Pinboard (Vaguery)

Pinboard (Vaguery) https://pinboard.in/u:Vaguery/public/ recent bookmarks from Vaguery DefensePredictor: A machine learning model to discover prokaryotic immune systems | Science 2026-04-26T12:32:02+00:00 https://www.science.org/doi/10.1126/science.adv7924 Vaguery structural-biology machine-learning bioinformatics indistinguishable-from-magic learning-from-data to-understand https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d94701a9a214/ A bacterial host factor confines phage localization for excluding the infected compartment through cell division - PubMed 2025-08-09T21:01:11+00:00 https://pubmed.ncbi.nlm.nih.gov/40644298/ Vaguery an-extra-billion-years-can't-hurt structural-biology biology evolutionary-biology physiology life-finds-a-way it's-a-prokaryotic-world-we-just-here-for-the-ride to-write-about bacteria-are-alien-but-from-here https://pinboard.in/ https://pinboard.in/u:Vaguery/b:aad9bce074ce/ Site-saturation mutagenesis of 500 human protein domains | Nature 2025-04-12T13:22:20+00:00 https://www.nature.com/articles/s41586-024-08370-4 Vaguery structural-biology biochemistry molecular-biology impressive looking-to-see neural-networks protein-folding to-write-about evolutionary-biology variation-as-a-source-of-innovation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:604c7c235a9a/ [2301.01929] Two-dimensional tile displacement can simulate cellular automata 2024-07-05T19:02:54+00:00 https://arxiv.org/abs/2301.01929 Vaguery nanotechnology DNA-computing indistinguishable-from-magic cellular-automata everything-looks-like-a-nail-made-of-DNA to-write-about nonlinear-dynamics structural-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:48db3c7121ab/ [1907.13371] Proteins: the physics of amorphous evolving matter 2022-03-10T17:11:41+00:00 https://arxiv.org/abs/1907.13371 Vaguery structural-biology review everything-is-physics-again complexology oversimplifications-as-a-route-to-papers https://pinboard.in/ https://pinboard.in/u:Vaguery/b:df77874dd62d/ [1804.05003] Higher order molecular organisation as a source of biological function 2022-02-05T13:33:25+00:00 https://arxiv.org/abs/1804.05003 Vaguery structural-biology systems-biology rather-interesting hypergraphs interaction-graphs bioinformatics structure-function-relations consider:components-in-Push to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:06c5ffeda0b0/ Some Proteins Change Their Folds to Perform Different Jobs | Quanta Magazine 2022-01-20T16:29:55+00:00 https://www.quantamagazine.org/metamorphic-proteins-change-their-folds-for-different-jobs-20210203/ Vaguery structural-biology protein-folding biological-engineering multitask-learning rather-interesting examples https://pinboard.in/ https://pinboard.in/u:Vaguery/b:b97926810368/ Predicting improved protein conformations with a temporal deep recurrent neural network | bioRxiv 2021-06-04T11:19:21+00:00 https://www.biorxiv.org/content/10.1101/275008v1?rss=1 Vaguery protein-folding structural-biology machine-learning recurrent-neural-network deep-learning rather-interesting dynamical-systems to-simulate to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:82ac88eb634f/ RNA polymerase organizes into distinct spatial clusters independent of ribosomal RNA transcription in E. coli | bioRxiv 2020-07-11T18:58:21+00:00 https://www.biorxiv.org/content/10.1101/320481v1?rss=1 Vaguery cell-biology structural-biology ultrastructure supramolecular-complexes cytoskeleton but-in-bacteria??? it's-more-complicated-than-you-think https://pinboard.in/ https://pinboard.in/u:Vaguery/b:b2578693849a/ DR. HERBERT H. TSANG - http://www.herberttsang.org 2020-02-09T01:14:49+00:00 http://htsang.wikidot.com/research Vaguery structural-biology polymer-folding biochemistry biophysics simulation metaheuristics energy-landscapes rather-interesting to-write-about to-simulate to-visualize https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d531cf9636cd/ Short How-To