https://pinboard.in/u:Vaguery/public/ recent bookmarks from Vaguery 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/ 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/ 2021-01-21T21:00:34+00:00 https://arxiv.org/abs/2002.06786 Vaguery strings bioinformatics algorithms rather-interesting hard-problems pattern-matching to-write-about to-simulate consider:representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:9a95cb8f1ca9/ 2020-05-23T13:23:17+00:00 https://arxiv.org/abs/1801.04087 Vaguery gene-regulatory-networks inverse-problems bioinformatics systems-biology rather-interesting modeling to-write-about to-simulate consider:data-quality consider:representation consider:genetic-programming https://pinboard.in/ https://pinboard.in/u:Vaguery/b:3c46f24714c8/ 2020-02-18T22:52:54+00:00 https://www.biorxiv.org/content/10.1101/393835v1 Vaguery bioinformatics systems-biology nonlinear-dynamics machine-learning regularization statistics numerical-methods heuristics to-write-about to-simulate consider:symbolic-regression consider:robustness https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f08dfb1849d5/ 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/ 2019-04-17T10:49:17+00:00 https://arxiv.org/abs/1810.07800 Vaguery discrete-mathematics optimization alignments combinatorics hey-I-know-this-guy bioinformatics rather-interesting formalization to-write-about consider:multiobjective-optimization consider:fitness-landscapes question:transitivity https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cdd8a5b8e59e/ 2019-03-17T12:28:35+00:00 https://www.sciencedirect.com/science/article/pii/S2452310019300022 Vaguery cannot-access dammit fitness-landscapes scanning-mutagenesis bioinformatics theoretical-biology looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ec4a0e226b25/ 2019-02-24T15:29:46+00:00 https://arxiv.org/abs/1711.08477 Vaguery machine-learning bioinformatics hey-I-know-this-guy feature-selection benchmarking epistasis algorithms to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:2c11820a8280/ 2019-02-22T23:08:22+00:00 https://arxiv.org/abs/1804.02045 Vaguery approximation fitness-landscapes dimension-reduction rather-interesting statistics modeling bioinformatics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:319a7d7a9e80/ 2019-02-13T10:43:47+00:00 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411762/ Vaguery via:arthegall bioinformatics clustering visualization data-analysis rather-interesting consider:nonbiological-genomes review https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8e2e925902f0/ 2018-12-28T11:42:59+00:00 https://gcbias.org/2018/03/14/polygenic-scores-and-tea-drinking/ Vaguery genetics bioinformatics GWAS good-example nature-and-nurture-sittin-in-a-tree population-biology cultural-norms https://pinboard.in/ https://pinboard.in/u:Vaguery/b:906b1be19f45/ 2018-05-28T12:03:17+00:00 https://kappalanguage.org/ Vaguery bioinformatics representation hey-I-know-this-guy complexology pattern-discovery rather-interesting to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:2f4be5227079/ 2018-02-27T12:43:44+00:00 http://www.mdpi.com/2073-4425/9/2/61/htm Vaguery GWAS bioinformatics medicine machine-learning epistasis it's-more-complicated-than-you-think https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d478a0f637e2/ 2018-02-25T12:50:22+00:00 https://www.biorxiv.org/content/early/2017/11/25/225003?rss=1 Vaguery origin-of-life bioinformatics exploration exploitation robustness evolutionary-biology self-organization rather-interesting to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:09b654789fc6/ 2018-02-04T13:44:32+00:00 https://arxiv.org/abs/1404.6520 Vaguery diversity population-biology bioinformatics philosophy-of-science algorithms statistics rather-interesting to-write-about to-understand consider:genetic-programming define-your-terms https://pinboard.in/ https://pinboard.in/u:Vaguery/b:c21c80ffcd46/ 2018-02-02T16:46:54+00:00 https://arxiv.org/abs/1611.03144 Vaguery reaction-networks boolean-networks Kauffmania bioinformatics systems-biology rather-interesting nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:828e912cdc36/ 2017-11-12T12:35:05+00:00 https://www.biorxiv.org/content/early/2017/09/25/193599?rss=1 Vaguery epigenetics gene-regulatory-networks bioinformatics theoretical-biology simulation biological-engineering rather-interesting to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:0666921dd3d3/ 2017-10-09T11:33:08+00:00 https://arxiv.org/abs/1709.05701 Vaguery