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%A M. Held
%A R. M. Karp
%T A dynamic programming approach to sequencing problems
%J Proc. 1961 16th ACM nat. mtg
%P 71.201-71.204
%M JAN
%D 1961
%K conf, c1961, c196x, c19xx, zz0720, travelling salesman problem, TSP, DPA,
   scheduling, problem, algorithm, Held, Karp, Bellman
%X "... explores a DP approach to the soln of three sequencing problems: a
   scheduling problem involving arbitrary cost fns, the TSP, and an assembly
   line balancing problem. ..."
   -- [doi:10.1145/800029.808532]['20].
   [Also search for: travelling salesman problem DPA].
   (Also see TSP@[wikip]['20].)

%A R. Bellman
%T Dynamic programming treatment of the travelling salesman problem
%J JACM
%V 9
%N 1
%P 61-?
%M JAN
%D 1962
%K jrnl, JACM, c1962, c196x, c19xx, zz0720, travelling salesman problem, TSP,
   DPA, algorithm, Held, Karp, Bellman
%X -- [doi:10.1145/321105.321111]['20].
   [Also search for: travelling salesman problem DPA].
   (Also see TSP@[wikip]['20].)

%A N. Cotumaccio
%A N. Prezza
%T On indexing and compressing finite automata
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0720, FSA, FSM, DFA, DFSA, NFA, NFSA, automaton,
   machine, index, indexing, compress, BWT
%X "An index for a finite automaton is a powerful [DS] that supports locating
   paths labeled with a query pattern, thus solving pattern matching on the
   underlying regular language. ... we solve the long-standing problem of
   indexing arb. fin.automata. Our soln consists in finding a partial
   co-lexicographic order of the states & proving, as in the total order case,
   that states reached by a given string form one interval on the partial order,
   thus enabling indexing. ... lwb stating that such an interval requires O(p)
   words to be represented, p being the order's width ... show that p determines
   the complexity of several fundamental problems on fin.automata: (i) Letting
   sigma be the alphabet size, we provide an encoding for NFAs using
   ceil(log sigma)+2ceil(log p)+2 bits per transition & a smaller encoding for
   DFAs ... generalizing the Burrows-Wheeler transform to arbitrary automata.
   ..."
   -- 2007.07718@[arXiv]['20].

%A L. Kowalik
%A K. Majewski
%T The asymmetric travelling salesman problem in sparse digraphs
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0720, TSP, ATSP, maths, graph, directed, graphs,
   directed Hamiltonicity, algorithm
%X "Asymmetric Travelling Salesman Problem (ATSP) and its special case Directed
   Hamiltonicity are among the most fundamental problems in CS. The DPA running
   in time O^*(2^n) developed almost 60 years ago by Bellman, Held & Karp, is
   still the state of the art for both of these problems. ... We present two new
   det. algs.: the first running in time O(2^{0.441(d-1)n}) & polynomial space,
   & the second in exponential space with running time of O^*(t(d)^{n/2}) for
   a function t(d) <= d."
   -- 2007.12120@[arXiv]['20].
   [Also search for: travelling salesman problem].
   (Also see TSP@[wikip]['20].)

%A A. M. Lesk
%A A. S. Konagurthu
%A L. Allison
%A M. Garcia de la Banda
%A P. J. Stuckey
%A D. Abramson
%T Computer modelling of a potential agent against SARS-Cov-2 (COVID-19)
   protease
%J Proteins: Structure, Function and Bioinformatics
%V ?
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, SARS-CoV-2, SARSCoV2, protease,
   protein, Mpro, 3CLpro, nsp5, covid19, covalent, inSilico, ligand,
   inhibitor, Cys145, AMLesk, LAllison, ArunK
%X "We have modelled modifications of a known ligand to the SARS‐CoV‐2
   (COVID‐19) protease, that can form a covalent adduct, plus additional
   ligand‐protein hydrogen bonds."
   -- [doi:10.1002/prot.25980]['20]  (online 14/7/2020).
   [Also search for: SARSCoV2 protease].

%A Qi-Shi Du
%A et al ...
%A Kuo-Chen Chou
%T Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of
   the octapeptide
%J Peptides
%V 25
%N 11
%P 1857-1864
%M NOV
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, zz0720, KuoChenChou, SARS CoV 1, SARSCoV,
   SARSCoV1, SARS1, Mpro, protease, protein, mechanism, cleave, cleaves,
   cleaving, polyprotein, octaprotein, octapeptide, AVLQSGFR,
   3CLpro, His41, Cys, Cys145, active site, sites, distorted key, working, works
%X "The cleavage mechanism of severe acute respiratory syndrome (SARS)
   coronavirus main proteinase (Mpro or 3CLpro) for the octapeptide AVLQSGFR ...
   The catalytic dyad His-41 & Cys-145 in the active pocket between domain I
   & II seem to polarize the pi-electron density of the peptide bond between
   Gln & Ser ..."    [cleaves after the 'Q'}.
   -- [doi:10.1016/j.peptides.2004.06.018]['20].
   [Also search for: KuoChenChou] & [also search for: MolBio SARS Mpro cleaves].

