog physics manifesto
10.1016/0378-2166(89)90027-1
Gamma-SLAM: Using stereo vision and variance grid maps for SLAM in unstructured environments
10.1109/ROBOT.2008.4543781
SUN: Top-down saliency using natural statistics
10.1080/13506280902771138
Toward connectionist semantics
10.3115/980304.980318
Phase space learning in an autonomous dynamical neural network
10.1016/j.neucom.2006.04.006
Central and peripheral vision for scene recognition: A neurocomputational modeling exploration
10.1167/17.4.9
Author Correction: Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research (Scientific Reports, (2017), 7, 1, (14243), 10.1038/s41598-017-13923-x)
10.1038/s41598-020-60108-0
Degenerative Grammar: The Story of Outa
10.1080/095400996116983
Prosopagnosia in modular neural network models
10.1016/s0079-6123(08)63073-3
On the Epistemological Status of Dog Breath, or Will the Real Qualia Please Stand Up?: A Reply to Sirloin
10.1080/09540099008915678
Experience matters: Information acquisition optimizes probability gain
10.1177/0956797610372637
Experience with selecting exemplars from clean data
10.1016/0893-6080(95)00099-2
Deep active object recognition by joint label and action prediction
10.1016/j.cviu.2016.10.011
A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products
10.1021/jacs.9b13786
Color-to-grayscale: Does the method matter in image recognition?
10.1371/journal.pone.0029740
Predicting the performance of linearly combined IR systems
10.1145/290941.290991
DynamicRec: A Dynamic Convolutional Network for Next Item Recommendation
10.1145/3340531.3412118
New life for neural networks
10.1126/science.1129813
Empath: A neural network that categorizes facial expressions
10.1162/089892902760807177
Are face and object recognition independent? A neurocomputational modeling exploration
10.1162/jocn_a_00919
Not all visual expertise is holistic, but it may be leftist: The case of Chinese character recognition: Research Article
10.1111/j.1467-9280.2009.02315.x
A dual-stage attention-based recurrent neural network for time series prediction
10.24963/ijcai.2017/366
Visual saliency model for robot cameras
10.1109/ROBOT.2008.4543572
A computational model which learns to selectively attend in category learning
10.1109/DEVLRN.2005.1490981
A connectionist simulation of the empirical acquisition of grammatical relations
10.1007/10719871_12
Evidence and a Computational Explanation of Cultural Differences in Facial Expression Recognition
10.1037/a0020019
A probabilistic model of eye movements in concept formation
10.1016/j.neucom.2006.02.026
Dynamic rate adaptation
10.1007/BF00849055
Organization of face and object recognition in modular neural network models
10.1016/S0893-6080(99)00050-7
A technique for adapting to speech rate
10.1109/NNSP.1993.471850
Robust classification of objects, faces, and flowers using natural image statistics
10.1109/CVPR.2010.5539947
Humans have idiosyncratic and task-specific scanpaths for judging faces
10.1016/j.visres.2015.01.013
Principal components analysis of images via back propagation
10.1117/12.969060
DeePr-ESN: A deep projection-encoding echo-state network
10.1016/j.ins.2019.09.049
Transmitting and decoding facial expressions
10.1111/j.0956-7976.2005.00801.x
Cognitive binding: A computational-modeling analysis of a distinction between implicit and explicit memory
10.1162/jocn.1992.4.3.289
Time-delay neural networks: Representation and induction of finite-state machines
10.1109/72.623208
Programming the User-friendly Dog
10.1080/09540099509696197
Convergence of the visual field split: Hemispheric modeling of face and object recognition
10.1162/jocn.2008.20162
The ventral striatum dissociates information expectation, reward anticipation, and reward receipt
10.1073/pnas.1911778117
Content and cluster analysis: Assessing representational similarity in neural systems
10.1080/09515080050002726
WALKING WALKing walking: Action recognition from action echoes
10.24963/ijcai.2017/342
Observed, executed, and imagined action representations can be decoded from ventral and dorsal areas
10.1093/cercor/bhu110
Optimizing similarity using multi-query relevance feedback
10.1002/(sici)1097-4571(199806)49:8<742::aid-asi8>3.0.co;2-h
Looking around the backyard helps to recognize faces and digits
10.1109/CVPR.2008.4587631
Learning grammatical structure with Echo State Networks
10.1016/j.neunet.2007.04.013
New Directions in Connectionist Dog Modeling
10.1080/09540099108946574
An examination of simultaneous lineup identification decision processes using eye tracking
10.1002/acp.1711
Early selection of diagnostic facial information in the human visual cortex
10.1016/j.visres.2005.09.016
What evidence supports special processing for faces? A cautionary tale for fMRI interpretation.
