This is a list of all the questions and their associated study carrel identifiers. One can learn a lot of the "aboutness" of a text simply by reading the questions.
| identifier | question |
|---|---|
| cord-018459-isbc1r2o | Integrating alignment- based and alignmentfree sequence similarity measures for biological sequence classification Hidden Markov models with applications to DNA sequence analysis Is multiple- sequence alignment required for accurate inference of phylogeny? |
| cord-011565-8ncgldaq | Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing MetaPalette: a k- mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation MISSION: ultra large- scale feature selection using count- sketches Large- scale machine learning for metagenomics sequence classification How much metagenomic sequencing is enough to achieve a given goal? |
| cord-000642-mkwpuav6 | Perkinsus marinus Evidence indicating the existence of a novel family of serine protease inhibitors that may be involved in marine invertebrate immunity Serine protease inhibitor cvSI-1 potential role in the eastern oyster host defense against the protozoan parasite Perkinsus marinus Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? |
| cord-017932-vmtjc8ct | The Salmonella pathogenicity island-1 type III secretion system Capsule switching of Neisseria meningitides Capsules and cassettes: genetic organization of the capsule locus of Streptococcus pneumoniae Genetic and molecular characterization of capsular polysaccharide biosynthesis in Streptococcus pneumoniae type 3 Massive gene decay in the leprosy bacillus Yersinia pestis-etiologic agent of plague Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis Microbial proteomics From proteins to proteomes: large scale protein identification by twodimensional electrophoresis and amino acid analysis Membrane proteins and proteomics: un amour impossible? |
| cord-266960-kyx6xhvj | your research? |
| cord-253436-dz84icdc | Human coronaviruses: what do they cause? |
| cord-213136-euv6pqh5 | How long does it take for the final droplet to form? |
| cord-010499-yefxrj30 | : where will it stop? |
| cord-103297-4stnx8dw | bioRxiv Methods for interpreting and understanding deep neural networks Layer- wise relevance propagation: an overview How many different clonotypes do immune repertoires contain? |
| cord-103297-4stnx8dw | bioRxiv Methods for interpreting and understanding deep neural networks Layer- wise relevance propagation: an overview How many different clonotypes do immune repertoires contain? |
| cord-321762-7kiahjyy | What appears to be lost in the process is the target: How useful are these representations to the practicing biologist? |
| cord-023647-dlqs8ay9 | If and Sequence Similarity to Yeast Pt~2 StguCttU'e and Evolution of the 02 Small Nuclear RNA Multigene Family in Primates: Gene Amplification Under Nat-¢wal Selectinn? |
| cord-023647-dlqs8ay9 | Transcription Factors An Element of Symmetry in Ytmst TATA- box Binding Protein Transcription Factor- liD--Consequence of an Ancestra/ Duplication? |
| cord-264296-0x90yubt | Could she be in contact with Patient Zero of Greece or any other who had been contaminated by the latter, before returning to London on February 20? |
| cord-264296-0x90yubt | Once- in- a- Century Pandemic? |
| cord-265857-fs6dj3dp | how big? |
| cord-265857-fs6dj3dp | how fast? |
| cord-302161-ytr7ds8i | reverse genetics Genomic RNA sequence of feline coronavirus strain FCoV C1Je Feline Coronavirus 3c Protein: A Candidate for a Virulence Marker? |
| cord-325043-vqjhiv7p | chance or common ancestry? |
| cord-001974-wjf3c7a7 | How Does Multiple Testing Correction Work? |
| cord-001974-wjf3c7a7 | What's in Your next- Generation Sequence Data? |
| cord-193356-hqbstgg7 | bioRxiv Methods for interpreting and understanding deep neural networks Layer- wise relevance propagation: an overview How many different clonotypes do immune repertoires contain? |
| cord-193356-hqbstgg7 | bioRxiv Methods for interpreting and understanding deep neural networks Layer- wise relevance propagation: an overview How many different clonotypes do immune repertoires contain? |
| cord-102766-n6mpdhyu | The reverse complement Here a virus, there a virus, everywhere the same virus? |
| cord-102766-n6mpdhyu | Why are RNA virus mutation rates so damn high? |
| cord-252347-vnn4135b | Secondly, is the biology of these novel strains similar to that of other HRV? |
| cord-252347-vnn4135b | Seventeen new strains( blue) belonged to HRVA group, and 9 strains( red) cluster into a new group(''C'') that is separate from groups A and B. doi:10.1371/ journal.pone.0000966.g004 putative''group C''HRV? |
| cord-023208-w99gc5nx | Are aza- β3 amino acids γ- turn mimetics? |