guides — GROMACS 2019 documentation 2020-02-09T01:06:09+00:00 http://manual.gromacs.org/documentation/2019/how-to/index.html Vaguery structural-biology simulation software open-source rather-interesting to-simulate to-write-about consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:9395b17ef4db/ [1803.07114] Slipknotting in Random Diagrams 2020-02-09T00:45:31+00:00 https://arxiv.org/abs/1803.07114 Vaguery knot-theory combinatorics sampling random-walks structural-biology rather-interesting theoretical-biology to-simulate to-write-about consider:representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:6e72fdda6ed0/ [2001.11709] Gaussian Random Embeddings of Multigraphs 2020-02-05T12:22:13+00:00 https://arxiv.org/abs/2001.11709 Vaguery structural-biology probability-theory random-walks rather-interesting to-simulate constraint-satisfaction polymers to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8473fce4e2d9/ [1806.03333] The rainbow-spectrum of RNA secondary structures 2020-01-10T21:01:53+00:00 https://arxiv.org/abs/1806.03333 Vaguery structural-biology RNA-folding hey-I-know-this-guy molecular-design simulation rather-interesting feature-construction to-write-about to-simulate consider:extreme-cases consider:feature-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:a438e8d14c51/ [1705.00721] Single microtubules and small networks become significantly stiffer on short time-scales upon mechanical stimulation 2019-06-12T13:50:33+00:00 https://arxiv.org/abs/1705.00721 Vaguery phrasing! biophysics cytoskeleton microtubules structural-biology nanotechnology rather-interesting experiment looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:c7766fc0c267/ [1608.03145] Physical model of the genotype-to-phenotype map of proteins 2019-04-24T15:24:51+00:00 https://arxiv.org/abs/1608.03145 Vaguery complexology rather-interesting theoretical-biology abstract-models combinatorics bioinformatics structural-biology structure-function-cartoons to-write-about to-simulate lattice-polymers https://pinboard.in/ https://pinboard.in/u:Vaguery/b:63c4d1b88c21/ [1904.04610] Buckling Soft Tensegrities: Fickle Elasticity and Configurational Switching in Living Cells 2019-04-24T15:14:58+00:00 https://arxiv.org/abs/1904.04610 Vaguery theoretical-biology cell-biology structural-biology tensegrity statics dynamics mechanical-engineering mechanical-design rather-interesting to-write-about to-do to-simulate consider:genetic-programming cytoskeleton https://pinboard.in/ https://pinboard.in/u:Vaguery/b:0275e9f42a66/ [1610.07277] Rapid calculation of side chain packing and free energy with applications to protein molecular dynamics 2017-10-12T10:56:57+00:00 https://arxiv.org/abs/1610.07277 Vaguery structural-biology approximation heuristics algorithms protein-folding to-write-about nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:afdc2b1f0a08/ [1109.6459] Folding Kinetics of a Polymer 2017-09-25T11:40:12+00:00 https://arxiv.org/abs/1109.6459 Vaguery lattice-proteins biophysics structural-biology simulation energy-landscapes to-write-about rather-interesting feature-construction https://pinboard.in/ https://pinboard.in/u:Vaguery/b:87cd953887c9/ [1702.01994] Polyomino Models of Surface Supramolecular Assembly: Design Constraints and Structural Selectivity 2017-09-23T12:01:03+00:00 https://arxiv.org/abs/1702.01994 Vaguery tiling supramolecular-complexes biological-engineering rather-interesting to-write-about energy-landscapes self-assembly molecular-design structural-biology nanotechnology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d7c71fe82a17/ [1506.08747] Faceted particles formed by the frustrated packing of anisotropic colloids on curved surfaces 2017-01-04T13:07:47+00:00 https://arxiv.org/abs/1506.08747 Vaguery self-assembly rather-interesting nanotechnology packing structural-biology engineering-design simulation to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:875cbef2530e/ [1608.06971] Protein Collapse is Encoded in the Folded State Architecture 2016-12-31T11:50:08+00:00 https://arxiv.org/abs/1608.06971 Vaguery structural-biology protein-folding rather-interesting bioinformatics theoretical-biology self-organization engineering-design dynamical-systems https://pinboard.in/ https://pinboard.in/u:Vaguery/b:81ce4c9f7934/ [1611.00842] Symmetry and size of membrane protein polyhedral nanoparticles 2016-12-28T12:02:14+00:00 https://arxiv.org/abs/1611.00842 Vaguery packing engineering-design rather-interesting structural-biology nanotechnology nudge-targets consider:feature-discovery consider:classification https://pinboard.in/ https://pinboard.in/u:Vaguery/b:9fd5c30c80a3/ Exploring the mutational robustness of nucleic acids by searching genotype neighbourhoods in sequence space | bioRxiv 2016-12-17T13:53:57+00:00 http://biorxiv.org/content/early/2016/12/03/091389?rss=1%2522 Vaguery biophysics structural-biology fitness-landscapes combinatorial-libraries aptamers rather-interesting to-write-about experiment https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f84e913f3f8f/ Chromatin structure shapes the search process of transcription factors | bioRxiv 2016-05-01T11:57:47+00:00 http://biorxiv.org/content/early/2016/04/25/050146?rss=1%2522 Vaguery structural-biology molecular-design molecular-biology systems-biology bioinformatics it's-more-complicated-than-you-think https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f151d98280fe/ [1511.01848] Binding of bivalent transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and domains 2016-03-26T22:15:09+00:00 http://arxiv.org/abs/1511.01848 Vaguery structural-biology simulation macromolecular-complexes cell-biology rather-interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cf9efa46ddc2/ [1511.00139] Chaos of Protein Folding 2016-03-26T20:51:51+00:00 http://arxiv.org/abs/1511.00139 Vaguery protein-folding Devaney-Model theoretical-biology structural-biology nudge-targets consider:representation consider:looking-to-see metaheuristics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:01bc08b528b6/ [1501.03971] Bayesian protein structure alignment 2016-02-27T21:43:28+00:00 http://arxiv.org/abs/1501.03971 Vaguery biochemistry structural-biology protein-folding bioinformatics algorithms machine-learning statistics metrics nudge-targets consider:distance-measure https://pinboard.in/ https://pinboard.in/u:Vaguery/b:eefeff02cf1a/ [1512.00268] Chromatin assortativity: integrating epigenomic data and 3D genomic structure 2016-02-25T11:23:58+00:00 http://arxiv.org/abs/1512.00268 Vaguery bioinformatics structural-biology it's-more-complicated-than-you-think supramolecular-complex cell-biology molecular-machinery experiment https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d7eadedfcdd2/ [1509.03434] Improving protein threading accuracy via combining local and global potential using TreeCRF model 2015-12-25T17:11:31+00:00 http://arxiv.org/abs/1509.03434 Vaguery structural-biology biophysics protein-folding models optimization algorithms representation nudge-targets bioinformatics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ad99a83404f6/ [1507.08335] Dissecting the roles of local packing density and longer-range effects in protein sequence evolution 2015-08-07T11:19:19+00:00 http://arxiv.org/abs/1507.08335 Vaguery biophysics structural-biology theoretical-biology elegant-demonstrations it's-crowded-in-there complexology models-and-modes https://pinboard.in/ https://pinboard.in/u:Vaguery/b:700a45381acb/ [1412.3138] Computational Protein Design Using AND/OR Branch-and-Bound Search 2015-07-25T11:29:08+00:00 http://arxiv.org/abs/1412.3138 Vaguery structural-biology biochemistry constraint-satisfaction biological-engineering engineering-design nudge-targets consider:rediscovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:fcb821ffbd3e/ [1410.4465] On the abundance of intrinsically disordered proteins