10.1162/jocn_a_00448
Two fixations suffice in face recognition
10.1111/j.1467-9280.2008.02191.x
Understanding Dogs and Dognition: A New Foundation for Design
10.1080/09540099008915672
Recognizing and curating photo albums via event-specific image importance
10.5244/c.31.94
Pagoamide A, a Cyclic Depsipeptide Isolated from a Cultured Marine Chlorophyte, Derbesia sp., Using MS/MS-Based Molecular Networking
10.1021/acs.jnatprod.9b01019
Nimble: A kernel density model of saccade-based visual memory
10.1167/8.14.17
Imaging Reveals Synaptic Targets of a Swim-Terminating Neuron in the Leech CNS
10.1523/jneurosci.23-36-11402.2003
Learning in recurrent finite difference networks.
10.1142/S0129065795000184
Image compression within visual system constraints
10.1016/0893-6080(88)90509-6
The Connectionist Air Guitar: A Dream Come True
10.1080/09540098908915651
Function of identified interneurons in the leech elucidated using neural networks trained by back-propagation
10.1038/340468a0
Time series classification with Echo Memory Networks
10.1016/j.neunet.2019.05.008
Understanding Convolution for Semantic Segmentation
10.1109/WACV.2018.00163
Jimi hendrix meets the giant screaming buddha: Recreating the sixties via backpropagation in time
10.1080/09540099208946610
Why is the fusiform face area recruited for novel categories of expertise? A neurocomputational investigation
10.1016/j.brainres.2007.06.079
Research Note: A Hybrid Model of the Intentional Behavior of the Dog
10.1080/09540098908915645
Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research
10.1038/s41598-017-13923-x
Belief tree search for active object recognition
10.1109/IROS.2017.8206290
Behavior recognition via sparse spatio-temporal features
10.1109/VSPETS.2005.1570899
A model of the leech segmental swim central pattern generator
10.1016/S0925-2312(00)00214-9
Triple-shapelet networks for time series classification
10.1109/ICDM.2019.00155
Representing documents using an explicit model of their similarities
10.1002/(SICI)1097-4571(199505)46:4<254::AID-ASI3>3.0.CO;2-S
Gamma-SLAM: Visual SLAM in unstructured environments using variance grid maps
10.1002/rob.20273
Automatic combination of multiple ranked retrieval systems
10.1007/978-1-4471-2099-5_18
Analysis of oscillations in a reciprocally inhibitory network with synaptic depression
10.1162/089976602317250906
Skeleton key: Image captioning by skeleton-Attribute decomposition
10.1109/CVPR.2017.780
Tau Net: A neural network for modeling temporal variability
10.1016/S0925-2312(97)00009-X
Mauricio Caraballo
Caraballo Mauricio
/ Mauricio Caraballo
/ Andres M Caraballo-Rodriguez
ORCID: 0000-0001-5499-2728
Amphotericin B as an inducer of griseofulvin-containing guttate in the endophytic fungus Xylaria cubensis FLe9
10.1007/s00049-017-0243-3
Molecular inter-kingdom interactions of endophytes isolated from Lychnophora ericoides
10.1038/s41598-017-05532-5
Expanding the Chemical Repertoire of the Endophyte Streptomyces albospinus RLe7 Reveals Amphotericin B as an Inducer of a Fungal Phenotype
10.1021/acs.jnatprod.6b00870
Endophytic Actinobacteria from the Brazilian Medicinal PlantLychnophora ericoidesMart. and the Biological Potential of Their Secondary Metabolites
10.1002/cbdv.201500225
Protocol for Community‐created Public MS/MS Reference Spectra Within the Global Natural Products Social Molecular Networking Infrastructure
10.1002/rcm.8725
Mass spectrometry searches using MASST
10.1038/s41587-019-0375-9
Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in Palau
10.1021/acs.jnatprod.9b01128
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
10.1016/j.foodchem.2019.125290
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
10.1038/s41587-019-0209-9
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization
10.1038/s41467-019-09944-x
Propagating annotations of molecular networks using in silico fragmentation
10.1371/journal.pcbi.1006089
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
10.1038/nbt.3597
Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales
10.1016/j.ddmod.2019.08.012
Chemical signaling involved in plant–microbe interactions
10.1039/c7cs00343a
A Convolutional Neural Network-Based Approach for the Rapid Characterization of Molecularly Diverse Natural Products
10.1021/jacs.9b13786
