Search engine run on: http://users.monash.edu.au/


Glookbib search for: zz0820

%T Int. Symp. on the Implementation & Application of Functional Languages
%K IFL, IFL15,2003, IFL16,2004, IFL17,2005, IFL18,2006, IFL19,2007, IFL20,2008,
   IFL21,2009, IFL22,2010, IFL23,2011, IFL25,2013, IFL29,2017, IFL30,2018,
   IFL31,2019, IFL32,2020,
   CFP,conf,wShop,FP,programming,www,HREF,http, zz0820, zz0721, zz0722
%X [2-4 Sep 2020], U.Kent, deadline 17 Aug 2020
   [2019 25-27/9], Singapore, deadline 31/5/2019
   [2018 5-7/9], U Mass Lowell, deadline 25/5/2018
   [2017 30/8-1/9] Bristol, deadline 31/7/2017
   ...
   [2004 Sept 8-10] Luebeck .de, deadline 20 Aug '04
      ("application" added to title in 2004)
   [2003 Sept 8-10] Edinburgh (see ISTFP) deadline 22 Aug '03
       LNCS 16pp (w-shop papers *submitted* to a LNCS volume)
   ...an open forum for researchers who wish to present & discuss new ideas...

%A C. Finn
%A P. Abbeel
%A S. Levine
%T Model-agnostic meta-learning for fast adaptation of deep networks
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0820, ANN, model agnostic, meta learning
%X "We propose an alg. for meta-learning that is model-agnostic, in the sense
   that it is compatible with any model trained with gradient descent &
   applicable to a variety of different learning problems, inc. class'n,
   regres'n, & reinf.learning. The goal of meta-l. is to train a model on a
   variety of ... such that a small # of gradient steps with a small amount of
   training data from a new task will produce good generalization performance
   on that task. ...  demonstrate that this approach leads to state-of-the-art
   performance on two few-shot image class'n benchmarks, produces good results
   on few-shot reg'n, & accelerates fine-tuning for policy gradient reinf.
   learning with n.n/wk policies."
   -- [arXiv]['20].

%A L. P. Kaelbling
%T The foundation of efficient robot learning
%J Science
%V 369
%N 6506
%P 915-916
%M AUG
%D 2020
%K news, views, c2020, c202x, c20xx, zz0820, AI, machine learning, intro,
   robotic, robotics, robots, realWorld
%X "The past 10 y. have seen enormous breakthroughs[*] in mach.l., resulting
   in game-changing applications in comp.vision & lang.proc.. The field of
   intell. robotics ... has not yet been revolutionized by these breakthroughs.
   A critical difficulty is that the nec. learning depends on data that can only
   come from acting in a variety of real-world environments. Such data are
   costly to acquire because there is enormous variability in the situations a
   general-purpose robot must cope with. It will take a combination of new
   alg.techniques, inspiration from natural syss, & multiple levels of
   m.learning to revolutionize robotics with general-purpose intell.. ..."
   -- [doi:10.1126/science.aaz7597]['20].
   [*][Also search for: progress AI 6494].

%A J. W. Cooley
%A J. W. Tukey
%T An algorithm for the machine calculation of complex Fourier series
%J Math. Comp.
%V 19
%P 297-301
%D 1965
%K jrnl, maths, c1965, c196x, c19xx, zz0820, Fast Fourier Transform, FFT, DFT,
   series, algorithm, Yates, Good, history
%X "An efficient method for the calculation of the interactions of a 2^m
   factorial experiment was introduced by Yates & is widely known by his name.
   The generalization to 3^m was given by Box et al.[1]. Good[2] generalized
   these methods & gave elegant algs. for which one class of applications is the
   calculation of Fourier series. ..."
   -- [doi:10.1090/S0025-5718-1965-0178586-1]['20].
   (Also see FFT@[wikip]['20] and
             DFT@[wikip]['20].)

%A J. Cooley
%A P. Lewis
%A P. Welch
%T The finite Fourier transform
%J IEEE Trans. on Audio and Electroacoustics
%V 17
%N 2
%P 77-85
%M JUN
%D 1969
%K jrnl, c1969, c196x, c19xx, zz0820, finite Fourier transform, fast, FFT,
   discrete, DFT, algorithm
%X "... The convolution & term-by-term product op'ns are defined & their equiv.
   ops. in transform space are given. A discussion of the transforms of
   stretched & sampled fns leads to a sampling theorem for finite seqs.. Finally
   these results are used to give a simple derivation of the fast Fourier
   transform algorithm."
   -- [doi:10.1109/TAU.1969.1162036]['20].
   (Also see DFT@[wikip]['20].)
   [Also search for: FFT algorithm].

%A Bing Jian
%A B. C. Vamuri
%T Robust point set registration using Gaussian mixture models
%J IEEE Trans. Patt. Analysis and Mach. Intell.
%V 33
%N 8
%P 1633-1645
%M AUG
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0820, point set registration, defn, sets,
   point cloud, alignment, match, matching, transformation, Wahba problem, pose,
   RANSAC
%X "... present a unified framework for the rigid and nonrigid point set
   registration problem in the presence of sig. amounts of noise ... represent
   the input point sets using GMMs ..."
   -- [doi:10.1109/TPAMI.2010.223]['20],
    & code@[gith'b]['20].
 [*Also see PSR@[wikip]['20].*]
   [Also search for: point set].

%A E. Karstadt
%A O. Schwartz
%T Matrix multiplication, a little faster
%J Proc. 29th ACM Symp. on Parallelism in Algs. and Arch.
%P 101-110
%M JUL
%D 2017
%K conf, SPAA17, c2017, c201x, c20xx, zz0820, fast, matrix multiplication,
   algorithm
%X "... The leading coeff. of Strassen-Winograd's alg. was believed to be
   optimal for m.mult. algs. with 2x2 base case, due to a [lwb] of Probert
   (1976).  Surprisingly, we obtain a faster m.m.alg., with the same base case
   size & asymptotic complexity as S.-W.'s alg., but with the coeff. reduced
   from 6 to 5. To this end, we extend Bodrato's (2010) method for m.squaring,
   & transform matrices to an alternative basis. ... apply our technique to
   other S.-like algs., improving their arithmetic & communication costs by
   sig. const. factors."
   -- [doi:3087556.3087579]['20].
   [Also search for: fast matrix miltiplication].

%A G. Beniamini
%A N. Cheng
%A O. Holtz
%A E. Karstadt
%A O. Schwartz
%T Sparsifying the operators of fast matrix multiplication algorithms
%J arXiv
%M AUG
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, matrix multiplication algorithm
%X "... Many sub-cubic algs. have large leading coeffs., rendering them
   impractical. Karstadt & Schwartz (SPAA17, JACM20) demonstrated how to reduce
   these coeffs. by sparsifying an alg's bilinear operator. Unfortunately, the
   ... finding optimal spars. is NP-Hard. We obtain three new methods to this
   end ... These methods have an exponential worst case running time, but run
   fast in practice & improve the performance of many fast m.mult. algs.. Two of
   [them] are guaranteed to produce leading coeffs. that, under some assumptions
   are optimal."
   -- 2008.03759@[arXiv]['20].
   [Also search for: fast matrix multiplication].