%A S. C. Madeira
%A A. L. Oliveira
%T A polynomial time biclustering algorithm for finding approximate expression
   patterns in gene expression time series
%J Algs. for Molec. Biol.
%V 4
%N #8
%M JUN
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0720, gene ecpression, time series, timeSeries,
   biclustering, coclustering
%X "... propose e-CCC-Biclustering, a biclustering alg. that finds & reports all
   maximal contiguous column coherent biclusters with approx. expression
   patterns in time polynomial in the size of the time series gene expression
   matrix. This polynomial time complexity ..."
   -- [doi:10.1186/1748-7188-4-8]['20].
   (Also see bicl@[wikip]['20].)

%T CurlySMILES: a chemical language to customize and annotate encodings of
   molecular and nanodevice structures
%J J. Cheminform.
%V 3
%N 1
%M JAN
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0720, CurlySMILES, SMILES, chemical
%X "CurlySMILES is a chemical line notation which extends SMILES with
   annotations for storage, retrieval & modeling of interlinked, coordinated,
   assembled & adsorbed molecules in supramolecular structures & nanodevices.
   Annotations are enclosed in curly braces & anchored to an atomic node or at
   the end of the molecular graph depending on the annotation type. ..."
   -- [doi:10.1186/1758-2946-3-1]['20].
   [Also search for: SMILES chemical].

%A R. Lister
%A et al ...
%A J. R. Ecker
%T Hotspots of aberrant epigenomic reprogramming in human induced pluripotent
   stem cells
%J Nature
%V 471
%P 68-73
%M FEB
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0720, cell, cellular differentiation,
   cells, tissue types, kinds, epigenetic, induced pluripotent stem cells,
   iPSCs, histone, regulation
%X "... Somatic cell reprogramming involves epigenomic reconfig., conferring
   iPSCs with characteristics similar to embryonic stem (ES) cells. However, it
   remains unknown how complete the reestablishment of ES-cell-like DNA
   methylation patterns is throughout the genome. Here we report the first
   whole-genome profiles of DNA methylation at single-base resolution in five
   human iPSC lines, along with methylomes of ES cells, SCs, & differentiated
   iPSCs & ES cells. iPSCs show sig. reprogramming variability ... iPSCs share
   megabase-scale differentially methylated regions proximal to centromeres &
   telomeres that display incomplete reprogramming of non-CG m., & differences
   in CG m. & histone modifications. Lastly, differentiation of iPSCs into
   trophoblast cells revealed that errors in reprogramming CG m. are transmitted
   at a high freq., providing an iPSC reprogramming signature that is maintained
   after differentiation."
   -- [doi:10.1038/nature09798]['20].
   (Also see cellDiff@[wikip]['20].)

%A J. Hopper
%A E. Makalic
%A D. Schmidt
%A M. Bui
%A J. Stone
%A M. Kapuscinski
%A D. Park
%A M. Jenkins
%A M. Southey
%T 'Next-generation' genome wide association studies
%J Hered. Cancer in Clin. Pract.
%V 10
%P #A48
%M APR
%D 2012
%K jrnl, MolBio, GWAS, c2012, c201x, c20xx, zz0720, stats, Illumina 5M SNP,
   SNPs, breast cancer
%X "The 1st wave of cancer ... (GWAS) have revealed tens of indep. loci marked
   by common variants of unknown or likely no functional significance that
   explain about 5-10% of familial risk for the particular disease. The approach
   taken to date has been conservative ... the Bonferroni procedure for
   selecting candidate phase II SNPs ignores many SNPs that happen to fail an
   extremely low p-value threshold. While ... does guarantee control of false
   ^ves, it seems counterintuitive to the purpose of phase I, which is to gen.
   hypotheses based on promising candidates. ... It is plausible that more info.
   should be extracted if: (i) higher order interactions are fitted, (ii) highly
   selected cases and controls are used in phase I, (iii) large replication
   studies are used, esp. if involving existing GWAS data, (iv) the non-indep.
   of SNPs is taken into account using, e.g. BEAGLE CALL or haplotype analyses,
   (v) focus is on candidate gene pathways, and/or functional SNPs, and
   (vi) rarer and more SNPs, such as is available from the Illumina 5M SNP chip,
   are used. ... also discuss the design of a large int. breast cancer GWAS
   using the Illumina 5M SNP chip, phase I cases enriched for family history,
   pop'n-based phase II cases and controls, pop'n-based family study of
   candidate SNPs, and GxG analyses using 'massively parallel' super computing."
   -- [doi:10.1186/1897-4287-10-S2-A48]['20].
   [Also search for: GWAS].