in the human proteome and its relation to diseases: there is no enrichment 2015-03-15T20:39:42+00:00 http://arxiv.org/abs/1410.4465 Vaguery bioinformatics biochemistry structural-biology protein-folding Thom-LaBean's-thesis it's-more-complicated-than-you-think Oh Science. https://pinboard.in/ https://pinboard.in/u:Vaguery/b:e941d1fa5934/ [1501.04071] Structures of Spherical Viral Capsids as Quasicrystalline Tilings 2015-02-02T18:22:31+00:00 http://arxiv.org/abs/1501.04071 Vaguery geometry structural-biology quasicrystals tiling stamp-collecting nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:50e41de9cec1/ [1410.4530] Fatigueless response of spider draglines in cyclic torsion facilitated by reversible molecular deformation 2014-12-06T17:13:09+00:00 http://arxiv.org/abs/1410.4530 Vaguery materials-science biological-engineering spiders-rock biochemistry structural-biology mechanical-engineering https://pinboard.in/ https://pinboard.in/u:Vaguery/b:87ddee18247e/ [1403.2269] Virus Assembly on a Membrane is Facilitated by Membrane Microdomains 2014-04-20T10:28:46+00:00 http://arxiv.org/abs/1403.2269 Vaguery structural-biology simulation membrane-biochemistry self-assembly molecular-design molecular-machinery well-duh it's-crowded-inside-a-cell https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f4c5e15ddc07/ [1312.4146] Unfolding kinetics of periodic DNA hairpins 2014-01-17T14:57:29+00:00 http://arxiv.org/abs/1312.4146 Vaguery structural-biology molecular-machinery experiment modeling DNA biochemistry https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cd0bd3a00371/ [1311.3573] Improved design and screening of high bioactivity peptides for drug discovery 2013-12-16T23:16:06+00:00 http://arxiv.org/abs/1311.3573 Vaguery biological-engineering structural-biology systems-biology combinatorial-chemistry bioinformatics at-least-somebody-did-it-finally hey-that's-my-Penn-thesis (fifteen-years-later) https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ba1e928fd825/ [1310.7249] A Spatial Simulation Approach to Account for Protein Structure When Identifying Non-Random Somatic Mutations 2013-12-05T12:50:47+00:00 http://arxiv.org/abs/1310.7249 Vaguery structural-biology biophysics bioinformatics I-thought-Alan-Perelson-did-this-years-ago https://pinboard.in/ https://pinboard.in/u:Vaguery/b:18f8659471df/ [1310.4309] Optimizing water permeability through the hourglass shape of aquaporins 2013-12-04T23:11:35+00:00 http://arxiv.org/abs/1310.4309 Vaguery molecular-design molecular-machinery biological-engineering structural-biology engineering-design https://pinboard.in/ https://pinboard.in/u:Vaguery/b:b530f83e2d6e/ [1310.3185] Optimization of collective enzyme activity via spatial localization 2013-12-04T21:33:15+00:00 http://arxiv.org/abs/1310.3185 Vaguery structural-biology systems-biology space-matters departures-from-the-ideal molecular-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d3a2dfd26eeb/ [1311.4514] The importance of crowding in signaling, genetic, and metabolic networks 2013-12-04T21:31:10+00:00 http://arxiv.org/abs/1311.4514 Vaguery systems-biology structural-biology molecular-machinery dynamical-systems space-matters simulation departures-from-the-ideal interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f5cfd1d5738f/ [1310.6741] Design principles governing the motility of myosin V 2013-11-21T13:09:19+00:00 http://arxiv.org/abs/1310.6741 Vaguery biophysics structural-biology cytoskeleton biological-engineering experiment https://pinboard.in/ https://pinboard.in/u:Vaguery/b:32a9a1ded380/ [1310.1403] Sequence-Structure Relationship in Proteins: a Computational Analysis of Proteins that Differ in Sequence but Share the Same Fold 2013-11-16T19:56:16+00:00 http://arxiv.org/abs/1310.1403 Vaguery structural-biology protein-folding biological-engineering biophysics interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f6a4059c8d99/ [1310.4223] Exact Learning of RNA