rather-interesting bioinformatics community-detection symbiosis machine-learning to-write-about consider:feature-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f0b72c056f4a/ 2017-10-03T11:01:27+00:00 https://www.biorxiv.org/content/early/2016/08/18/070151?rss=1%2522 Vaguery gene-regulatory-networks bioinformatics systems-biology rather-interesting modeling experiment nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:2f149bc59c46/ 2017-09-26T11:54:18+00:00 https://arxiv.org/abs/1701.08085 Vaguery representation philosophy-of-science theoretical-biology bioinformatics systems-biology modeling to-write-about define-your-terms https://pinboard.in/ https://pinboard.in/u:Vaguery/b:591b903d92f0/ 2017-09-19T11:46:41+00:00 https://arxiv.org/abs/1709.02293 Vaguery image-processing software-development-is-not-programming rather-interesting bioinformatics medinformatics user-experience scaling to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:133bf8473bc9/ 2017-04-30T12:44:39+00:00 https://arxiv.org/abs/1702.01780 Vaguery hey-I-know-this-guy bioinformatics machine-learning meta-optimization workflows framework https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f1ddc6939c05/ 2017-04-30T12:40:00+00:00 https://arxiv.org/abs/1306.5667 Vaguery bioinformatics software-synthesis algorithms genetic-programming hey-I-know-this-guy nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:5ff9a0ec790f/ 2017-04-26T11:37:21+00:00 https://arxiv.org/abs/1704.06530 Vaguery boolean-networks Kauffmania rather-interesting heuristics algorithms bioinformatics systems-biology nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:a806a8f6fa56/ 2017-04-26T10:18:03+00:00 https://arxiv.org/abs/1606.09370 Vaguery text-mining bioinformatics salience-detection algorithms neural-networks nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:acffcca1b7cc/ 2017-04-25T10:11:50+00:00 http://biorxiv.org/content/early/2017/04/13/125542?rss=1 Vaguery bioinformatics visualization representation rather-odd to-understand ultrabubbles https://pinboard.in/ https://pinboard.in/u:Vaguery/b:157d64c026ca/ 2017-04-17T10:35:26+00:00 https://arxiv.org/abs/1608.04048 Vaguery feature-selection data-analysis big-data bioinformatics statistics algorithms to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ef2072225004/ 2017-04-17T10:30:55+00:00 https://arxiv.org/abs/1703.04823 Vaguery machine-learning representation rather-interesting hypergraphs to-write-about nudge-targets consider:representation consider:looking-to-see bioinformatics clustering metrics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d6f591f5708d/ 2017-03-24T22:32:49+00:00 http://biorxiv.org/content/early/2016/05/24/055020?rss=1%2522 Vaguery microbiology bioinformatics microbial-ecology wow indistinguishable-from-magic algorithms to-understand to-learn https://pinboard.in/ https://pinboard.in/u:Vaguery/b:6949e50e44e0/ 2017-03-22T11:53:42+00:00 https://arxiv.org/abs/1511.02393 Vaguery strings bioinformatics search-algorithms algorithms computational-complexity nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:e4f8cfc93713/ 2017-02-27T14:57:21+00:00 http://www.nature.com/nmeth/journal/v12/n3/abs/nmeth.3254.html Vaguery archetypal-analysis clustering bioinformatics systems-biology machine-learning algorithms rather-interesting to-write-about nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cdfd7e23fcd5/ 2017-02-11T15:31:11+00:00 https://arxiv.org/abs/1702.00318 Vaguery combinatorics bioinformatics metaheuristics strings rather-interesting nudge-targets consider:looking-to-see consider:representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:62e2723cdce4/ 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/ 2016-12-25T22:11:09+00:00 https://arxiv.org/abs/1605.02948 Vaguery natural-language-processing bioinformatics topic-modeling machine-learning algorithms nudge-targets consider:feature-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:07802c3a0242/ 2016-10-31T13:08:42+00:00 https://arxiv.org/abs/1605.01639 Vaguery systems-biology reaction-networks bioinformatics simulation theoretical-biology control-theory nonlinear-dynamics rather-interesting nudge-targets consider:feature-discovery consider:simulation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8930897a6abf/ 2016-08-06T13:29:35+00:00 http://arxiv.org/abs/1605.07151 Vaguery bioinformatics combinatorics rather-interesting puzzles algorithms uniqueness nudge-targets consider:rediscovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:93925600eef6/ 