%A S. C. Madeira
%A M. C. Teixeira
%A I. Sa-Correia
%A A. L. Oliveira
%T Identification of regulatory modules in time series gene expression data
   using a linear time biclustering algorithm
%J IEEE/ACM Trans. on Comp. Biol. and Bioinf.
%V 7
%N 1
%M JAN-MAR
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0720, CCC biclustering, coclustering,
   contiguous, consecutive, columns, time series, timeSeries, gene expression
%X "... most biclustering formulations are NP-hard [but] restrict the problem to
   the identification of maximal biclusters with contiguous columns, which
   corr.to coherent exp'n patterns shared by a group of genes in consec. time
   pts. This restriction leads to a tractable problem. ... linear time
   complexity of CCC-Biclustering relies on the use of a discretized matrix &
   efficient string proc. techniques based on suff'x trees. ... Results obtained
   using the transcriptomic expression patterns occurring in Saccharomyces
   cerevisiae in response to heat stress ..."
   -- [doi:10.1109/TCBB.2008.34]['20],
    & [.pt]['20].
   (Also see bicl@[wikip]['20].)

%A J.-B. Petit
%A et al ...
%A J. Marioni
%T Identifying cell types from spatially referenced single-cell expression
   datasets
%J PLoS Comp. Biol.
%V ?
%M SEP
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0720, scRNAseq, cell expression profile,
   tissue, 3D, spatial, HMRF, MRF, Markov random field, clustering,
   Wholemount, WiSH
%X "...  experimental technology, such as Wholemount in Situ Hybridizations
   (WiSH) & single-cell RNA-sequencing. ... now possible to study gene expn
   levels in thousands of cells from the same tissue type. After generating such
   data one of the key goals is to cluster the cells into groups that correspond
   to both known & putatively novel cell types. Whilst many clustering algs.
   exist, they are typically unable to incorporate information about the spatial
   dependence between cells within the tissue under study. When such info.
   exists it provides important insights that should be directly inc. in the
   clustering scheme. To this end we have developed a clustering method that
   uses a Hidden Markov Random Field (HMRF) model to exploit both quantitative
   measures of expression & spatial information. ..."
   -- [doi:10.1371/journal.pcbi.1003824M]['20].
   [Also search for: Markov random field].

%A K. Achim
%A et al ...
%A J. C. Marioni
%T High-throughput spatial mapping of single-cell RNA-seq data to tissue of
   origin
%J Nat. Biotechnol.
%V 33
%N 5
%P 503-509
%M MAY
%D 2015
%K jrnl, eJrnl, c2015, c201x, c20xx, zz0720, scRNAseq, scRNA-seq, RNA, mRNA,
   cell expression profile, tissue
%X "... cell type identity ... we present a high-throughput method to identify
   the spatial origin of cells assayed by single-cell RNA-sequencing within a
   tissue of interest. ... mRNA profiles ..."
   -- [doi:10.1038/nbt.3209]['20].
   [Also search for: scRNAseq].

%A J. Shin
%A et al ...
%A H. Song
%T Single-cell RNA-seq with Waterfall reveals molecular cascades underlying
   adult neurogenesis
%J Cell Stem Cell
%V 17
%N 3
%P 360-372
%M SEP
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0720, Waterfall, single cell RNA seq,
   RNAseq, scRNAseq, expression, trajectory
%X "... single-cell transcriptomes of adult hippocampal quiescent neural stem
   cells (qNSCs) and their immediate progeny. We further developed Waterfall, a
   bioinformatic pipeline ... reconstructed cts developmental trajectory. ..."
   -- [doi:10.1016/j.stem.2015.07.013]['20].
   (Also see RNAseq@[wikip]['20].)
   [Also search for: scRNAseq].

%A D. Grun
%A et al ...
%A A. van Oudenaarden
%T De novo prediction of stem cell identity using single-cell transcriptome data
%J Cell Stem Cell
%V 19
%N 2
%P 266-277
%M AUG
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0720, single cell RNA seq, RNAseq,
   scRNAseq, trajectory, expression, stemCell
%X "... StemID, an alg. for id. stem cells among all detectable cell types
   within a popn. We demonstrate that StemID recovers two known adult stem cell
   popns, Lgr5+ cells in the small intestine & hematopoietic stem cells in the
   bone marrow. We apply StemID to predict candidate multipotent cell ..."
      "... reduce the dimensionality ... single inter-cluster link [linkage]
       ... medoid ..."
   -- [doi:10.1016/j.stem.2016.05.010]['20].
   [Also search for: scRNAseq]  and  [also search for: single link].