Energy Parameters From Structure 2013-11-03T13:36:47+00:00 http://arxiv.org/abs/1310.4223 Vaguery learning-by-watching structural-biology nudge-targets algorithms https://pinboard.in/ https://pinboard.in/u:Vaguery/b:fc85db7f46c4/ [1310.5778] Interplay between single-stranded binding proteins on RNA secondary structure 2013-11-03T13:23:36+00:00 http://arxiv.org/abs/1310.5778 Vaguery RNA structural-biology molecular-biology molecular-machinery bioinformatics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4857b22685c7/ [1310.1579] Distribution of lifetimes of kinetochore-microtubule attachments:interplay of energy landscape, molecular motors and microtubule (de-)polymerization 2013-10-18T12:27:35+00:00 http://arxiv.org/abs/1310.1579 Vaguery structural-biology cellular-biology simulation molecular-machinery cell-physiology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d7548cf5d108/ [1309.7694] Self Organizing Maps to efficiently cluster and functionally interpret protein conformational ensembles 2013-10-06T13:20:50+00:00 http://arxiv.org/abs/1309.7694 Vaguery SOMs protein-folding structural-biology biophysics metaheuristics feature-extraction clustering https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cdf3f860bb4c/ [1308.6510] A perturbation density functional theory for the competition between inter and intramolecular association 2013-08-31T20:44:12+00:00 http://arxiv.org/abs/1308.6510 Vaguery biophysics simulation polymer-chemistry about-damned-time structural-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:38359628df84/ [1307.1009] Systems Biophysics of Gene Expression 2013-07-21T14:30:23+00:00 http://arxiv.org/abs/1307.1009 Vaguery systems-biology structural-biology sittin-in-a-tree https://pinboard.in/ https://pinboard.in/u:Vaguery/b:c65733ca7906/ [1306.2852] Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space 2013-06-17T12:28:07+00:00 http://arxiv.org/abs/1306.2852 Vaguery structural-biology protein-folding energy-landscapes algorithms heuristics tiling interesting nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:118950cd383b/ [1305.6096] A Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision 2013-06-17T12:20:18+00:00 http://arxiv.org/abs/1305.6096 Vaguery biophysics simulation structural-biology nudge-targets physics monte-carlo-modeling algorithms https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d0936f6da268/ [1304.7241] pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study 2013-04-30T21:56:20+00:00 http://arxiv.org/abs/1304.7241 Vaguery biochemistry protein-folding structural-biology engineering-design biological-engineering nudge-targets simulation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8e7ba4a2acc9/ [1212.4312] pH-dependent coarse-grained model of peptides 2013-04-30T21:55:33+00:00 http://arxiv.org/abs/1212.4312 Vaguery structural-biology protein-folding biochemistry models simulation interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8d8919003693/ [1303.2543] Estimation of Persistence Lengths of Semiflexible Polymers: Insight from Simulations 2013-04-25T11:18:13+00:00 http://arxiv.org/abs/1303.2543 Vaguery structural-biology simulation experiment nudge-targets higher-order-predictions aggregation-heuristic https://pinboard.in/ https://pinboard.in/u:Vaguery/b:64e7a48e1f62/ [1301.4092] Encounter dynamics of a small target by a polymer diffusing in a confined domain 2013-04-25T11:15:42+00:00 http://arxiv.org/abs/1301.4092 Vaguery structural-biology simulation what-happens-if-project molecular-crowding nudge-targets parameter-tuning benchmarking https://pinboard.in/ https://pinboard.in/u:Vaguery/b:03502be8630d/ [1303.6231] From mechanical folding trajectories to intrinsic energy landscapes of biopolymers 2013-04-21T15:09:06+00:00 http://arxiv.org/abs/1303.6231 Vaguery structural-biology biological-engineering experiment energy-landscapes protein-folding https://pinboard.in/ https://pinboard.in/u:Vaguery/b:651b230099ee/ [1304.3704] Pearls Are Self-Organized Natural Ratchets 2013-04-16T12:09:50+00:00 http://arxiv.org/abs/1304.3704 Vaguery via:cshalizi self-organization biological-engineering biomaterials structural-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:3febfc1bf268/ [1209.6379] Crowding induced entropy-enthalpy compensation in protein association equilibria 2013-04-14T12:00:09+00:00 http://arxiv.org/abs/1209.6379 Vaguery simulation molecular-machinery structural-biology biophysics macromolecules nudge-targets experiment https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d095d98ce5d0/ [1303.5889] A Graph Theoretic Approach to Utilizing Protein Structure to Identify Non-Random Somatic Mutations 2013-04-08T20:24:09+00:00 http://arxiv.org/abs/1303.5889 Vaguery structural-biology bioinformatics genetics graph-theory algorithms heuristics nudge-targets cancer https://pinboard.in/ https://pinboard.in/u:Vaguery/b:bc1b5c4b2e0d/ [1303.3898] Crumpled globule possesses the properties of molecular machines 2013-03-30T14:09:53+00:00 http://arxiv.org/abs/1303.3898 Vaguery molecular-design molecular-machinery structural-biology energy-landscapes protein-folding nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d43fda22c6ea/ [1211.6493] RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity 2013-03-20T21:09:18+00:00 http://arxiv.org/abs/1211.6493 Vaguery structural-biology bioinformatics macromolecules simulation control-structures emergent-design nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:5ed1a5d25fe2/ [1003.2811] Refining the Protein-Protein Interactome using Gene Expression Data 2013-03-10T22:59:58+00:00 http://arxiv.org/abs/1003.2811 Vaguery protein–protein-iteraction contact-maps GWAS structural-biology systems-biology nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:773f7caa9177/ [1211.0662] Hidden Complexity in the Isomerization Dynamics of Holliday Junctions 2013-03-06T19:06:36+00:00 http://arxiv.org/abs/1211.0662 Vaguery molecular-design molecular-machinery biochemistry experiment protein-folding structural-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:95b009c64a0f/ [1211.1281] Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models 2013-02-03T14:15:03+00:00 http://arxiv.org/abs/1211.1281 Vaguery structural-biology multimodal-modeling inference domain-specific-knowledge nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:c7fbd7ea9e00/ [1207.3289] The Origin, Evolution and Development of Bilateral Symmetry in Multicellular Organisms 2012-08-04T12:29:43+00:00 http://arxiv.org/abs/1207.3289 Vaguery evo-devo artificial-life simulation structural-biology complexology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:40cc1da713b3/ [1206.3789] Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots 2012-07-02T22:27:51+00:00 http://arxiv.org/abs/1206.3789 Vaguery RNA structural-biology folding bioinformatics algorithms nudge-targets modeling https://pinboard.in/ https://pinboard.in/u:Vaguery/b:5a557133a984/ [1206.1098] The interplay of intrinsic and extrinsic bounded noises in genetic networks 2012-06-08T15:09:03+00:00 http://arxiv.org/abs/1206.1098 Vaguery biochemistry structural-biology reaction-networks biological-engineering noise its-complicated-inside-a-cell simulation nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:5b5907dd51b0/ [1206.0766] Why Optimal States Recruit Fewer Reactions in Metabolic Networks 2012-06-07T11:36:23+00:00 http://arxiv.org/abs/1206.0766 Vaguery network-theory biological-engineering metabolic-networks systems-biology engineering-design structural-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:39a7aeaeefae/ [1203.3353] Solving Structure with Sparse, Randomly-Oriented X-ray Data 2012-03-18T10:21:56+00:00 http://arxiv.org/abs/1203.3353 Vaguery structural-biology image-analysis crystallography algorithms inverse-problems nudge-targets statistics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:66baf5a1cb02/