%A R. Anderson
%A R. May
%T The logic of vaccination
%J New Sci.
%V 96
%N 1332
%P 410-415
%M NOV
%D 1982
%K MolBio, c1982, c198x, c19xx, zz0820, BobMay, vaccine, vaccination, infection,
   disease, epidemic, pandemic, measles, smallpox, polio, herd immunity
%X -- ref@[ncbi]['20].
   [Also search for: vaccination].

%A R. Anderson
%A R. May
%T Vaccination and herd immunity to infectious diseases
%J Nature
%V 318
%P 323-329
%M NOV
%D 1985
%K jrnl, c1985, c198x, c19xx, zz0820, BobMay, vaccination, vaccine, infection,
   disease, epidemic, pandemic, measles, smallpox, polio, herd immunity,
   human health, medicine, spread, Robert Bob May
%X "An understanding of the relationship between the transmission dynamics of
   infectious agents & herd immunity provides a template for the design of
   effective control programmes based on mass immunization. Math. models of the
   spread & persistence of infection provide important insights into the problem
   of how best to protect the community against disease."
   -- [doi:10.1038/318323a0]['20].

%A V. R. Iyer
%A C. E. Horak
%A C. S. Scafe
%A D. Botstein
%A M. Snyder
%A P. O. Brown
%T Genomic binding sites of the yeast cell-cycle transcription factors SBF and
   MBF
%J Nature
%M JAN
%D 2001
%V 409
%N 6819
%P 533-538
%K jrnl, MolBio, c2001, c200x, c20xx, zz0820, Chiponchip, Chipchip, defn, chip,
   seq, yeast, cell cycle, Swi4, Swi6, Mbp1, mitotic, binding site
%X "Proteins interact with genomic DNA ... SBF & MBF are seq.-specific
   transcription factors that activate gene expression during the G1/S
   transition of the cell cycle in yeast. ... we define the genomic binding
   sites of the SBF & MBF transc.factors in vivo, by using DNA microarrays. ..."
   -- [doi:10.1038/35054095]['20].
   [*Also see ChIP-on-chip@[wikip]['20].*]

%A D. S.Latchman
%T Transcription factors: An overview
%J Int. J. Biochem. and Cell Biol.
%V 29
%N 12
%P 1305-1312
%M DEC
%D 1997
%K MolBio, c1997, c199x, c19xx, zz0820, Transcription factor, defn, TF, TFs,
   intro, survey, transcriptionFactor, gene expression, regulation
%X -- [doi:10.1016/S1357-2725(97)00085-X]['20].
   [*Also see,  "a transcription factor (TF) (or seq.-specific DNA-binding
   factor) is a protein that controls the rate of transcription of genetic
   info. from DNA to mRNA, by binding to a specific DNA seq."
   -- TFs@[wikip]['20].*]

%A S. E. Boyd
%A M. Garcia de la Banda
%A R. N. Pike
%A J. C. Whisstock
%A G. B. Rudy
%T PoPS: A computational tool for modeling and predicting protease specificity
%J Proc. IEEE Comput. Syst. Bioinf. Conf.
%P 372-381
%D 2004
%K Boyd, MonashUni, conf, MolBio, c2004, c200x, c20xx, zz0820, PoPS, protease,
   proteinase, peptidase, substrate, specificity, cleave
%X "... we present PoPS, a publicly accessible bio'nf. tool
   [pops.csse.monash.edu.au] which provides a novel method for building
   comp. models of protease specificity that, while still being based on these
   amino acid seqs., can be built from any experimental data or expert knowledge
   available to the user ..."
   -- [doi:10.1109/csb.2004.1332450]['20].
   (Also see [JBCB_'05]['20].)

%T The Cancer Genome Atlas
%D 2005
%K TCGA, NCI, MolBio, c2005, c200x, c20xx, zz0820, cancer, cell, cells, data,
   stats, genomic, epigenomic, transcriptomic, proteomic, dataBase
%X [TCGA]['20],
   TCGA@[wikip]['20].

%A C. B. Do
%A M. S. P. Mahabhashyam
%A M. Brudno
%A S. Batzoglou
%T ProbCons: Probabilistic consistency-based multiple sequence alignment
%J Gen. Res.
%V 15
%P 330-340
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0820, protein alignment, gap, gaps,
   indel, costs
%X "... alignments, however, is a difficult comp. problem because of not only
   the high computational cost but also the lack of proper objective fns for
   measuring alignment quality. ... we introduce probabilistic consistency, a
   novel scoring fn for multiple seq. comparisons. We present ProbCons, a
   practical tool for progressive protein multiple seq. al. based on prob.
   consistency, & evaluate its performance on several std al.benchmark
   d.sets. ..."
   -- [doi:10.1101/gr.2821705]['20].
   [Also search for: MolBio protein alignment].

%A M. A. Apostol
%A et al ...
%A D. Eisenberg
%T Atomic structures of amyloid cross-beta spines reveal varied steric zippers
%J Nature
%V 447
%P 454-457
%M APR
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, zz0820, amyloid fibril, prion, disease,
   2OL9, GNNQQNY, protein, prions, alpha, beta spine, tau, Sup35, folded,
   misfolded, Alzheimer's, Alzheimers
%X "Amyloid fibrils formed from different proteins, each assoc. with a
   particular disease, contain a common cross-beta spine. ... the fibril-forming
   segment GNNQQNY of the yeast prion protein Sup35, was recently revealed ...
   ... It is a pair of beta-sheets, with the facing side chains of the two
   sheets interdigitated in a dry 'steric zipper'. ... report some 30 other
   segments from fibril-forming proteins ... include segs from the Alzheimer's
   amyloid-beta & tau proteins, the PrP prion protein, insulin, islet amyloid
   polypeptide (IAPP), lysozyme, myoglobin, alpha-synuclein & beta-microglobulin
   suggesting that common structural features are shared by amyloid diseases ...
   13 of these microcrystals all reveal steric zippers, but with variations ..."
   -- [doi:10.1038/nature05695]['20] (online 29/4/2007).
   Also see 2OL9@[PDB]['20].
   [Also search for: prion disease].

%A J. J. W. Wiltzius
%A et al ...
%A D. Eisenberg
%T Molecular mechanisms for protein-encoded inheritance
%J Nat. Struct. & Molec. Biol.
%V 16
%P 973-978
%M AUG
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0820, protein, fibril, folded,
   elk prion, disease, prions, beta sheet, mechanism, misfolded, 3FVA, NNQNTF
%X "... phenotypic variants encoded by protein 'conformations'. However, it is
   unclear how a protein conformation can be stable enough to endure
   transmission between cells or organisms. ... describe new polymorphic crystal
   structures of segments of prion & other amyloid proteins, which offer two
   structural mechanisms for the encoding of prion strains. ... prion strains
   are encoded by alternative packing arrangements (polymorphs) of beta-sheets
   formed by the same segment of a protein; in segmental polymorphism, prion
   strains are encoded by distinct beta-sheets built from different segments of
   a protein. ..."
   -- [doi:10.1038/nsmb.1643]['20].
   Also see 3FVA@[PDB]['20].
   [Also search for: prion disease].