%A Zhicheng Ji
%A Hongkai Ji
%T TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq
   analysis
%J NAR
%V 44
%N 13
%P e117
%M JUL
%D 2016
%K jrnl, eJrnl, MolBio, c2016, c201x, c20xx, zz0720, single cell RNA seq,
   RNAseq, scRNAseq, expression, time series, timeSeries
%X "... Tools for Single Cell Analysis (TSCAN) is a s/w tool [for] in silico
   pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis. ... uses a
   cluster-based min.span.tr. (MST) approach to order cells. Cells are
   1st grouped into clusters & an MST is then constructed to connect cluster
   centers. Pseudo-time is obtained by projecting each cell onto the tree, & the
   ordered seq. of cells can be used to study dynamic changes of gene expression
   along the pseudo-time. Clustering cells before MST construction reduces the
   complexity of the tree space. ... often leads to improved cell ordering. ..."
   -- [doi:10.1093/nar/gkw430]['20].
   Also see TSCAN@[g'thub]['20].
   (Also see RNAseq@[wikip]['20].)
   [Also search for: scRNAseq].

%A G. La Manno
%A et al ...
%A S. Linnarsson
%T Molecular diversity of midbrain development in mouse, human, and stem cells
%J Cell
%V 167
%N 2
%P 566-580.e19
%M OCT
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0720, LaManno, human, mouse, brain,
   glia, stem cells, stemCell, scRNA-seq, scRNAseq
%X "... We performed single-cell RNA seq. to examine ventral midbrain
   development in human & mouse. We found 25 molecularly defined human cell
   types, inc. five subtypes of radial glia-like cells & four progenitors. In
   the mouse, two mature fetal dopaminergic neuron subtypes diversified into
   five adult classes during postnatal development. Cell types & gene expression
   were generally conserved across species, but with clear differences in cell
   proliferation, developmental timing, & dopaminergic neuron development. ..."
   -- [doi:10.1016/j.cell.2016.09.027].
   [Also search for: MolBio stem cell].

%A T. Muramatsu
%A et al ...
%A S. Yokoyama
%T SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel
   subsite cooperativity
%J PNAS
%V 113
%N 46
%P 12997-13002
%M NOV
%D 2016
%K jrnl, PNAS, MolBio, c2016, c201x, c20xx, zz0720, SARS CoV 1, SARS1, 3CLpro,
   Mpro, protease, cleave, cleaves, cleaving, polyprotein, pp1a, pp1b, works,
   working, specificity, Cys, Cys145, site, sites, concensus, profile
%X "The 3C-like protease (3CLpro) of severe acute respiratory syndrome
   coronavirus (SARS-CoV) cleaves 11 sites in the polyproteins, inc. its own
   N- and C-terminal autoprocessing sites, by recognizing P4-P1 and P1'. In this
   study, we determined the crystal structure of 3CLpro with the C-terminal
   prosequence & the catalytic-site C145A mutation, in which the enzyme binds
   the C-terminal prosequence of another molecule. ..."
    [cleaves RQCSGVTFQGKFKKIVKG,
             TSITSAVLQSGFRKMAFP,
             PCIKVATVQSKMSDVKCT,
             MLDNRATLQAIASEFSSL,
             RANSAVKLQNNELSPVAL,
             SLAATVRLQAGNATEVPA,
             DQLREPLMQSADASTFLN,
             MYTPHTVLQAVGACVLCN,
             PRRNVATLQAENVTGLFK,
             LWNTFTRLQSLENVAYNV,
             VETFYPKLQASQAWQPGV, after the Q I think. & concensus logo profile]
   -- [doi:10.1073/pnas.1601327113]['20].
   [Also search for: MolBio SARS Mpro cleaves].

%A R. Rostom
%A V. Svensson
%A S. A. Teichmann
%A G. Kar
%T Computational approaches for interpreting scRNA-seq data
%M MAY
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0720, single cell RNA seq, RNAseq,
   scRNAseq, analysis, cell types, gene expression levels
%X "... new modes of data analysis, building on high-dimensional data mining
   techniques. Here, we consider biological questions for which scRNA-seq data
   is used, both at a cell & gene level, & describe tools available for these
   types of analyses. This is an exciting & rapidly evolving field, where
   clustering, pseudotime inference, branching inference & gene-level analyses
   are particularly informative areas of computational analysis."
   -- [doi:10.1002/1873-3468.12684]['20].
   [Also search for: scRNAseq].

%A K. Street
%A et al ...
%A S. Dudoit
%T Slingshot: cell lineage and pseudotime inference for single-cell
   transcriptomics
%J BMC Genomics
%V 19
%N 477
%M JUN
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0720, single cell RNA seq, RNAseq,
   scRNAseq, expression, cell type, lineage, TSCAN, Monocle, DPT
%X "... Slingshot, a novel method for inferring cell lineages and pseudotimes
   from single-cell gene expression data. In prev. published datasets, Slingshot
   correctly identifies the biological signal for one to three branching
   trajectories. ..."
      "... first stage uses a cluster-based MST ... second stage, we propose a
      novel method called simultaneous principal curves, to fit smooth branching
      curves to these lineages ..."
   -- [doi:10.1186/s12864-018-4772-0]['20].
   (Also see RNAseq@[wikip]['20].)
   [Also search for: scRNAseq].