2016-07-04T18:04:22+00:00 http://biorxiv.org/content/early/2016/06/21/060111?rss=1%2522 Vaguery bioinformatics algorithms statistics models rather-interesting systems-biology nudge-targets approximation consider:feature-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ff270eb6af8f/ 2016-06-06T10:55:29+00:00 http://biorxiv.org/content/early/2016/05/27/055715?rss=1%2522 Vaguery bioinformatics deep-learning neural-networks machine-learning prediction nudge-targets consider:rediscovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:6d5a8c061369/ 2016-05-28T21:04:34+00:00 http://biorxiv.org/content/early/2016/05/26/055624 Vaguery via:numerous neural-networks inference modeling experiment rather-interesting big-data bioinformatics looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cd7d452bf53f/ 2016-05-16T12:25:04+00:00 http://arxiv.org/abs/1605.03043 Vaguery0 then the solution is unique. This solves a conjecture of Mossel and Ross (Shotgun assembly of labeled graphs, arXiv:1504.07682). ]]> probability-theory proof combinatorics graph-theory bioinformatics rather-interesting nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:e85c734bda20/ 2016-05-13T23:44:27+00:00 http://arxiv.org/abs/1605.01941 Vaguery bioinformatics algorithms DNA-assembly molecular-biology statistics inference nudge-targets consider:performance-measures https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cec42b767669/ 2016-05-08T13:53:08+00:00 http://biorxiv.org/content/early/2016/04/28/050732?rss=1%2522 Vaguery protein-structure biophysics systems-biology machine-learning algorithms rather-interesting bioinformatics nudge-targets consider:feature-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:44fa91e27326/ 2016-05-03T13:08:00+00:00 http://biorxiv.org/content/early/2016/04/26/050187?rss=1%2522 Vaguery95% of all models). Whilst 99.3% of the core reactions were classified as housekeeping also in normal tissues, we identified reactions catalyzed by ARG2, RHAG, SLC6 and SLC16 family gene members, and PTGS1 and PTGS2 as core exclusively in cancer. The remaining 26% of the reactions were contextual reactions. Their inclusion was dependent in one case (GLS2) on the absence of TP53 mutations and in 94.6% of cases on differences in cancer types. This dependency largely resembled differences in expression patterns in the corresponding normal tissues, with some exceptions like the presence of the NANP-encoded reaction in tumors not from the female reproductive system or of the SLC5A9-encoded reaction in kidney-pancreatic-colorectal tumors. In conclusion, tumors expressed a metabolic network virtually overlapping the matched normal tissues, raising the possibility that metabolic reprogramming simply reflects cancer cell plasticity to adapt to varying conditions thanks to redundancy and complexity of the underlying metabolic networks. At the same time, the here uncovered exceptions represent a resource to identify selective liabilities of tumor metabolism. ]]> systems-biology network-theory bioinformatics medical-technology machine-learning feature-extraction nudge-targets consider:feature-discovery classification https://pinboard.in/ https://pinboard.in/u:Vaguery/b:3dcc3f3401d0/ 2016-05-02T10:06:52+00:00 http://biorxiv.org/content/early/2016/04/23/049999?rss=1%2522 Vaguery rather-interesting physiology bioinformatics statistics machine-learning also-not-machine-learning feature-extraction feature-construction nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:55ac7c01d000/ 2016-05-02T10:00:07+00:00 http://biorxiv.org/content/early/2016/04/28/050757?rss=1%2522 Vaguery cell-biology image-processing image-analysis deep-learning bioinformatics rather-interesting nudge-targets consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:7fbb74767e1e/ 2016-05-01T12:50:48+00:00 http://arxiv.org/abs/1604.08354 Vaguery bioinformatics machine-learning systems-biology algorithms prediction nudge-targets consider:feature-discovery consider:representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f945fc799b7b/ 2016-05-01T12:14:42+00:00 http://biorxiv.org/content/early/2016/04/25/049627?rss=1%2522 Vaguery bioinformatics machine-learning gene-regulatory-networks systems-biology engineering-design rather-interesting nudge-targets consider:rediscovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:297d50ef9c6f/ 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/ 2016-03-20T16:40:19+00:00 http://arxiv.org/abs/1510.02356 Vaguery bioinformatics cladistics classification