%A C. Trapnell
%A L. Pachter
%A S. L. Salzberg
%T TopHat: Discovering splice junctions with RNA-Seq
%J Bioinformatics
%V 25
%N 9
%N 1
%P 1105-1111
%M MAY
%D 2009
%K MolBio, cjrnl, c2009, c200x, c20xx, zz0820, TopHat, mRNA, RNAseq, RNAseq,
   splice junction, splicing, isoForm
%X "... millions of short seq. fragments ...  We mapped the RNA-Seq reads from a
   recent mammalian RNA-Seq experiment & recovered more than 72% of the splice
   junctions reported by the annotation-based s/w from that study, along with
   nearly 20,000 prev. unreported junctions. The TopHat pipeline is much faster
   than prev. systems, mapping nearly 2.2 million reads per CPU hour ..."
   -- [doi:10.1093/bioinformatics/btp120]['20] (online March 2009).
   (Also see TopHat2@[doi:10.1186/gb-2013-14-4-r36][25/4/2013].)
   [Also search for: MolBio RNAseq].

%A M. D. Robinson
%A A. Oshlack
%T A scaling normalization method for differential expression analysis of
   RNA-seq data
%J Geno. Biol.
%V 11
%N R25
%M MAR
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0820, RNA-seq, RNAseq, normalization,
   normalisation, stats
%X "... we show that normalization continues to be an essential step in the
   analysis. We outline a simple and effective method for performing n. & show
   dramatically improved results for inferring differential expression in
   simulated & publicly available data sets."
   -- [doi:10.1186/gb-2010-11-3-r25]['20].
   [Also search for: RNAseq normalization].

%A C. Trapnell
%A et al ...
%A L. Pachter
%T Transcript assembly and quantification by RNA-Seq reveals unannotated
   transcripts and isoform switching during cell differentiation
%J Nature Biotech.
%V 28
%P 511-515
%M MAY
%D 2010
%K MolBio, jrnl, c2010, c201x, c20xx, zz0820, Cufflinks, mRNA, RNAseq, RNA seq,
   isoform, gene expression
%X "... we intro. such algs. in an open-source s/w program called Cufflinks. To
   test Cufflinks, we sequenced & analyzed > 430 million paired 75-bp RNA-Seq
   reads from a mouse myoblast cell line over a differentiation time series. We
   detected 13,692 known transcripts & 3,724 prev. unannotated ones ... Over the
   time series, 330 genes showed complete switches in the dominant transcription
   start site (TSS) or splice isoform, and we observed more subtle shifts in
   1,304 other genes. ..."
   -- [doi:10.1038/nbt.1621]['20].

%A D. T. Barken
%A et al
%T Prediction of protease substrates using sequence and structure features
%J Bioinformatics
%V 26
%N 14
%P 1714-1722
%M JUL
%D 2010
%K MolBio, c2010, c201x, c20xx, zz0820, salilab, protease, proteinase, cleave,
   substrate, specificity, Granzyme B, GranzymeB, GrB, caspases, GrBah
%X "... we present a BioI. method based on support vector machine (SVM)
   learning that identifies seq. & structural features important for protease
   recognition of substrate peptides & then uses these features to predict
   novel substrates. ..."
   -- [doi:/10.1093/bioinformatics/btq267]['20].

%A Yuan-Ping Pang
%A S. Brimijoin
%A D. W  Ragsdale
%A Kun Yan Zhu
%A R. Suranyi
%T Novel and viable acetylcholinesterase target site for developing effective
   and environmentally safe insecticides
%J Curr. Drug Targets
%A. 2012 Apr;
%V 13
%N 4
%P 471-482
%M APR
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0820, pest, insect, aphid, insecticide,
   acetylcholinesterase, AChE, anticholinesterase, cysteine, cys, Cys289, 2AZG,
   inhibitor, AMTS13, anti-malaria, mosquito
%X "... This review summarizes the lit. data that support the hypothesis that an
   insect-specific cysteine residue located at the opening of the
   acetylcholinesterase active site is a promising target site for developing
   new insecticides with reduced off-target toxicity & low propensity for insect
   resistance. ... discuss the differences between targeting the insect-specific
   cysteine residue & targeting the ubiquitous catalytic serine residue of
   acet... ... Also discussed is the prospect of developing cysteine-targeting
   antichol... as effective & environmentally safe insecticides for control of
   disease vectors, crop damage, & residential insect pests within the financial
   confines of the present insecticide market."
   -- [doi:10.2174/138945012799499703]['20].
   [Also search for: MolBio insecticide].

%A P. Doherty
%T Pandemics: What Everyone Needs to Know
%I OUP
%P 272
%M AUG
%D 2013
%K book, text, c2013, c201x, c20xx, zz0820, PCDoherty, infection, disease,
   epidemic, pandemic, vaccine, vaccination, spread, resistance, pathogen,
   virus, viruses, Spanish flu, influenza, SARS, Wuhan, human, public health
%X 1st ed 2013; hb us$82; uk us isbn:0199898103; uk us isbn13:978-0199898107.
  "... an essential guide to one of the truly life-or-death issues of our age.
   In concise, question-and-answer format, he explains the causes of pandemics,
   how they can be counteracted with vaccines and drugs, and how we can better
   prepare for them in the future. ..."

%A A. Dobin
%A et al ...
%A T. R. Gingeras
%T STAR: ultrafast universal RNA-seq aligner
%J Bioinformatics
%V 29
%N 1
%P 15-21
%M OCT
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0820, RNA seq, RNAseq, mapping,
   reference, reads, splice junction, splicing
%X "... align our large (> 80 billon reads) ENCODE Transcriptome RNA-seq dataset
   we developed the Spliced Transcripts Alignment to a Reference (STAR) s/w ...
   550 million 2x76bp paired-end reads per hour on a modest 12-core server ...
   can discover non-canonical splices and chimeric (fusion) transcripts ..."
   -- [doi:10.1093/bioinformatics/bts635]['20].
   [Also search for: MolBio RNAseq].

%A M. A. Lancaster
%A J. A. Knoblich
%T Organogenesis in a dish: Modeling development and disease using
   organoid technologies
%J ScienceMag
%V 345
%N 6194
%P ?-?
%M JUL
%D 2014
%K jrnl, Biol, MolBio, c2014, c201x, c20xx, zz0820, organoid, organelle, organs,
   tissue types
%X "... Organoids are derived from pluripotent stem cells or isolated organ
   progenitors that differentiate to form an organlike tissue exhibiting
   multiple cell types that self-organize to form a structure not unlike the
   organ in vivo ..."
   -- [doi:10.1126/science.1247125]['20].
   [Also search for: organelle].