%A K. Michailidou
%A et al (!)
%T Association analysis identifies 65 new breast cancer risk loci
%J Nature
%V 551
%N 7678
%P 92-94
%M OCT
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0720, breast cancer, GWAS, Schmidt, Makalic,
   SNPs
%X "... report the results of a genome-wide association study of breast cancer
   in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases
   and 13,104 controls of East Asian ancestry1. We identified 65 new loci that
   are associated with overall breast cancer risk at P < 5x10^{-8}. The majority
   of credible risk single-nucleotide polymorphisms in these loci fall in
   distal regulatory elements ..."
   -- [doi:10.1038/nature24284]['20].
   (Also see GWAS@[wikip]['20].)

%A F. A. Wolf
%A et al ...
%A F. J. Theis
%T PAGA: graph abstraction reconciles clustering with trajectory inference
   through a topology preserving map of single cells
%J Genome Biol.
%V 20
%P #59
%M MAR
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0720, single cell RNA seq, RNAseq,
   scRNAseq
%X "... Partition-based graph abstraction (PAGA) provides an interpretable
   graph-like map of the arising data manifold, based on est. connectivity of
   manifold partns [g'thub]."
   -- [doi:10.1186/s13059-019-1663-x]['20].
   [Also search for: scRNAseq].

%A Haoji Wu
%A et al ...
%A B. D. Humphries
%T Comparative analysis and refinement of human PSC-derived kidney organoid
   differentiation with single-cell transcriptomics
%J Cell Stem Cell
%V 23
%N 6
%P 869-881.e8
%M DEC
%D 2018
%K jrnl, MolBio, organoid, c2018, c201x, c20xx, zz0720, kidney, transcriptome,
   PSC, BDNF, Dropseq, scRNAseq. scRNA-seq
%X "...We compared two directed differentiation protocols by single-cell
   transcriptomics of 83,130 cells from 65 organoids with single-cell
   transcriptomes of fetal and adult kidney cells. Both protocols generate a
   diverse range of kidney cells with differing ratios, but organoid-derived
   cell types are immature, and 10%-20% of cells are non-renal. Reconstructing
   lineage relationships by pseudotemporal ordering identified ligands,
   receptors, & transcr'n factor networks associated with fate decisions. ..."
   -- [doi:10.1016/j.stem.2018.10.010]['20].
   [Also search for: scRNAseq MolBio].

%A S. Mayer
%A et al ...
%A A. R. Kriegstein
%T Multimodal single-cell analysis reveals physiological maturation in the
   developing human neocortex
%J Neuron
%V 102
%N 1
%P 143-158.e7
%M APR
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0720, cell, human, brain, neocortex,
   neurons, glia, HTR2A, neurotransmitter, differentiation
%X "... While single-cell RNA sequencing has revealed cellular diversity,
   physiological heterogeneity has yet to be mapped onto these developing &
   diverse cell types. By combining measurements of intracellular Ca2+
   elevations in response to neurotransmitter receptor agonists & RNA sequencing
   of the same single cells, we show that Ca2+ responses are cell-type-specific
   & change dynamically with lineage progression. Physiological response
   properties predict molecular cell identity & additionally reveal diversity
   not captured by single-cell transcriptomics. ..."
   -- [doi:10.1016/j.neuron.2019.01.027]['20].
   [Also search for: MolBio cell differentiation].

%A T. N. Tran
%A G. D. Bader
%T Tempora: cell trajectory inference using time-series single-cell RNA
   sequencing data
%J bioRxiv
%M NOV
%D 2019
%K TR, MolBio, c2019, c201x, c20xx, zz0720, cell, RNA seq, RNAseq, scRNAseq,
   trajectory, time series, timeSeries, Monocle, TSCAN, Slingshot, PAGA,
   StemID
%X "Single-cell RNA sequencing (scRNAseq) can map cell types, states &
   transitions during dynamic biol. processes such as development & regen.. Many
   trajectory inference methods have been developed ... Tempora, a novel cell
   trajectory inference method that orders cells using time info. from
   time-series scRNAseq data. ... Tempora accurately inferred developmental
   lineages in human skeletal myoblast differentiation & murine cerebral cortex
   development ..."
   -- [doi:10.1101/846907 ]['20].
   (Also see RNAseq@[wikip]['20].)
   [Also search for: scRNAseq].

%A J. Liang
%A et al ...
%A T. C. Karagiannis
%T Interaction of the prototypical alpha-ketoamide inhibitor with the SARS-CoV-2
   main protease active site in silico: Molecular dynamic simulations highlight
   the stability of the ligand-protein complex
%J Comput. Biol. Chem.
%V 87
%P 107292
%M MAY
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, SARS-CoV-2, SARSCoV2, protease,
   Mpro, alpha-ketoamide, MonashUni
%X "... An important target is the SARS-CoV-2 main protease (Mpro), involved in
   processing translated viral proteins. Peptidomimetic A-ketoamides represent
   prototypical inhibitors of Mpro. A recent attempt at designing a compound
   with enhanced pharmacokinetic properties has resulted in the synthesis &
   evaln of the A-ketoamide 13b analogue. Here, we performed molecular docking &
   molec.dynamics simulations to further characterize the interaction of
   A-ketoamide 13b with the active site of the SARS-CoV-2 Mpro. ..."
   -- [doi:10.1016/j.compbiolchem.2020.107292]['20] (online May 2020),
      32485652@[pubm'd]['20].
   [Also search for: SARSCoV2 Mpro].