statistics algorithms theoretical-biology nudge-targets consider:alternatives https://pinboard.in/ https://pinboard.in/u:Vaguery/b:19c5dbb24aae/ 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/ 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/ 2016-02-09T17:48:33+00:00 http://arxiv.org/abs/1508.05990 Vaguery reaction-networks dynamical-systems simulation models-and-modes modeling-is-not-mathematics theoretical-biology bioinformatics nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:854bafa52318/ 2015-12-27T21:48:14+00:00 http://arxiv.org/abs/1512.05055 Vaguery gene-regulatory-networks boolean-networks Kauffmania inference bioinformatics models nudge-targets consider:representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:60795608658c/ 2015-12-27T13:46:54+00:00 http://arxiv.org/abs/1512.03094 Vaguery systems-biology gene-regulatory-networks bioinformatics inference nudge-targets representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:dfc186d58fa7/ 2015-12-27T13:34:27+00:00 http://arxiv.org/abs/1512.02786 Vaguery boolean-networks theoretical-biology bioinformatics systems-biology engineering-design representation nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:395589621b21/ 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/ 2015-12-25T16:37:08+00:00 http://arxiv.org/abs/1510.08513 Vaguery gene-regulatory-networks systems-biology models bioinformatics inference network-theory inverse-problems nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:261731ed3d67/ 2015-12-10T12:32:37+00:00 http://arxiv.org/abs/1511.07662 Vaguery bioinformatics network-theory interaction-models systems-biology inference statistics nudge-targets consider:stress-testing https://pinboard.in/ https://pinboard.in/u:Vaguery/b:434056c61fa2/ 2015-11-13T22:20:59+00:00 http://arxiv.org/abs/1509.00896 Vaguery bioinformatics reaction-networks inference statistics rather-interesting community-detection network-theory nudge-targets consider:feature-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:944048fd76da/ 2015-11-05T02:05:42+00:00 http://arxiv.org/abs/1501.04648 Vaguery RNA molecular-biology biophysics bioinformatics optimization simulation approximation algorithms nudge-targets consider:representation rather-interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:fe8151cde260/ 2015-11-03T20:57:49+00:00 http://biorxiv.org/content/early/2015/10/22/029710 Vaguery workflow framework representation software-development design-patterns bioinformatics distributed-processing rather-interesting consider:for-GP https://pinboard.in/ https://pinboard.in/u:Vaguery/b:3b3bf92b0890/ 2015-10-16T12:54:23+00:00 http://arxiv.org/abs/1505.05815 Vaguery bioinformatics cladistics taxonomy inference algorithms topology rather-interesting representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d55ab49e29ad/ 2015-09-30T11:57:30+00:00 http://arxiv.org/abs/1407.2812 Vaguery machine-learning bioinformatics probability-theory nudge-targets signal-processing information-theory https://pinboard.in/ https://pinboard.in/u:Vaguery/b:dd6ee046718b/ 2015-09-20T11:25:54+00:00 http://arxiv.org/abs/1509.02975 Vaguery strings metrics clustering similarity feature-construction information-theory bioinformatics algorithms rather-interesting nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4ddbd2e129b9/ 2015-09-13T21:56:11+00:00 http://arxiv.org/abs/1412.4967 Vaguery feature-extraction deep-learning bioinformatics rather-interesting horse-races algorithms machine-learning nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:5846b66126f2/ 2015-09-06T14:34:02+00:00 http://arxiv.org/abs/1303.3692 Vaguery GPU bioinformatics algorithms to-learn https://pinboard.in/ https://pinboard.in/u:Vaguery/b:467cff5c87f7/ 2015-08-28T23:29:43+00:00 http://biorxiv.org/content/early/2015/08/21/025262 Vaguery data-fusion bioinformatics medinformatics statistics algorithms rather-interesting nudge-targets consider:feature-discovery consider:looking-to-see https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f6d2ae6a30b7/ 2015-08-22T12:32:38+00:00 http://arxiv.org/abs/1508.04174 Vaguery network-theory complexology information-theory bioinformatics nudge-targets consider:feature-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:adf398c3dc4a/ 2015-08-09T14:51:25+00:00 http://arxiv.org/abs/1412.1074 Vaguery bioinformatics genomics modeling modeling-is-not-mathematics representation interpretability performance-measure nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:3301527c1269/