%A S. Verma
%A R. Dixit
%A K. C. Pandey
%T Cysteine proteases: Modes of activation and future prospects as
   Pharmacological targets
%J Front. Pharmacol.
%M APR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0820, MolBio, cysteine, protease, Cys, cystine,
   target, drug design, proteinase
%X "... Proteases are classified according to their catalytic site, &
   distributed into four major classes: cysteine p., serine p., aspartic p., &
   metalloproteases. ... involved in multiple fns such as extracellular matrix
   turnover, antigen presentation, processing events, digestion, immune
   invasion, hemoglobin hydrolysis, parasite invasion, parasite egress, &
   processing surface proteins. ..."
   -- 1604.03587@[doi:10.3389/fphar.2016.00107]['20].
   [Also search for: cysteine protease].

%A N. L Bray
%A H. Pimentel
%A P. Melsted
%A L. Pachter
%T Near-optimal probabilistic RNA-seq quantification
%J Nat. Biotech.
%V 34
%P 525-527
%M APR
%D 2016
%K MolBio, jrnl, c2016, c201x, c20xx, zz0820, kallisto, RNAseq, PseudoAlignment,
   pseudo, mRNA, mapping, reference
%X "... kallisto, an RNA-seq quantification program that is two orders of
   magnitude faster than prev. approaches & achieves similar accuracy. Kallisto
   pseudoaligns reads to a reference, producing a list of transcripts that are
   compatible with each read while avoiding alignment of individual bases. We
   use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in
   < 10 min on a standard laptop computer. This removes a major computational
   bottleneck in RNA-seq analysis."
   -- [doi:10.1038/nbt.3519]['20].
   [Also search for: PseudoAlignment].

%A D. van Dijk
%A et al ...
%A D. Pe'er
%T MAGIC: A diffusion-based imputation method reveals gene-gene interactions in
   single-cell RNA-sequencing data
%J bioRxiv
%M FEB
%D 2017
%O Cell 174(3), pp.716-729, 26/7/2018 [doi:10.1016/j.cell.2018.05.061]['20].
%K MAGIC, MolBio, c2017, c201x, c20xx, zz0820, Dana Peer, scRNAseq, scRNA seq,
   impute, imputation, abundance, zero, dropout, colinearity, manifold,
   nearest neighbour, trajectory, diffusion, graph, cell, cells, gene expression
%X "... scRNA-seq technologies suffer from many sources of sig. technical noise,
   the most prominent of which is 'dropout' due to inefficient mRNA capture. ...
   MAGIC (Mark'v Affinity-based Graph Imputation of Cells), a method for
   imputing missing values, & restoring the structure of the data. After MAGIC,
   we find that two- & three-D gene interactions are restored & that MAGIC is
   able to impute complex & non-linear shapes of interactions ..."
   -- [doi:10.1101/111591]['20].
   (A seminar@[ubend]['20].)
   [Also search for: scRNAseq].

%A R. Patro
%A et al ...
%A C. Kingsford
%T Salmon: Fast and bias-aware quantification of transcript expression using
   dual-phase inference
%J Nat. Methods
%V 14
%P 417-419
%M MAR
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0820, scRNAseq, scRNA seq, RNAseq,
   Salmon, pseudo, PseudoAlignment, map mRNA reference, gene expression profile
%X "... Salmon, a lightweight method for quantifying transcript abundance from
   RNA-seq reads. Salmon combines a new dual-phase parallel inference alg. &
   feature-rich bias models with an ultra-fast read mapping procedure. ... the
   1st transcriptome-wide quantifier to correct for fragment GC-content bias,
   which, as we demo. here, substantially improves the accuracy of abundance
   estimates & the sensitivity of subsequent differential expression analysis."
   -- [doi:10.1038/nmeth.4197]['20].
   [Also search for: PseudoAlignment].

%A E. Qi
%A D. Wang
%A B. Gao
%A Y. Li
%A G. Li
%T Block-based characterization of protease specificity from substrate sequence
   profile
%J BMC Bioinformatics
%V 18
%N #438
%M OCT
%D 2017
%K MolBio, jrnl, c2017, c201x, c20xx, zz0820, protease, distance, cleave, pops,
   cleaves, cleaving, cleavage, site, profile, sites, substrate, specificity,
   octopeptide, prosper, MEROPS
%X "... propose a novel block-based approach to reveal the potential combns of
   [AAs] which may regulate the action of proteases. Using the entropies of
   eight blocks centered at a cleavage bond, we created a distance matrix for
   61 proteases to compare their specificities. After quantitative analysis, we
   discovered a # of prominent blocks, each of which consists of successive
   [AAs] near a cleavage bond, intuitively characterizing the site cooperation
   of the substrate sequences.  ..."
   -- [doi:10.1186/s12859-017-1851-1]['20].
   [Also search for: protease specificity].
   (Also see [MEROPS]['20].)

%A J. D. Welch
%A A. J. Hartemink
%A J. F. Prins
%T MATCHER: Manifold alignment reveals correspondence between single cell
   transcriptome and epigenome dynamics
%J Genome Biol
%V 18
%N 138
%M JUL
%d 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0820, manifold alignment, scRNA-seq,
   scRNAseq, matcher, gene expression, epigenetic, scM&T-seq, scMTseq,
   sc-GEM, scGEM, ATACseq, cell types, pseudoTime
%X "... an approach for integrating multiple types of single cell measurements.
   MATCHER uses manifold alignment [Ham03] to infer single cell multiomic
   profiles from transcriptomic & epigenetic measurements performed on different
   cells of the same type. Using scM&T-seq & sc-GEM data ... predicts true
   s.cell correlations between DNA methylation & gene expression ..."
      ["... [assume] variation among cells can be explained mainly by a single
       latent variable ('pseudotime') ... cells in each experiment are sampled
       from the same population, process, and cell type ..."]
   -- [doi:10.1186/s13059-017-1269-0]['20].
   [Also search for: MolBio scRNAseq].

%A N. D. Rawlings
%A et al ...
%A R. D Finn
%T The MEROPS database of proteolytic enzymes, their substrates and inhibitors
   in 2017 and a comparison with peptidases in the PANTHER database
%J NAR
%V 46
%N D1
%P D624-D632
%M JAN
%D 2018
%K NRA, jrnl, MolBio, c2018, c201x, c20xx, zz0820, MEROPS, protease, proteinase,
   peptidase, enzyme, inhibitor, substrate, cleave, cleavage, specificity, pops,
   database, collection, DB,
%X "... an integrated source of info. about peptidases, their substrates
   & inhibitors. The hier.class'n is: protein-species, family, clan,
   with an id. at each level. ..."
   -- [doi:10.1093/nar/gkx1134]['20].
   Also see MEROPS@[www]['20].

%A T. Nawy
%T Spatial transcriptomics
%J Nat. Methods
%V 15
%M JAN
%D 2018
%K news, views, MolBio, c2018, c201x, c20xx, zz0820, spatial, transcriptome,
   RNA, mRNA, cells, gene expression levels, tissue
%X -- [doi:10.1038/nmeth.4542]['20].