%A J. Lee
%A et al ...
%A K. R. Koehler
%T Hair-bearing human skin generated entirely from pluripotent stem cells
%j Nature
%V 582
%P 399-404
%M JUN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, human, stem cells, stemCell, hair,
   skin, organoid, scRNA-seq, scRNAseq
%X "The skin is a multilayered organ, equipped with appendages (that is,
   follicles and glands), that is critical for regulating body temperature and
   the retention of bodily fluids, guarding against external stresses and
   mediating the sensation of touch and pain. ... report an organoid culture
   system that generates complex skin from human pluripotent stem cells. ..."
   -- [doi:10.1038/s41586-020-2352-3]['20].
   [Also search for: organoid] and [also search for: scRNAseq].

%A H. J. Abel
%A et al ...
%A I. M. Hall
%T Mapping and characterization of structural variation in 17,795 human genomes
%J Nature
%V 583
%P 83-89
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, human genomes, DNA,
   structural variations
%X "... used a scalable pipeline to map & characterize structural variants in
   17,795 deeply sequenced human genomes. ... release site-freq. data to create
   the largest, to our knowledge, whole-genome-seq.-based struct.variant
   resource so far. On average, individuals carry 2.9 rare s.variants that
   alter coding regions; these variants affect the dosage or struct. of 4.2
   genes & account for 4.0-11.2% of rare high-impact coding alleles. Using a
   comp'l model, we est. that s.variants account for 17.2% of rare alleles
   genome-wide, with predicted deleterious effects that are equiv. to
   loss-of-fn coding alleles; ~90% of such s.variants are noncoding deletions
   (mean 19.1 per genome). We report 158,991 ultra-rare s.variants & show that
   2% of individuals carry ultra-rare megabase-scale s.variants, nearly half of
   which are balanced or complex rearrangements. Finally, we infer the dosage
   sensitivity of genes & noncoding elts, & reveal trends that relate to elt
   class & conservation. ..."
   -- [doi:10.1038/s41586-020-2371-0]['20],  pub. 27/5/2020.

%A J. C. Wheat
%A et al
%A U. Steidl
%T Single-molecule imaging of transcription dynamics in somatic stem cells
%J Nature
%V 583
%P 431-436
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, smFISH, single molecule RNA,
   fluorescent insitu hybridization, PU1, Spi1, Gata1, Gata2, stemCell,
   somatic, adult
%X "... we use single-molec. RNA fluorescent in situ hybridization (smFISH) on
   mouse stem cells derived from haematopoietic tissue to measure the
   transcription dynamics of three key genes that encode transcription factors:
   PU.1 ([AKA] Spi1), Gata1 & Gata2. ... infrequent, stochastic bursts of
   transcription result in the co-expression of these antagonistic transcription
   factors in the majority of haematopoietic stem & progenitor cells. Moreover,
   by pairing smFISH with time-lapse microscopy & the analysis of pedigrees, we
   find that although individual stem-cell clones produce descendants that are
   in transcriptionally related states - akin to a trans.priming phenomenon -
   the underlying transition dynamics between states are best captured by
   stochastic & reversible models. As such, a stoch. process can produce
   cellular behaviours that may be incorrectly inferred to have arisen from
   deterministic dynamics. We propose a model whereby the intrinsic stoch'y of
   gene expn facilitates, rather than impedes, the concomitant maintenance of
   transcriptional plasticity & stem cell robustness."
   -- [doi:10.1038/s41586-020-2432-4]['20].
   (Also see StemC@[wikip]['20].)

%A A. M. Andrianov
%A Y. V. Kornoushenko
%A A. D. Karpenko
%A I. P. Bosko
%A A. V. Tuzikov
%T Computational discovery of small drug-like compounds as potential inhibitors
   of SARS-CoV-2 main protease
%J J. Biomolec. Structs. and Dynamics
%V ?
%P ?-?
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, SARS-CoV-2, SARSCoV2, Mpro,
   3CLpro, protease, protein, inhibitor, ligand, X77, Pharmit, His41, Met49,
   Cys145, Met165, Gln189, inSilico
%X "... mimicry of the high affinity ligand X77, potent non-covalent inhibitor
   of SARS-COV-2 main protease (MPro). In doing so, the X77-mimetic candidates
   were predicted based on the crystal X77-MPro structure by a public
   web-oriented virtual screening platform Pharmit. ... Calculation revealed
   5 top-ranking compounds that exhibited a high affinity to the active site of
   SARS-CoV-2 MPro. ... van der Waals interactions with the functionally
   important residues of the enzyme, such as His-41, Met-49, Cys-145, Met-165, &
   Gln-189 ..."
   -- [doi:10.1080/07391102.2020.1792989]['20]  (online 7/2020),
      12275390/1@[chemRxiv]['20].
   [Also search for: SARSCoV2 protease].