| cord-023208-w99gc5nx | These cells were multilayered on day-3 and expressed various keratinocyte markers, including cytokeratin-1, involculin, and laminin? |
| cord-340907-j9i1wlak | The question that we must first address is: what constitutes an under- represented sequence in a coding region? |
| cord-353290-1wi1dhv6 | Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? |
| cord-328644-odtue60a | The latter originated RGTFPDL on one side, and the ancestor of Radiation 2( RGTLLGL) that originated both KRTLLGL( through KG unfit strains?) and later RGILLGL. |
| cord-324021-y1vr1db0 | how do ribosomes find the correct AUG codon for initiation of translation?; and ii) |
| cord-324021-y1vr1db0 | how is the efficiency of translation modulated by aspects of mRNA structure, especially near the 5'end? |
| cord-334127-wjf8t8vp | Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource Is there any value to hepatitis B virus genotype analysis? |
| cord-344782-ond1ziu5 | Molecular comparison of isolates of an emerging fish pathogen, Koi herpesvirus, and the effect of water temperature on mortality of experimentally infected Koi Is horizontal transmission of the ostreid herpesvirus OsHV-1 in Crassostrea gigas affected by unselected or selected survival status in adults to juveniles? |
| cord-304607-td0776wj | Molecular detection of multiple emerging pathogens in sputa from cystic fibrosis patients ALLPATHS: de novo assembly of whole- genome shotgun microreads Evolution of pathogenicity and sexual reproduction in eight Candida genomes New tools for discovering and characterizing microbial diversity Cytolethal distending toxin( CDT): a bacterial weapon to control host cell proliferation? |
| cord-304607-td0776wj | The death of microarrays? |
| cord-328259-3g4klpyg | https://www.mg-rast.org/linkin.cgi? |
| cord-330312-1pjolkql | how big? |
| cord-355075-ieb35upi | inflammasome activation: the convergence of multiple signalling pathways on ROS production? |
| cord-341879-vubszdp2 | Global trends in emerging infectious diseases Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat- borne zoonosis Geographic expansion of dengue: the impact of international travel Spread of a novel influenza A( H1N1) virus via global airline transportation Hantavirus epidemic in Europe Emergence of new forms of totally drug- resistant tuberculosis bacilli: super extensively drug- resistant tuberculosis or totally drug- resistant strains in Iran Is Neisseria gonorrhoeae initiating a future era of untreatable gonorrhea?: |
| cord-263987-ff6kor0c | A generalization of substitution evolution models of nucleotides to genetic motifs Empirical and structural models for insertions and deletions in the divergent evolution of proteins Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont Alignment of phylogenetically unambiguous indels in Shewanella Identification of transposable elements using multiple alignments of related genomes Statistical alignment: computational properties, homology testing and goodness- of- fit General continuous- time Markov model of sequence evolution via insertions/ deletions: are alignment probabilities factorable? |
| cord-263987-ff6kor0c | General continuous- time Markov model of sequence evolution via insertions/ deletions: local alignment probability computation Erratum to: General continuous- time Markov model of sequence evolution via insertions/ deletions: are alignment probabilities factorable? |
| cord-263987-ff6kor0c | The question naturally arises: how to extend the model to describe the evolution of an entire sequence, not just individual sites? |
| cord-343863-q1y8uscj | It allows the researcher to ask the question:"what new sequences match my sequences since the last time I searched?" |
| cord-310734-6v7oru2l | A comparison of bats and rodents as reservoirs of zoonotic viruses: Are bats special? |
| cord-310734-6v7oru2l | Important Reservoir Hosts of Emerging Viruses Bats and zoonotic viruses: Can we confidently link bats with emerging deadly viruses? |
| cord-015850-ef6svn8f | A compromise solution to the introns- early versus introns- late debate? |
| cord-015850-ef6svn8f | The evolution of spliceosomal introns: Patterns, puzzles and progress Genes in pieces: Were they ever together? |
| cord-015850-ef6svn8f | What kind of the relationship exists between the genome size and mutation rates? |
| cord-015850-ef6svn8f | Why genes in pieces? |
| cord-342785-55r01n0x | For instance, in this article an assay for human corona virus OC43[ 6] What about such a match in a clinical lab in Africa? |