%A S. Lamarre
%A et al ...
%A E. Maza
%T Optimization of an RNA-Seq differential gene expression analysis depending
   on biological replicate number and library size
%J Front. Plant Sci.
%V ?
%P ?-?
%M FEB
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0820, gene expression levels, RNAseq,
   stats, RNA-seq, replicate number, library size, DESeq, DESeq2, edgeR,
   normalization, normalisation
%X "... we conducted both an analysis of a two-condition experiment (with eight
   biol. replicates per condition) to compare the results with prev. benchmark
   studies, & a meta-analysis of 17 experiments with up to 18 biol. conditions
   eight biological replicates & 100 million (M) reads per sample. ..."
   -- [doi:10.3389/fpls.2018.00108]['20].
  [Also search for: RNAseq MolBio].

%A M. Amodio
%A S. Krishnaswamy
%T MAGAN: Aligning biological manifolds
%J arXiv
%M FEB
%D 2018
%O 35th ICML
%K Conf, ICML, MolBio, c2018, c201x, c20xx, zz0820, MAGAN, scRNAseq,
   mass cytometry, manifold alignment
%X "... many types of natural and physical systems ... different types of
   measurements ... important to align the manifolds arising from each
   measurement in order to integrate such data and gain an improved picture of
   the system. We tackle this problem using generative adversarial networks
   (GANs). ... present a new GAN called the Manifold-Aligning GAN (MAGAN) that
   aligns two manifolds s.t. related points in each measurement space are
   aligned together. ... [e.g.] single-cell biology ... scRNAseq and proteomic
   (mass cytometry) ..."
   -- 1803.00385@[arXiv]['20],
      [mlrPress]['20].
   [Also search for: Ham03].

%A M. Gehringer
%A S. A. Laufer
%T Emerging and re-emerging warheads for targeted covalent inhibitors:
   Applications in Medicinal Chemistry and Chemical Biology
%J J. Med. Chem.
%V 62
%N 12
%P 5673-5724
%M DEC
%D 2018
%K MolBio, jrnl, c2018, c201x, c20xx, zz0820, drug design, warhead, ligand,
   inhibitor, Cys, TCI, TCIs, reactivity, anions
%X "... Currently, targeting noncatalytic cysteine residues with acrylamides &
   other alpha,beta-unsaturated carbonyl compounds is the predominant strategy
   in TCI development. ... provides an overview of warheads - beyond
   a,b-unsaturated amides - recently used in the design of targeted covalent
   ligands. Promising reactive groups that have not yet demonstrated their
   utility in TCI development are also highlighted. ..."
   -- [doi:10.1021/acs.jmedchem.8b01153]['20],
      [www]['20].

%A R. Molania
%T Identification and removal of unwanted variation in large gene expression
   data
%I Uni. Melb.
%D 2018
%K PhD thesis, MolBio, stats, c2018, c201x, c20xx, zz0820, RNAseq, RNA-seq,
   mRNA, Nanostring, nCounter, gene expression levels, microarray, purity,
   batch effects, normalisation, normalization, screening,
   The Cancer Genome Atlas, TCGA
%X "Gene expression experiments ...  include: identifying & classifying disease
   types, assessing the transcriptional differences between the state of a
   disease & normal cells, & identifying biomarkers to predict clinical outcome
   of diseases such as cancer, ..."
   -- [www]['20].
   [WEHIseminar 4/8/'20].
   [Also search for: MolBio RNAseq].

%A R. Salomon
%A et al
%T Droplet-based single cell RNAseq tools: a practical guide
%J Lab. Chip
%V 19
%N 10
%P 1706-1727
%M MAY
%D 2019
%K MolBio, c2019, c201x, c20xx, zz0820, droplet, flow cell, flowCell, intro,
   survey, guide, scRNA seq, scRNAseq, RNAseq, DropSeq, inDrop, 10X
%X "Droplet based scRNA-seq sys. such as Drop-seq, inDrop & Chromium 10X ...
   scRNA-seq technologies in the res.lab.. ...  we provide a practical guide
   through all the steps involved in a typical scRNA-seq experiment. ..."
   -- [doi:10.1039/c8lc01239c]['20],
      abs@[p'bmed]['20].
   [Also search for: MolBio flowCell].

%A R. Molania
%A J. A. Gagnon-Bartsch
%A A. Dobrovic
%A T. P. Speed
%T A new normalization for Nanostring nCounter gene expression data
%J NAR
%V 47
%N 12
%P 6073-6083
%M JUL
%D 2019
%K jrnl, NAR, MolBio, c2019, c201x, c20xx, zz0820, stats, normalisation,
   amount, batch effects, RUV-III, RUVIII, RUV3, technical replicate,
   pseudoreplicate, expression levels, RNA-seq, RNAseq
%X "The Nanostring nCounter gene expression assay uses molecular barcodes &
   single molecule imaging to detect & count hundreds of unique transcripts in a
   single reaction. These counts need to be normalized to adjust for the amount
   of sample, variations in assay efficiency & other factors. ... we present a
   new n.method, Removing Unwanted Variation-III (RUV-III), which makes vital
   use of technical replicates & suitable control genes. We also propose an
   approach using pseudo-replicates when tech.replicates are not available. ..."
   -- [doi:10.1093/nar/gkz433]['20].

%A V. Kiselev
%A et al ...
%A M. Hemberg
%T Analysis of single cell RNA-seq data
%I Sanger Inst.
%M JUL
%D 2019
%K intro, course, MolBio, c2019, c20x, c20xx, zz0820, scRNA-seq, scRNAseq,
   Sanger, uk, cells, transcriptome data, mRNA, RNA, gene expression
%X "Today it is possible to obtain genome-wide transcriptome data from single
   cells using high-throughput sequencing (scRNA-seq). ..."
   -- [www]['20].

%A D. Kim
%A et al ...
%A S. L. Salzberg
%T Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
%J Nat. Biotechnology
%V 37
%P 907-915
%M AUG
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0820, HISAT, HISAT2, DNA, RNA, mRNA,
   mapping, reference, scRNAseq, scRNA seq, BWT, FMindex, GFM
%X "... HISAT2 (hierarchical indexing for spliced alignment of transcripts 2)
   that can align both DNA & RNA seqs. using a graph Ferragina Manzini index. We
   use HISAT2 to represent & search an expanded model of the human reference
   genome in which over 14.5 million genomic variants in combination with
   haplotypes  ... outperforms other computational methods & matches or exceeds
   the performance of laboratory-based assays."
   -- [doi:10.1038/s41587-019-0201-4]['20],
    & s/w@[gith'b]['20].
   [Also search for: scRNAseq].

%A S. R. Hackett
%A et al
%A R. S. McIsaac
%A Learning causal networks using inducible transcription factors and
   transcriptome-wide time series
%J Mol. Syst. Biol.
%N 16
%P e9174
%M MAR
%D 2020
%K jrnl, eJrnl, MolBio, c2020, c202x, c20xx, zz0820, IDEA, Bnet, network,
   model, transcription factor, TF, TFs, gene expression, budding yeast, Aft1
%X "... IDEA (the Induction Dynamics gene Expression Atlas), a dataset
   constructed by indep. inducing hundreds of transcription factors (TFs) &
   measuring time-courses of the resulting gene exp'n responses in budding
   yeast. Each experiment captures a regulatory cascade connecting a single
   induced regulator to the genes it causally regulates. ... IDEA contains
   >200 TF induction experiments with 20 million individual observations &
   100,000 signal-containing dynamic responses. As an application of IDEA, we
   integrate all timecourses into a whole-cell transcriptional model ..."
   -- [doi:10.15252/msb.20199174]['20].
   (some auths @Calico Life Sci.)