%A P. M. Folegatti
%A et al ...
%A A. J. Pollard
%T Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2:
   a preliminary report of a phase 1/2, single-blind, randomised controlled
   trial
%J The Lancet
%V 396
%N 10249
%P P467-478
%M AUG
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0720, SARS-CoV-2, SARSCoV2, covid19, covid-19,
   ChAdOx1, vaccine, Oxford, UniOxford, clinical trial
 %X "... We did a phase 1/2, single-blind, randomised controlled trial in five
   trial sites in the UK of a chimpanzee adenovirus-vectored vaccine
   (ChAdOx1 nCoV-19) expressing the SARS-CoV-2 spike protein compared with a
   meningococcal conjugate vaccine (MenACWY) as control. ... ChAdOx1 nCoV-19
   showed an acceptable safety profile, and homologous boosting increased
   antibody responses. ..."
   -- [doi:10.1016/S0140-6736(20)31604-4]['20]  (online JUL 2020).
   [Also search for: SARSCoV2].

%A M. Di Antonio
%A et al ...
%A S. Balasubramanian
%T Single-molecule visualization of DNA G-quadruplex formation in live cell
%J Nat. Chem.
%V 12
%P 832-837
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, DiAntonio, DNA, quadruplex, G4s,
   four stranded, gene expression, cell cycle, SiR-PyPDS
%X "Substantial evidence now exists to support that formation of DNA
   G-quadruplexes (G4s) is coupled to altered gene expression. ..."
      ("G-quadruplexes (G4s) are non-canonical structures that can form within
       guanine-rich nucleic-acid sequences ... over 700,000 distinct sites that
       can form G4s ...")
   -- [doi:10.1038/s41557-020-0506-4]['20]  (18 refs, online 20/7/2020).
  (4 guanines can form a square.)

%A D. Jebb
%A et al ...
%A E. C. Teeling
%T Six reference-quality genomes reveal evolution of bat adaptations
%J Nature
%V 583
%P 578-584
%M JUL
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0720, MolBio, bat, bats, Chiroptera, Ngenome,
   genome, genomes, evolution, Scrotifera, echolocation, immunity,
   immune system, APOBEC3, LRRC70, IL36G, viral, viruses
%X "... the first reference-quality genomes of six bat species (Rhinolophus
   ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis,
   Pipistrellus kuhlii & Molossus molossus). ... identified a basal origin for
   bats within Scrotifera. ... found selection & loss of immunity-related genes
   (including pro-inflammatory NF-kB regulators) & expansions of anti-viral
   APOBEC3 genes, which highlights molecular mechanisms that may contribute to
   the exceptional immunity of bats...."
   -- [doi:10.1038/s41586-020-2486-3]['20].
   [Also search for: MolBio bat genome].

%A M. Trump
%T Too Much And Never Enough: How My Family Created the World's Most
   Dangerous Man
%I SimonAndSchuster
%P 240
%M JUL
%D 2020
%K book, c2020, c202x, c20xx, zz0720, USA, politics, president, Trump, Potus,
   niece, uncle, Trumpery
%X 1st ed 2020; hb us$25; uk us isbn:1982141468; uk us isbn13:978-1982141462.
   "... Donald's only niece, shines a bright light on the dark history of their
   family in order to explain how her uncle became the man who now threatens the
   world's health, economic security, and social fabric. ..."
   (Also see the [bbc][16/6/2020].)
   [Also search for: USA President Trump].

%A J. Bolton
%T The Room Where It Happened: A White House Memoir
%I SimonAndSchuster
%P 592
%M JUL
%D 2020
%K book, memoir, c2020, c202x, c20xx, zz0720, USA, politics, president,
   National Security Advisor, Oval Office, West Wing, White House, Washington,
   foreign policy, Trump, Trumpery, Ukraine, Putin, Russia, Xi, China, election,
   interference
%X 1st ed 2020; hb us$41; uk us isbn:1982148039; uk us isbn13:978-1982148034.
   "... comprehensive and substantial account of the Trump Administration, and
   one of the few to date by a top-level official. With almost daily access to
   the President ..."
   [Also search for: USA President Trump].

%A S. Richie
%T Science Fictions: How Fraud, Bias, Negligence, and Hype Undermine the
   Search for Truth
%I MetropolitanBooks
%P 368
%M JUL
%D 2020
%K book, c2020, c202x, c20xx, zz0720, science, scientific, university, research,
   ethics, fraud, misconduct, manipulation, stats, errors, mistake, peer review,
   reviewing, pressure, impact, KPI, KPIs, Hindex, Phacking
%X 1st ed 2020; hb us$23; uk us isbn:1250222699; uk us isbn13:978-1250222695.
   "... failures in peer review and mistakes in statistics have rendered a
   shocking number of scientific studies useless - or, worse, badly misleading.
   ... reveals the very human biases, misunderstandings, and deceptions that
   undermine the scientific endeavor: from contamination in science labs to the
   secret vaults of failed studies that nobody gets to see; from outright
   cheating with fake data to the more common, but still ruinous, temptation to
   exaggerate mediocre results for a shot at scientific fame. ..."