| cord-031957-df4luh5v | Rapid and sensitive sequence comparison with FASTP and FASTA Comparative analysis of the quality of a global algorithm and a local algorithm for alignment of two sequences Programming techniques: regular expression search algorithm Profile hidden Markov models Hidden Markov models and their applications in biological sequence analysis What are the ideal properties for functional food peptides with antihypertensive effect? |
| cord-031957-df4luh5v | parvifolia Isolation, solution structure, and insecticidal activity of kalata B2, a circular protein with a twist: do Möbius strips exist in nature? |
| cord-031957-df4luh5v | pore formers or metabolic inhibitors in bacteria? |
| cord-001786-ybd8hi8y | However, it remains an open question, what is the actual size of biological sequence space? |
| cord-001786-ybd8hi8y | However, it remains an open question, what is the actual size of biological sequence space? |
| cord-001786-ybd8hi8y | The classical questions in metagenomics that are asked about the sampled microbial community are"Who is there?" |
| cord-001786-ybd8hi8y | and"What are they doing?. |
| cord-103029-nc5yf6x4 | Do overlapping genes violate molecular biology and the theory of evolution? |
| cord-103029-nc5yf6x4 | Functional? |
| cord-103029-nc5yf6x4 | How many protein sequences fold to a given structure? |
| cord-103029-nc5yf6x4 | Is genetic code redundancy related to retention of structural information in both DNA strands? |
| cord-103029-nc5yf6x4 | The combinatorics of overlapping genes Overlapping genes: more than anomalies? |
| cord-010260-8lnpujip | Consensus regions with preferred conformation in homologous proteins Prediction of protein secondary structure at better than 70% accuracy Secondary structure prediction of all- helical proteins in two states PHD-An automatic mail server for protein secondary structure prediction Progress in protein structure prediction? |
| cord-010260-8lnpujip | How can these cases be identified in a reliable way? |
| cord-010260-8lnpujip | How do serine proteases really work? |
| cord-010260-8lnpujip | Predicting protein secondary structure with a nearest- neighbor algorithm Database of homologyderived protein structures and the structural meaning of sequence alignment An winexpensive, versatile sample illuminator for photo- CIDNP on any NMR spectrometer Pancreatic lipases: Evolutionary intermediates in a positional change of catalytic carboxylates? |
| cord-010260-8lnpujip | Some central questions arise: Do we know enough to undertake such tasks, and what goals can we define? |
| cord-010260-8lnpujip | Will future computers be all wet? |
| cord-325750-x7jpsnxg | , Mandrillus leucophaeus Isolation of a cDNA from the virus responsible for enterically transmitted non- A, non- B hepatitis Quantitative monitoring of gene expression patterns with a complementary DNA microarray Viral discovery and sequence recovery using DNA microarrays Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant Prostate cancer: XMRV-contaminant, not cause? |
| cord-325750-x7jpsnxg | For example, how far has this new viral metagenomics discipline evolved in its first decade? |
| cord-325750-x7jpsnxg | The discovery of the poliovirus Smallpox and Its Eradication The Greatest Killer-Smallpox in History Discovery of the first virus, the tobacco mosaic virus: 1892 or 1898? |
| cord-325750-x7jpsnxg | What has been learned so far that can be applied to viral discovery and the forecasting of future viral outbreaks? |
| cord-016293-pyb00pt5 | : Is There Ample Evidence? |
| cord-016293-pyb00pt5 | According to anecdotal evidence when visiting his namesake centre, Sanger asked:"What does this machine do then?""Dideoxy sequencing"came the reply, to which Fred retorted:"Have n't they come up with anything better yet?" |
| cord-016293-pyb00pt5 | According to anecdotal evidence when visiting his namesake centre, Sanger asked:"What does this machine do then?""Dideoxy sequencing"came the reply, to which Fred retorted:"Have n't they come up with anything better yet?" |
| cord-016293-pyb00pt5 | Issues of justice and resource allocation also have been raised: In a time of strain on our health care system, can we afford such expensive therapy? |
| cord-016293-pyb00pt5 | That finding led plant pathologist Roger Beachy, then at Washington University in Saint Louis, to wonder exactly how such"cross- protection"worked-did part of the virus prompt it? |
| cord-016293-pyb00pt5 | When Steve Fodor was asked in 2003"How do you really take the Human genome sequence and transform it into knowledge?" |
| cord-016293-pyb00pt5 | Who should receive gene therapy? |
| cord-017354-cndb031c | Molecular virology: was the 1918 flu avian in origin? |
| cord-017354-cndb031c | The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis Large- Scale Sequence Analysis of Avian Influenza Isolates Making Better Influenza Virus Vaccines? |
| cord-017354-cndb031c | Understanding the Impact on Animal and Human Health Phylogenetic analysis of nucleoproteins suggests that human influenza A viruses emerged from a 19th century avian ancestor Pandemic Planning and Preparedness Feldblyum and 14 others, Large- scale sequencing of human influenza reveals the dynamic nature of viral genome evolution Was the 1918 pandemic caused by a bird flu? |
| cord-017354-cndb031c | When are phylogency estimates from molecular and morphological data incongruent? |
| cord-017354-cndb031c | bound algorithms to determine minimal evolutionary trees Pandemics and Pandemic Scares in the 20th Century Part 2 Public Health Guidance for State and Local Partners Is Sparse Taxon Sampling a Problem for Phylogenetic Inference? |
| cord-017354-cndb031c | other data Optimization Alignment: the end of multiple sequence alignment in phylogenetics? |
| cord-023209-un2ysc2v | And, is Abeta modifi ed by 1( 2) able to aggregate at low concentrations on a biologically relevant time scale? |
| cord-023209-un2ysc2v | Because these compounds were rationally designed by using the co- crystallized structure of VEGF with the immunoglobulin like fragment 2 of VEGFR-1, we raise the following question: do these antagonists really target the immunoglobulin like domain 2 of VEGFR-1? |
| cord-023209-un2ysc2v | C more or less resistant to denaturation conditions? |
| cord-023209-un2ysc2v | Conformational preferences of investigated systems were obtained on base of ROESY and NOESY experiments and calculations by use of X- PLOR and quantum chemical calculation Is concentration overload or volume overload the best strategy for synthetic peptide purifi cation? |
| cord-023209-un2ysc2v | Peptido2.rotaxanes: can a tetramide macrocycle travel to a station by wrapping up around a helical peptide thread? |
| cord-023209-un2ysc2v | lower the CC of Abeta aggregation into the PC range? |
| cord-018963-2lia97db | A fit well with structural fold B? |
| cord-018963-2lia97db | A fit well with structural fold B? |
| cord-018963-2lia97db | A unified statistical framework for sequence comparison and structure comparison Emergence of preferred structures in a simple model of protein folding Are protein folds atypical? |
| cord-018963-2lia97db | Bioinformatics in the driver's seat Prediction of transcription regulatory sites in Archaea by a comparative genomic approach Can sequence determine function? |
| cord-018963-2lia97db | How representative are the known structures of the proteins in a complete genome? |
| cord-018963-2lia97db | This observation has also raised an interesting question:"Is there something special about the topology of protein structures, which could be further and more rigorously exploited for efficient threading algorithm development?" |
| cord-018963-2lia97db | Why do globular proteins fit the limited set of folding patterns? |
| cord-000257-ampip7od | For instance, how many gene encoding sequences are present in one genome? |
| cord-000257-ampip7od | How did alternative splicing evolve? |
| cord-000257-ampip7od | How frequent are correlated changes in families of protein sequences? |
| cord-000257-ampip7od | How many sequences are repetitive and are these sequences similar in the various organisms on Earth? |
| cord-000257-ampip7od | Is there any significant correlation between the propensity to distribute and the functional roles domains have in cellular pathways? |
| cord-000257-ampip7od | The linkage between protein folding and functional cooperativity: two sides of the same coin? |
| cord-000257-ampip7od | Which genes were involved in the large scale genome duplications that we see in animals? |
| cord-000257-ampip7od | Who's your neighbor? |
| cord-004879-pgyzluwp | A50$ 14- 28 Neutralization rates of TNF- a from eight animal species by a monoclonal antibody against human TNF: implication for receptor action? |
| cord-004879-pgyzluwp | Are these two activities encoded by a single mRNA? |
| cord-004879-pgyzluwp | Do their protein- chemical structure and organisation decipher us certain clues and parts of the path by which they have been selected and derived from a possible primordial reaction centre polypeptide? |
| cord-004879-pgyzluwp | Does the ALEP1 germ- line specific protein have a homologue in the somatic ribosomes? |
| cord-004879-pgyzluwp | However, in the presence of 1000 U/ ml interferon? |
| cord-004879-pgyzluwp | Is membranebound enzyme preferentially associated with a given cellular membrane? |
| cord-004879-pgyzluwp | What is the function of rpS 19? |
| cord-016594-lj0us1dq | Are high- scoring matches an artefact or are they real and meaningful? |
| cord-016594-lj0us1dq | But, is this practically useful for selecting candidate vaccines? |
| cord-016594-lj0us1dq | Have we cut ourselves too short in mapping CTL epitopes? |
| cord-016594-lj0us1dq | However, and say that we were offered a newly sequenced pathogen genome, is such a classification for AB toxins helpful when trying to identify a potential exotoxins? |
| cord-016594-lj0us1dq | The same old, familiar caveats apply here: are chosen thresholds appropriate? |
| cord-016594-lj0us1dq | This typically yields exact values for, say, the binding affinity of a peptide to a protein component of the immune system, or an unequivocal yes or no answer to the question: is this peptide sequence an epitope? |
| cord-016594-lj0us1dq | Using NERVE, the prioritisation of potential candidate antigens consists of several stages: prediction of subcellular localisation; is the antigen an adhesion?; identification of membrane- crossing domains; and comparison to pathogen and human proteomes. |
| cord-016594-lj0us1dq | Why should this be? |
| cord-016594-lj0us1dq | Why should this be? |
| cord-003316-r5te5xob | -what is an achievable turnaround time? |
| cord-003316-r5te5xob | Can current expertise in traditional clinical microbiology be maintained in the transition to WGS? |
| cord-003316-r5te5xob | How can clinical metagenomic data be managed safely in line with the ethical considerations applicable to identifiable human DNA? |
| cord-003316-r5te5xob | How can publicly available databases be reliably maintained to the required clinical accreditation standards over long time periods? |
| cord-003316-r5te5xob | How can unwieldy bioinformatics pipelines developed with academic research in mind be adapted for a clinical setting? |
| cord-003316-r5te5xob | Though, we can see an opportunity for low-/medium- income countries to Outstanding Questions Can WGS be used to develop robust classification schemes that account for the genetic diversity of organisms with open genomes? |
| cord-003316-r5te5xob | When are pathogen genome sequences informative of transmission events? |
| cord-003316-r5te5xob | Which clinically relevant phenotypes can be reliably predicted using WGS, and for which organisms? |
| cord-003316-r5te5xob | Will the true cost of generating a bacterial genome remain stable as the sequencing market consolidates in fewer hands? |
| cord-003316-r5te5xob | analyses of outbreaks be speeded up to meaningfully contribute to infection control at actionable time scales? |
| cord-014462-11ggaqf1 | Both ATP and GTP were utilized as phosporyl donors and Mn 2? |
| cord-014462-11ggaqf1 | Cut off was calculated as Mean negative control? |
| cord-014462-11ggaqf1 | FMDV P1- 3CD''O''vaccine gene constructs in pCDNA3.1? entrapped by the nanoparticles was prepared by using different molarity of calcium chloride and disodium hydrogen orthophosphate. |
| cord-014462-11ggaqf1 | Helicase activity of NSs was absolutely dependent on ATP and Mg 2? |
| cord-014462-11ggaqf1 | How do Indian journals perform in Maintaining quality? |
| cord-014462-11ggaqf1 | How do motivate the scientists to improve their scientific output? |
| cord-014462-11ggaqf1 | How to motivate the scientists to improve their scientific output? |
| cord-014462-11ggaqf1 | In this regard, rNSs is a unique enzyme which does not have the canonical helicase motifs but can catalyze dsDNA/ dsRNA unwinding in an ATP and Mg 2? |
| cord-014462-11ggaqf1 | Should we compare the growth of Indian science with other developed countries? |
| cord-014462-11ggaqf1 | What ails Indian Science? |
| cord-014462-11ggaqf1 | What criteria should be adopted to judge the quality and standard of scientific research? |
| cord-301827-a7hnuxy5 | A polypeptide chain at the folding- misfolding- nonfolding cross- roads: which way to go? |
| cord-301827-a7hnuxy5 | How can one develop tissue- specific drugs targeting such abundant proteins? |
| cord-301827-a7hnuxy5 | Polyglutamine diseases: a transcription disorder? |
| cord-301827-a7hnuxy5 | Prevalent structural disorder in E. coli and S. cerevisiae proteomes Large- scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome Archaic chaos: intrinsically disordered proteins in Archaea Reduction in structural disorder and functional complexity in the thermal adaptation of prokaryotes Intrinsic disorder in pathogenic and non- pathogenic microbes: discovering and analyzing the unfoldomes of early- branching eukaryotes How much of protein sequence space has been explored by life on Earth? |
| cord-301827-a7hnuxy5 | Regular arrangement on the peptidoglycan and unusual dodecyl sulfate binding Proposed knobs- intoholes packing for several membrane proteins Folding patterns of porin and bacteriorhodopsin Hydrophobic organization of membrane proteins Are membrane proteins"inside- out"proteins? |
| cord-301827-a7hnuxy5 | The effect of salts on the activity and stability of Escherichia coli and Haloferax volcanii dihydrofolate reductases Halophilic adaptation of protein- DNA interactions Unique amino acid composition of proteins in halophilic bacteria Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes Structural basis for the aminoacid composition of proteins from halophilic archea Electrostatic contributions to the stability of halophilic proteins Viral disorder or disordered viruses: do viral proteins possess unique features? |
| cord-301827-a7hnuxy5 | The importance of being unfolded Heterogeneity of the binding sites of bovine serum albumin Structural studies of p21 Waf1/ Cip1/ Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity What properties characterize the hub proteins of the protein- protein interaction network of Saccharomyces cerevisiae? |
| cord-301827-a7hnuxy5 | The refined crystal structures of the bovine trypsinogen- pancreatic trypsin inhibitor complex and of its ternary complex with Ile- Val at 1.9 A resolution Intrinsic disorder in the Protein Data Bank Protein disorder and the evolution of molecular recognition: theory, predictions and observations Intrinsically unstructured proteins: re- assessing the protein structurefunction paradigm Why are"natively unfolded"proteins unstructured under physiologic conditions? |
| cord-301827-a7hnuxy5 | What does it mean to be natively unfolded? |
| cord-301827-a7hnuxy5 | What's in a name? |
| cord-001835-0s7ok4uw | 3) Can an exhaustive statistical scan of a large, recent dataset identify new side chain interactions at helix termini? |
| cord-001835-0s7ok4uw | A Promoter or Inhibitor for IAPP aggregation? |
| cord-001835-0s7ok4uw | An empirical framework for binary interactome mapping Estimating the size of the human interactome Coming to peace with protein complexes? |
| cord-001835-0s7ok4uw | Are they essential in carrying out a specific cellular function? |
| cord-001835-0s7ok4uw | But the general effects on traits relevant at atomic/ residue resolutions have been less studied, and one fundamental issue remains unsolved: to what extent are proteins forced into interactions with highly concentrated solutes, and with what direct consequences? |
| cord-001835-0s7ok4uw | Can Bio- functionalities be deciphered from protein sequence information using computational approaches? |
| cord-001835-0s7ok4uw | Can site- directed mutagenesis shed light on the refolding pattern of human glucose 6-phosphate dehydrogenase( G6PD)? |
| cord-001835-0s7ok4uw | Can the structure of a protein( H3.1) depend on the treatment of a solvent medium( explicit vs effective) in a coarse- grained computer simulation? |
| cord-001835-0s7ok4uw | Do they play a regulatory role in controlling the on and off of a certain cellular process? |
| cord-001835-0s7ok4uw | How did enzymes, the catalysts of many crucial cellular processes, achieve this cold adaptation? |
| cord-001835-0s7ok4uw | In a protein engineering context, do we need to take into account the dynamics in order to maximize the fitness and function of the resulting proteins? |
| cord-001835-0s7ok4uw | Is there evolutionary pressure to conserve dynamics? |
| cord-001835-0s7ok4uw | Is this necessary to retain functionality, as it has been suggested? |
| cord-001835-0s7ok4uw | Protein engineering: what's next? |
| cord-001835-0s7ok4uw | Questions under- investigation includes what are the effects of mutations( e.g. b- and g- synuclein), how does the structure of an isolated ASN chain change in presence of many interacting protein chains, and how do they organize over the multiple length scales? |
| cord-001835-0s7ok4uw | To what extent are helix- terminal motifs that include multiple amino acids likely to represent genuine cooperative interactions between side chains, rather than chance alignments? |
| cord-001835-0s7ok4uw | Which particular helix- terminal loop geometries are favored by each side chain interaction? |
| cord-022348-w7z97wir | And if so, what is the virus adapting to? |
| cord-022348-w7z97wir | Are They Adapting or Merely Changing? |
| cord-022348-w7z97wir | But if it were non- linear? |
| cord-022348-w7z97wir | Can quasispecies define a transient molecular clock? |
| cord-022348-w7z97wir | Conservative perhaps, but is there any suggestion that viruses are more or less so than other replicons? |
| cord-022348-w7z97wir | Could symptomatic infections reflect bottleneck transmission of those fitter clones with asymptomatic( subclinical) infection representing fitness- compromised clones? |
| cord-022348-w7z97wir | Does the VP1 gene of foot- and- mouth disease virus behave as a molecular clock? |
| cord-022348-w7z97wir | For outbred populations, is it in fact virulence? |
| cord-022348-w7z97wir | Given the inevitability of mutation, is it possible that over the aeons natural selection has selected for proteins that are robust, those that are capable of absorbing endless substitutions? |
| cord-022348-w7z97wir | How are innate and adaptive immune responses coupled and how are they influenced by genetic polymorphisms? |
| cord-022348-w7z97wir | How good are viruses as machines? |
| cord-022348-w7z97wir | How many rounds of infection are necessary to fix mutations? |
| cord-022348-w7z97wir | Is not fourth best in any large population remarkable? |
| cord-022348-w7z97wir | Might this finding suggest that the optimum is actually away from mass production? |
| cord-022348-w7z97wir | Problems arise transposing it to the in vivo situation, notably: 9 First and foremost: how does one determine fitness in vivo? |
| cord-022348-w7z97wir | Should such measurements score intrahost viral titres or transmission probabilities from an index case? |
| cord-022348-w7z97wir | We come to the basic question- to what extent is genetic variation exploited by an RNAvirus, if at all? |
| cord-022348-w7z97wir | What fraction of amino acid residues is necessary for function? |
| cord-022348-w7z97wir | What is the value of n? |
| cord-022348-w7z97wir | What might a viral species be? |
| cord-022348-w7z97wir | While they are fit enough to survive, are they the best possible? |
| cord-022348-w7z97wir | Why do they mutate rapidly yet remain phenotypically stable? |
| cord-022348-w7z97wir | Why is the evolution of RNA viruses so conservative? |
| cord-022348-w7z97wir | Why is this? |
| cord-022348-w7z97wir | Yet is that correct? |
| cord-022348-w7z97wir | Yet who can remember the name of any Olympic athlete who came in fourth? |
| cord-264746-gfn312aa | & What is the chance of seeing a block of high G+C nucleotides shorter than 5000? |
| cord-264746-gfn312aa | ( e.g., is it likely for a block of high G+C to follow a block of low G+C?). |
| cord-264746-gfn312aa | 13.17? |
| cord-264746-gfn312aa | Do any of them have similar profiles? |
| cord-264746-gfn312aa | Furthermore, how does one select the scores for matches, mismatches, and indels? |
| cord-264746-gfn312aa | How does one determine which of the 129 possibilities is best? |
| cord-264746-gfn312aa | How large( or small) must the ratio be to say that the expression levels are really different?'' |
| cord-264746-gfn312aa | How long would it take to find the best alignment of two 1000 bp sequences by exhaustive search? |
| cord-264746-gfn312aa | How many chromosomes does it have? |
| cord-264746-gfn312aa | How many genes does it have? |
| cord-264746-gfn312aa | How many mammalian genomes have been completely sequenced? |
| cord-264746-gfn312aa | How many matches to that oligonucleotide would one expect to find in the human genome? |
| cord-264746-gfn312aa | How many possible proteins could be formed by a gene region containing four exons? |
| cord-264746-gfn312aa | How might this fact be used in gene finding algorithms? |
| cord-264746-gfn312aa | If each of the 13 SSR markers used by the FBI for identification purposes has 20 equally frequent alleles, what is the chance that two randomly chosen individuals have the same collection of alleles at those 13 markers? |
| cord-264746-gfn312aa | If one of these synonymous codons is energetically more efficient for the organism to use, what effect would that have on the organism's genome content? |
| cord-264746-gfn312aa | If the quantities are measured at the level of entire exons( e.g., did the algorithm correctly predict the location of the entire exon or not?), the values drop to around 70%. |
| cord-264746-gfn312aa | Phrased differently, would a ratio near 0.27 for spot 4 be likely if the experiment were repeated? |
| cord-264746-gfn312aa | The expression levels for two genes measured at four times are: implication of the correlation coefficient? |
| cord-264746-gfn312aa | This database makes it possible to take a query sequence and, for each of the 7500 families and their associated profile HMMs, ask the question,''Is the query sequence a member of this gene family?'' |
| cord-264746-gfn312aa | What are possible advantages and disadvantages of introns? |
| cord-264746-gfn312aa | What are they? |
| cord-264746-gfn312aa | What does the result tell you about zinc finger genes? |
| cord-264746-gfn312aa | What is the chance that a 20-nucleotide oligonucleotide matches a sequence other than the one it was designed to match? |
| cord-264746-gfn312aa | What is the length of the Drosphila melanogaster alcohol dehydrogenase gene? 9. |
| cord-264746-gfn312aa | What is the size of the Anopheles gambiae genome? |
| cord-018133-2otxft31 | Equally important, how are the proteins turned off? |
| cord-018133-2otxft31 | For example, they could provide:( 1) the ability to guess the function of a new protein by assessing its similarity to E. coli genes with a similar sequence,( 2) the ability to ask what the effect on an organism would be if a critical component of a pathway were removed( would other pathways be used to create the desired function, or would the organism lose a vital function and die?), and( 3) the ability to provide a rich user interface to the literature on E. coli metabolism. |
| cord-018133-2otxft31 | GENBANK can be searched efficiently with a number of algorithms and is usually the first stop for a scientist with a new sequence who wonders"Has a sequence like this ever been observed before? |
| cord-018133-2otxft31 | Given two sets of threedimensional coordinates for a set of atoms, what is the best way to superimpose them so that the similarities and differences between the two structures are clear? |
| cord-018133-2otxft31 | How can we analyze the structures of molecules to learn their associated function? |
| cord-018133-2otxft31 | How can we extend the limited structural data by using information in the sequence databases about closely related proteins from different organisms( or within the same organism, but performing a slightly different function)? |
| cord-018133-2otxft31 | How do the proteins function once there? |
| cord-018133-2otxft31 | How does it respond to these medications? |
| cord-018133-2otxft31 | How has the age of genomics changed the landscape of bioinformatics? |
| cord-018133-2otxft31 | How should structures be grouped for the purposes of classification? |
| cord-018133-2otxft31 | If one has, what is known about it? |
| cord-018133-2otxft31 | In addition, the neighbors of a sequence element are also critical, and it is important to be able to perform queries such as,"What sequence elements are seen 20 elements to the left of this element? |
| cord-018133-2otxft31 | It is necessary to support queries such as,"What sequence motifs are present in this sequence? |
| cord-018133-2otxft31 | It provides an excellent introduction to basic molecular biology and biochemistry what ways will bioinformatics and medical informatics interact in the future? |
| cord-018133-2otxft31 | Once genes are transcribed and translated into proteins, into what cellular compartment are the proteins directed? |
| cord-018133-2otxft31 | One of the critical questions facing the genome- sequencing projects is"Can genetic information be misused?" |
| cord-018133-2otxft31 | Should a chapter on bioinformatics appear in a clinical informatics textbook? |
| cord-018133-2otxft31 | Should a patient be informed that he or she is likely to get a disease for which there is no treatment? |
| cord-018133-2otxft31 | The simulation would be a complex mathematical model in which all the molecular details of each organ system would be represented in sufficient detail to allow complex"what if?" |
| cord-018133-2otxft31 | What are two computational challenges in bioinformatics for the future? |
| cord-018133-2otxft31 | What are two problems encountered in analyzing biological sequence, structure, and function? |
| cord-018133-2otxft31 | What is the standard course for this disease? |
| cord-018133-2otxft31 | What more natural user interface could there be for exploring physiology, anatomy, genetics, and biochemistry than the universally recognizable structure of a human that could be browsed at both macroscopic and microscopic levels of detail? |
| cord-018133-2otxft31 | What two changes should we anticipate in the medical record as a result of these new information sources? |
| cord-018133-2otxft31 | When are genes turned on? |
| cord-018133-2otxft31 | Where on the Internet should you look for a DNA sequence, a protein sequence, or a protein structure? |
| cord-018133-2otxft31 | Why have biologists and bioinformaticians embraced the Web as a vehicle for disseminating data so quickly, whereas clinicians and clinical informaticians have been more hesitant to put their primary data online? |
| cord-018133-2otxft31 | Why is sequence, structure, and biological pathway information relevant to medicine? |
| cord-018133-2otxft31 | Why should an awareness of bioinformatics be expected of clinical informatics professionals? |
| cord-018133-2otxft31 | Will the introduction of DNA and protein sequence information change the way that medical records are managed in the future? |
| cord-018133-2otxft31 | Will the same problems arise in basic biomedical research? |