%A I. Astuti
%A Ysrafil
%T Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of
   viral structure and host response
%J Diabetes Metab. Syndr.
%V 14
%N 4
%P 407-412
%M JUL-AUG
%D 2020
%K MolBio, survey, intro, review, c2020, c202x, c20xx, zz0820, SARSCoV2,
   SARS-CoV-2, virus, covd-19, covid19, ACE2, nsp, nsp3, nsp5, Wuhan, China,
   protein, immune response, system
%X "... provide a complete review related to structure, origin, & how the body
   responds to this virus infection & explain the possibility of an immune
   system over-reaction or cytokine storm. We also inc. an explanation of how
   this virus creates modes of avoidance to evade immune system attacks. ..."
   -- [doi:10.1016/j.dsx.2020.04.020]['20] (online 18/4/2020) (45 refs),
      PMC7165108@[ncbi]['20].
   [Also search for: MolBio SARSCoV2],  maybe add Intro.

%A Peng He
%A et al ...
%A B. J. Wold
%T The changing mouse embryo transcriptome at whole tissue and
   single-cell resolution
%J Nature
%V 583
%P 760-767
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0820, scRNAseq, scRNA-seq, mouse,
   embryo, development, cell, tissue, type, embryogenesis, gene expression,
   animal, mammal
%X "During mammalian embryogenesis, differential gene expression gradually
   builds the identity & complexity of each tissue & organ system. Here we
   systematically quantified mouse polyA-RNA from day 10.5 of embryonic
   development to birth, sampling 17 tissues & organs. The resulting
   developmental transcriptome ... Focusing on the developing limb, single-cell
   RNA data identified 25 candidate cell types ..."
   -- [doi:10.1038/s41586-020-2536-x]['20].
   [Also search for: scRNAseq].

%A Jingyun Yang
%A et al ...
%A Xiawei Wei
%T A vaccine targeting the RBD of the S protein of SARS-CoV-2 induces protective immunity
%J Nature
%V ?
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0820, SARS-CoV-2, SARSCoV2, vaccine,
   SARS2, S-RBD, SRBD, spike protein
%X "... Here we showed that a recombinant vaccine comprising residues 319-545
   of the S-RBD could induce a potent functional antibody response in the
   immunized mice, rabbits & non-human primates (Macaca mulatta) as early as
   7 or 14 days after a single dose injection ..."
   -- [doi:10.1038/s41586-020-2599-8]['20]  (online 29/7/2020).
   (Apparently over 100 *potential* vacs. are in the works.)
   [Also search for: SARSCoV2 vaccine].

%A M. Minguez-Toral
%A B. Cuevas-Zuviria
%A M. Garrido-Arandia
%A L. F. Pacios
%T A computational structural study on the DNA-protecting role of the
   tardigrade-unique Dsup protein
%J Sci. Reports
%V 10
%N #13424
%M AUG
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0820, MolBio, biol, tardigrade, invertebrate,
   animal, DNA, damage suppression, protection, Dsup, disordered protein
%X "The remarkable ability of t. to withstand a wide range of physical & chem.
   extremes ... By means of molec. mod., calculations of electrostatic
   potentials & electric fields, & all-atom molec. dynamics sim'ns, we obtained
   a dynamic picture of the Dsup-DNA interaction. ... suggest that the protein
   is intrinsically disordered, which enables Dsup to adjust its structure to
   fit DNA shape. Strong electrostatic attractions & high protein flexibility
   drive the formation of a molecular aggregate in which Dsup shields DNA. While
   the precise mechanism of DNA protection conferred by Dsup remains to be
   elucidated, our study provides some molec. clues of their assoc. that could
   be of interest for further investigation in this line."
   -- [doi:10.1038/s41598-020-70431-1]['20].

%A J. D. Stone
%T Algorithms for Functional Programming
%I Springer
%P 265
%M FEB
%D 2020
%K book, text, c2020, c20x, c20xx, zz0820, algorithm, FP, Scheme, L2Ref, L3Ref
%X 1st ed 2018; hb us$55; uk us isbn:0387955704; uk us isbn13:978-0387955704.
   [Also search for: book FP algorithm].

%A C. M. Case
%T Scholarship in Sociology
%J Sociology and Social Res.
%V 12
%P 323-340
%D 1928
%K c1928, c192x, c19xx, zz0820, publish or perish, quote, quotable, aphorism,
   academic, academia, university, scientific, research, management, journals,
   pressure, KPI, KPIs
%X "Publish or perish" attributed:
       "... The earliest known use of the term [P or P] in an
       academic context was in a 1928 journal article. ..."
   -- PorP@[wikip]['20].

%A M. V. Malin
%T The Science Citation Index: A new concept in indexing
%J Library Trends
%P 374-387
%M JAN
%D 1968
%K c1968, c196x, c19xx, zz0820, bibliometrics, citation index, source index,
   corporate index, SCI, history, scientific research, literature, papers,
   publications, citations, references
%X -- [www]['20].
   [Also search for: science citation index history].

%A H. E. Chandler
%A V. de P. Roper
%T Citation indexing: Uses and limitations
%J The Indexer
%V 17
%N 4
%M OCT
%D 1991
%K c1991, c199x, c19xx, zz0820, science citation index, history, SCI,
   scientific literature, source, citation index, corporate, permuterm,
   history, examples, use
%X "... Explanations, with examples, are given of the four parts of the C.I.
   published by the Inst. for Sci. Inf.: the Source i., Citation I., Permuterm
   I., & Corporate I.. ..."
   -- [www]['20].

%A J. D. Wren
%A C. Georgescu
%T Detecting potential reference list manipulation within a citation network
%J bioRxiv
%M AUG
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, publish, perish, KPI, KPIs, Hindex, impact,
   misconduct, paper, peer review, reviewing, cite, citation, abuse, reference,
   manipulation, scam, coercive, coercion, coercive, RLM, Kuo-Chen Chou, KCChou,
   KuoChenChou, Roukos, journals, JTB, Elsevier, Gini, GiniIndex
%X "... reference list manipulation (RLM) could take place during the
   peer-review process (e.g., coercive citation from editors or reviewers), or
   prior to it (e.g., a quid-pro-quo between authors). ... find the freq. of
   non-self citations (NSC) to one author coming from one paper ~ Zipf's law.
   We propose the Gini Index as a simple means of quantifying skew in this
   dist'n ... We estimate between 81 (FDR < 0.05) & 231 (FDR < 0.10) authors are
   outliers on the curve, suggestive of chronic, repeated RLM. Based upon the
   distribution, we est. ~ 3,284 (16%) of all authors may have engaged in RLM
   to some degree ..."
   -- [bioRxiv]['20],
      [doi:10.1101/2020.08.12.248369]['20].
   (Also see: "Signs of 'citation hacking' flagged in scientific papers",
   Nature 14/8/2020 [www]['20] and
   "Highly cited researcher banned from journal board for citation abuse",
   Nature 6/2/2020 [www]['20].)
   [Also search for: Hindex manipulation] and [also search for: KuoChenChou].