%A G. Hall
%A L. Massoulie
%T Partial recovery in the graph alignment problem
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0720, maths, graph, alignment, matching,
   graphAlignment, MCES, approximate, noisy isomorphism
%X "... the graph alignment problem ... recovering, given two graphs, a
   one-to-one mapping between nodes that maximizes edge overlap. ... can be
   viewed as a noisy version of the well-known graph isomorphism problem &
   appears in many applications, inc. social network deanonymization & cellular
   biology. Our focus here is on partial recovery, i.e., we look for a 1-to-1
   mapping which is correct on a fraction of the nodes of the g. rather than on
   all of them, & we assume that the two input gs to the problem are correlated
   ErdosRenyi gs of parameters (n,q,s). Our main contribution is then to give
   nec. & suff. conditions on (n,q,s) under which partial recovery is possible
   with high prob. as the # of nodes n goes to infinity. These conditions are
   compact, easily interpretable, & cover [most] of the parameter space."
   -- 2007.00533@[arXiv]['20].
   [Also search for: graphAlignment].

%A C. de Rham
%A A. J. Tolley
%T The speed of gravity
%J arXiv
%M SEP
%D 2019
%K TR, physics, c2019, c201x, c20xx, zz0720, deRham, speed, mass, gravity,
   light, cosmology, relativity, gravitational waves, quantum
%X "Within the std effective field theory of General Relativity, we show that
   the speed of gravitational waves deviates, ever so slightly, from luminality
   on cosmological & other spontaneously Lorentz-breaking backgrounds. This
   effect results from loop contributions from massive fields of any spin ...
   speed of grav.waves is in general superluminal at low-energies on NEC
   preserving backgrounds, meaning grav.waves travel faster than allowed by the
   metric to which photons & Std Model fields are minimally coupled. We show
   that departure of the speed from unity increases in the IR & argue that the
   speed inevitably returns to luminal at high energies as required by Lorentz
   invariance ..."
   -- 1909.00881@[arXiv]['20],
      CdeR@[Imp.C.]['20].

%A L. B. Thingholm
%A L. Andersen
%A E. Makalic
%A M. C. Southey
%A M. Thomassen
%A L. Lotte Hansen
%T Strategies for integrated analysis of genetic, epigenetic, and gene
   expression variation in cancer: Addressing the challenges
%J Front. Genet.
%M FEB
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0720, review, genetic, GWAS,
   UniMelb, UMelb
%X "... review article will provide an introduction to integration strategies
   used for analyzing genetic risk factors for cancer. We critically examine the
   ability of these strategies to handle the complexity of the human genome and
   also accommodate information about the biological and functional interactions
   between the elements that have been measured - making the assessment of
   disease risk against a composite genomic factor possible. The focus of this
   review is to provide an overview and introduction to the main strategies and
   to discuss where there is a need for further development."
   -- [doi:10.3389/fgene.2016.00002]['20].
   (Also see GWAS@[wikip]['20].)

%A D. F.Schmidt
%A E. Makalic
%T Minimum message length analysis of multiple short time series
%J Stats. and Prob. Lett.
%V 110
%P 318-328
%M MAR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0720, MML, mdl, multiple short time series,
   several, many, timeSeries, trajectory, stats, model, conditional likelihood
%X "... applies the Bayesian minimum message length principle to the multiple
   short time series problem, yielding satisfactory estimates for all model
   parameters as well as a test for autocorrelation. Connections with the method
   of conditional likelihood are also discussed."
   -- [doi:10.1016/j.spl.2015.09.021]['20], and
   2O15 preprint@[r'srchg'te]['20].

%A E. Makalic
%A D. F. Schmidt
%T High-dimensional Bayesian regularised regression with the BayesReg package
%J arXiv
%M NOV
%D 2016
%K TR, c2016, c201x, c20xx, zz0720, BayesReg, regression, stats, R, RR
%T "B. penalized regression techniques, such as the B. lasso & the B. horseshoe
   estimator ... However, s/w implementing state-of-the-art B.penalized
   regression, outside of general purpose Markov chain M.C. platforms such as
   STAN, is relatively rare. This paper introduces bayesreg, a new toolbox for
   fitting B.penalized regression models with continuous shrinkage prior
   densities. ... features B.linear regression with Gaussian or heavy-tailed
   error models & B. logistic regression with ridge, lasso, horseshoe &
   horseshoe+ ests.. ... is free, open-source & available for use with the
   MATLAB & R numerical platforms."
   -- 1611.06649@[arXiv]['20].


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