%Q Google AI Quantum and Collaborators
%T Hartree-Fock on a superconducting qubit quantum computer
%J Science
%V 369
%N 6507
%P 1084-1089
%M AUG
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0820, quantum computer, qubits, chemistry,
   fermion, physics
%X "... We performed several quantum simulations of chemistry with up to
   one dozen qubits, inc. modeling the isomerization mechanism of diazene. ..."
   -- 2004.04174@[arXiv]['20],
      pub49057@[go'gle]['20],
      [doi:10.1126/science.abb9811]['20].

%T 'Make research fun again': UK's powerful funding chief is on a mission to
   change scientific culture
%J Nature
%V 584
%P 508
%M AUG
%D 2020
%K news, views, c2020, c202x, c20xx, zz0820, Ottoline Leyser, UK, UKRI,
   scientific research, university, management, impact, KPI, KPIs, grant,
   grants, peer review
%X -- [doi:10.1038/d41586-020-02424-z]['20].
   [Also search for: scientific research grants].

%A F. Dagnino
%A D. Ancona
%A E. Zucca
%T Flexible coinductive logic programming
%J arXiv
%M AUG
%D 2020
%K TR, conf, ICLP, ICLP2019, LP, ILP, c2020, c202x, c20xx, zz0820, coinduction,
   coLP, inductive logic programming, coClause
%X "Recursive defns of predicates are usually interpreted either inductively or
   coinductively. Recently, a more powerful approach has been proposed, called
   flexible coinduction, to express a variety of intermediate interpretations,
   nec. in some cases to get the correct meaning. We provide a detailed formal
   a/c of an extension of LP supporting flexible coinduction. ... coclauses,
   clauses with a special meaning used to tune the interpretation of predicates.
   As usual, the declarative semantics can be expressed as a fixed pt which,
   however, is not nec. the least, nor the greatest one, but is determined by
   the coclauses. ... the op.semantics is a combination of std SLD resolution &
   coSLD res'n. We prove that the op.semantics is sound & complete ..."
   -- 2008.02140@[arXiv][5/8/2020].
      (Also see coI@[wikip]['20].)
   [Also search for: LP ILP]  and  [also search for coinduction].

%A E. P. Wigner
%T The unreasonable effectiveness of mathematics in the natural sciences.
%J Comm. on Pure and Appl. Maths
%V 13
%N 1
%P 1-14
%M FEB
%D 1960
%O Richard Courant lecture in Math. Sci., delivered at New York Univ.,
   11 May 1959
%K lecture, seminar, c1960, c196x, c19xx, zz0820, science, maths, model,
   prediction, predict, effective, useful, mathematics, physics, quote, quotable
%X -- [doi:10.1002/cpa.3160130102]['20],
      [wikip]['20].

%A M. Naor
%T Succinct representation of general unlabeled graphs
%J Discr. Applied Math.
%V 28
%N 3
%P 303-307
%M SEP
%D 1990
%K jrnl, c1990, c199x, c19xx, zz0820, maths, graph, compress, encode, decode
%X "We show that general unlabeled graphs on n nodes can be represented by
   (^n_2)-nlog2(n)+O(n) bits which is optimal up to the O(n) term. Both the
   encoding & decoding require linear time."
   -- [doi:10.1016/0166-218X(90)90011-Z]['20].
   [Also search for: graph compress].

%A V. A. Traag
%A L. Waltman
%A N. J. van Eck
%A From Louvain to Leiden: Guaranteeing well-connected communities
%J Sci. Reps.
%V 9
%N 5233
%M MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0820, vanEck, network, maths, graph,
   Louvain algorithm, louvian, modularity, modular, Leiden,
   community, detection, networks
%X "... We show that this [Lo.] alg. has a major defect that largely went
   unnoticed until now: the Lo.alg. may yield arbitrarily badly connected
   communities. In the worst case, communities may even be disconnected, esp.
   when running [it] iteratively. ... we introduce the Leiden alg.. We prove
   that the Le.alg. yields communities that are guaranteed to be connected. [&]
   prove that, when the Le.alg. is applied iteratively, it converges to a
   partition in which all subsets of all communities are locally optimally
   assigned. ... [&] runs faster ..."
   -- [doi:10.1038/s41598-019-41695-z]['20].
   (Also see Louvain@[wikip]['20].)
   [Also search for: community network].

%A L. Piccirillo
%T The Conway knot is not slice
%J Annals of Mathematics
%V 191
%N 2
%M MAR
%D 2020
%K maths, jrnl, c2020, c202x, c20xx, zz0820, maths, knot theory, Conway, slice,
   4ball, 11n34, Crossings, Lisa Piccirillo, women, STEM
%X "A knot is said to be slice if it bounds a smooth properly embedded disk in
   the 4-ball. We demonstrate that the Conway knot, 11n34 in the Rolfsen tables,
   is not slice. This completes the class'n of slice knots under 13 crossings,
   & gives the 1st example of a non-slice knot which is both topologically slice
   & a positive mutant of a slice knot."
   -- [doi:10.4007/annals.2020.191.2.5]['20],
      [arXiv]['20], and
   Auth@[wikip]['20].

%A D. Q. Huynh
%T Metrics for 3D rotations: Comparison and analysis
%J J. Math Imaging Vis.
%V 35
%P 155-164
%M JUN
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0820, maths, Matrix Lie group, Lie algebra,
   Quaternion, SO3, 3D rotation, distance, similarity, norm, UWA
%X "3D rotations arise in many computer vision ... evaluation of the distance
   between two 3D rotns is often an essential task. ... presents a detailed
   analysis of six fns for measuring dist. between 3D rotns that have been
   proposed in the lit.. ... we demonstrate that five of them are biinvariant
   metrics on SO(3) but that only four of them are boundedly equiv. to each
   other. We conclude that it is both spatially & computationally more efficient
   to use q. for 3D rotns. Lastly, by treating the two rotns as a true & an est.
   rotn matrix, we illustrate the geometry assoc. with iso-error measures."
   -- [doi:10.1007/s10851-009-0161-2]['20] (online 18/6/2009).

%A A. Gaikwad
%A S. Maity
%A S. K. Tripathi
%T The satisfactory partition problem
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, maths, satisfactory partition problem, SPP,
   adequate, network, community, graph, vertex, vertices, modularity,
   Gerber, Kobler
%X "The Satisfactory Partition problem consists in deciding if the set of
   vertices of a given undirected g. can be partitioned into two nonempty parts
   s.t. each vertex has at least as many neighbours in its part as in the other
   part. ... its parameterized complexity remains open until now. ... It is
   known that the SP problem [&] a variant where the parts are required to be
   of the same cardinality, are NP-complete. ...  showing that (1) the problem
   is FPT when parameterized by the neighbourhood diversity of the input g.,
   (2) it can be solved in O(n^{8cw})) where cw is the clique-width, (3) a
   generalized version ... is W[1]-hard when parameterized by the treewidth."
   -- 2007.14339@[arXiv][28/7/20].
   (Also see Mod@[wikip]['20].)
   [Also search for: network modularity] and [also search for: graph partition].

%A I. Kontoyiannis
%A Y. Heng Lim
%A K. Papakonstantinopoulou
%A W. Szpankowski
%T Compression and symmetry of small-world graphs and structures
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, maths, graph, model, graphModel, compress
%X "... a graph can be examined at three levels. Its structure can be described
   as the unlabeled version of the g.; then the labeling of its structure can be
   added; & finally, given the structure & labeling, the contents of the labels
   can be described ... we focus on a class of small-world gs.. These are
   geometric random gs. ... establish the degree dist'n of this model ... derive
   the relevant entropy & structural entropy of these random gs., in connection
   with g.compression."
   -- 2007.15981@[arXiv]['20].
   [Also search for: graphModel].

%A R. K. Gautam
%A A. S. Kare
%A S. D. Bhavani
%T Faster heuristics for graph burning
%J arXiv
%M AUG
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, maths, graph, burn, burning, NPH, heuristic
%X "Graph burning is a process of info. spreading through the n/wk by an agent
   in discrete steps. The problem is to find an optimal seq. of nodes which have
   to be given info. so that the n/wk is covered in least # of steps. G.burning
   problem is NP-Hard for which two approx'n algs. & a few heuristics have been
   proposed ...  we propose three heuristics, namely, Backbone Based Greedy
   Heuristic (BBGH), Improved Cutting Corners Heuristic (ICCH) & Component Based
   Recursive Heuristic (CBRH). These are mainly based on Eigenvector centrality
   measure. ..."
   -- 2008.08811@[arXiv]['20].

%A Jiahao Guo
%A P. Singh
%A K. E. Bassler
%T Reduced network extremal ensemble learning (RenEEL) scheme for
   community detection in complex networks
%J Sci. Rep.
%V 9
%P #14234
%M OCT
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz0820, community detection, algorithm,
   network
%X "... ensemble learning scheme for community detection ... found by a
   conventional base alg., to find a node partition that maximizes modularity.
   At each iter'n, core groups of nodes that are in the same community in every
   ensemble part'n are identified & used to form a reduced n/wk. Partitions of
   the reduced n/wk are then found & used to update the ensemble. ..."
   -- [doi:10.1038/s41598-019-50739-3]['20].
   (Also see ComStr@[wikip]['20].)
   [Also search for: community network].

%A J. E. Hirsch
%T Superconductivity, what the H? The Emperor has no clothes
%J Physics and Society
%M JAN
%D 2020
%K publish, perish, JEHirsch, TR, c2020, c202x, c20xx, zz0820, news, views,
   physics, superconductor, Hindex, misuse, abuse, jrnl, KPI, KPIs, impact,
   university, scientific research, bibliometrics, wry,
   quote, quotable, controversial
%X "... For better or for worse, I am most famous (or infamous) for the
   invention of the Hindex. ... In a nutshell, my observation is that about half
   the scientific community loves the Hindex & half hates it, & the Hindex of
   the scientist itself is a great predictor of whether s/he belongs to the 1st
   or the 2nd group, in addition to its other virtues. I am not completely
   unhappy with the impact of my paper, which is by far my most highly cited
   one. As Oscar Wilde said, 'There is only one thing in life worse than being
   talked about ...'. ...  But I have now come to believe that it can also fail
   spectacularly & have severe unintended -ve consequences. I can understand how
   the sorcerer's apprentice must have felt. ..."
   -- 2001.09496@[arXiv]['20].
   [Also search for: publish perish].

%A Kok-Wei Bong
%A et al ...
%A H. M. Wiseman
%T A strong no-go theorem on the Wigner's friend paradox
%J Nat. Physics
%V ?
%M AUG
%D 2020
%K jrnl, physics, c2020, c202x, c20xx, zz0820, quantum theory, Wigner, friend,
   paradox, measurement, collapse, fact, facts, observation, observer,
   observed, event, events, determinism, superdeterminism, locality,
   objectivity, weirdness, absoluteness, inequality, theorem, Bell,
   inequalities, Bells, KokWeiBong, HMWiseman, GriffithUni
%X "Does quantum theory apply at all scales, inc. that of observers? ... Here,
   by building on a scenario with two separated but entangled friends introduced
   by Brukner, we prove that if q.evol'n is controllable on the scale of an
   observer, then one of 'No-Superdeterminism', 'Locality' or 'Absoluteness of
   Observed Events' - that every observed event exists absolutely, not
   relatively - must be false. We show that although the violation of Bell-type
   inequalities in such scenarios is not in general suff. to demo. the
   contradiction between those three assumptions, new inequalities can be
   derive ..."
   -- [doi:10.1038/s41567-020-0990-x][17/8/2020].
   Also see, "Testing the reality of Wigner's friend's observations", 4/2020,
   at 1907.05607@[arXiv]['20], and
   WF@[wikip]['20].

%A J. H. Ham
%A D. D. Lee
%A L. K. Saul
%T Learning high dimensional correspondences from low dimensional manifolds
%I Dept. Elec. & Sys. Eng., U. Penn.
%M AUG
%D 2003
%O Workshop on The Continuum from Labeled to Unlabeled Data in M.Learning &
   DataMining, at 20th ICML 2003
%K Ham03, wkshop, UPenn, c2003, c200x, c20xx, zz0820, manifold, manifolds,
   stats, dimension, dimensionality, reduction, PCA, stats, FactorAnalysis
%X "Many different high-D data sets are characterized by the same underlying
   modes of variability. When ... continuous & few in #, they can be viewed as
   parameterizing a low-D manifold. ... provides a compact shared rep'n of the
   data, suggesting corr. b/ween the high-D examples from different data sets.
   ... difficult to learn using trad. methods in supervised learning. ... we
   generalize three methods in unsupervised learning - principal components
   analysis, factor analysis, & locally linear embedding - to discover subspaces
   & manifolds that provide common low-D repns of different high-D data sets. We
   use the shared repns ... to put high-D examples from different data sets into
   corr.. Finally, we show that a notion of 'self-correspondence' b/ween
   examples in the same dataset can be used to improve the performance of these
   algs on small data sets. ... demonstrated on images & text."
   -- [UPenn]['20].
   [Also search for: FactorAnalysis]  and  [also search for: PCA stats].

%A V. R. Tabar
%A F. Elahi
%T A novel method for aggregation of Bayesian networks without considering an
   ancestral ordering
%J Applied AI
%V 32
%N 2
%P 214-227
%D 2018
%K jrnl, Bnet, c2018, c201x, c20xx, zz0820, Bnets, network, aggregate, combine,
   merge, Feng, II
%X "... ensures a combined BN meets three important criteria of avoiding cycles,
   preserving cond.independencies ... first combine the BNs using the mods. of
   the method intro. by Feng et al. We then use the sim.ann.alg. for getting an
   acyclic g. in which the minimum arcs have been removed. ..."
   -- [doi:10.1080/08839514.2018.1451134]['20].
   [Also search for: Bayesian network].


Search string: