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-000556-uu1oz2ei | Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions? |
| cord-267714-ji88tvsl | The Century Foundation'Are bioterrorism dollars making us safer? |
| cord-265329-bsypo08l | What are pathogens, and what have they done to and for us? |
| cord-000902-ew8orn0z | Whole genome molecular phylogeny of large dsDNA viruses using composition vector method Evolutionary genomics of nucleo- cytoplasmic large DNA viruses Here a virus, there a virus, everywhere the same virus? |
| cord-007923-j3jpqd7k | What can we expect after the cat genome sequence becomes available? |
| cord-018437-yjvwa1ot | The size and conformation of Kaposi's sarcoma- associated herpesvirus( human herpesvirus 8) DNA in infected cells and virions Characterization of a novel coronavirus associated with severe acute respiratory syndrome Nucleotide sequence of the Kaposi sarcoma- associated herpesvirus( HHV8) Human bocavirus: passenger or pathogen in acute respiratory tract infections? |
| cord-018437-yjvwa1ot | What does virus evolution tell us about virus origins? |
| 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-348059-wa1gjbck | After two decades, have the aspirational aims of the HGP been realized? |
| cord-268795-tjmx6msm | Trends in biochemical sciences Are patients with hypertension and diabetes mellitus at increased risk for COVID-19 infection? |
| cord-265857-fs6dj3dp | how big? |
| cord-265857-fs6dj3dp | how fast? |
| cord-265581-pbv8mjfc | Can we develop a bio- based( mimicking living organisms), highfidelity, cheap, and fast nucleic acid synthesis platform to reach the stage of"made- to- order"DNA for desired purposes? |
| cord-265581-pbv8mjfc | Some laboratory and clinical experiences with a new antibiotic, vancomycin Avermectins, new family of potent anthelmintic agents: producing organism and fermentation Natural products as sources of new drugs from 1981 to 2014 Drug discovery and natural products: end of an era or an endless frontier? |
| cord-000012-p56v8wi1 | Science Are there bugs in our genome? |
| cord-000012-p56v8wi1 | The genome of Melanoplus sanguinipes entomopoxvirus Cloning and expression of a gene encoding a Campoletis sonorensis polydnavirus structural protein A gene encoding a polydnavirus structural polypeptide is not encapsidated What does structure tell us about virus evolution? |
| cord-000012-p56v8wi1 | redox considerations for HIV and SARS- coronavirus Genetic recombination of the DNA plant virus PBCV-1 in a chlorella alga Common origin of four diverse families of large eukaryotic DNA viruses Evolutionary genomics of nucleo- cytoplasmic large DNA viruses Effects of the nonoccluded virus of Spodoptera frugiperda( Lepidoptera: Noctuidae) on the development of a parasitoid Parasitoid- mediated transmission of an iridescent virus Non- poly- DNA viruses, their parasitic wasp, and hosts The few virus- like genes of Cotesia congragata Self- synthesizing DNA transposons in eukaryotes Marvericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses Evolution of viruses by acquisition of cellular RNA or DNA nucleotide sequences and genes: an introduction Microbialgenes in the human genome: lateral transfer or gene loss? |
| 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-330312-1pjolkql | how big? |
| cord-314594-xvc8hvpq | : has the single reference approach become obsolete? |
| cord-352619-s2x53grh | A review of porcine circovirus 2-associated syndromes and diseases Porcine circovirus diseases Experimental reproduction of severe wasting disease by co- infection of pigs with porcine circovirus and porcine parvovirus Concurrent infections are important for expression of porcine circovirus associated disease Circovirus in domestic and wild carnivores: An important opportunistic agent? |
| cord-005281-wy0zk9p8 | CRISPR/ Cas systems Cpf1 is a single RNA- guided endonuclease of a class 2 CRISPR- Cas system How many antiviral small interfering RNAs may be encoded by the mammalian genomes? |
| cord-005281-wy0zk9p8 | Can viruses make us human? |
| cord-005281-wy0zk9p8 | The next genetics revolution? |
| cord-316033-xg8eb2nm | A deep insight into the sialotranscriptome of the gulf coast tick, Amblyomma maculatum PCR- RFLP analyses of leishmania species causing cutaneous and mucocutaneous leishmaniasis revealed distribution of genetically complex strains with hybrid and mito- nuclear discordance in Ecuador Phylogenomic and biogeographic reconstruction of the Trichinella complex Circos: an information aesthetic for comparative genomics Fast gapped- read alignment with bowtie 2 Inference of population structure using dense haplotype data Signatures of mito- nuclear discordance in Schistosoma turkestanicum indicate a complex evolutionary history of emergence in Europe Popart: full- feature software for haplotype network construction Are Ascaris lumbricoides and Ascaris suum a single species? |
| cord-316033-xg8eb2nm | The genome of Onchocerca volvulus, agent of river blindness Disentangling hybridization and host colonization in parasitic roundworms of humans and pigs Landscape genetics reveals focal transmission of a human macroparasite Ascaris lumbricoides, Ascaris suum, or"Ascaris lumbrisuum"? |
| cord-302047-vv5gpldi | : What Have we Learned? |
| cord-302047-vv5gpldi | First, how stable are natural virus genomes, and under what conditions do they become unstable? |
| cord-302047-vv5gpldi | Second, since horizontal gene transfer( HGT) plays an important role in virus evolution, under what conditions are transferred sequences likely to be retained? |
| cord-297669-22fctxk4 | Far? Porcine reproductive and respiratory syndrome virus. |
| cord-297669-22fctxk4 | How does genome editing fit within existing selective breeding structures and how will it be regulated? |
| cord-297669-22fctxk4 | Made? |
| cord-340423-f8ab7413 | How does the genome structure and lifestyle of a virus affect its population variation? |
| cord-340423-f8ab7413 | Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? |
| cord-340423-f8ab7413 | The question that arises is: How do RNA viruses withstand mutation? |
| cord-340423-f8ab7413 | Why do RNA viruses recombine? |
| 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-350747-5t5xthk6 | First, why is elongation on the first template interrupted? |
| cord-350747-5t5xthk6 | Poliovirus neurovirulence depends on the presence of a cryptic AUG upstream of the initiator codon Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? |
| cord-350747-5t5xthk6 | Second, does the incomplete nascent strand dissociate alone or together with RdRP? |
| cord-350747-5t5xthk6 | Third, how is the site of the acceptor template chosen to resume synthesis? |
| cord-016588-f8uvhstb | Are we measuring the right thing? |
| cord-016588-f8uvhstb | Estimating phenotypic drug resistance from HIV-1 genotypes Mycobacterium du jour: what's on tomorrow's menu? |
| cord-016588-f8uvhstb | How do we compare hundreds of bacterial genomes? |
| cord-016588-f8uvhstb | Mauve: multiple alignment of conserved genomic sequence with rearrangements Harnessing bioinformatics to discover new vaccines Integration of omics data: how well does it work for bacteria? |
| cord-016588-f8uvhstb | Microb Infect Ten years of bacterial genome sequencing: comparative- genomics- based discoveries Integration and mining of malaria molecular, functional and pharamacological data: how far are we from a chemogenomic knowledge space? |
| cord-016588-f8uvhstb | What would you do if you could sequence everything? |
| 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-022128-r8el8nqm | A unique intra- molecular fidelity- modulating mechanism identified in a viral RNA- dependent RNA polymerase Defective or effective? |
| cord-022128-r8el8nqm | Coxsackievirus B3 mutator strains are attenuated in vivo A single- nucleotide synonymous mutation in the gag gene controlling human immunodeficiency virus type 1 virion production Is sex necessary for the proliferation and transmission of Pneumocystis? |
| cord-022128-r8el8nqm | Linking RNA sequence, structure, and function on massively parallel highthroughput sequences Defective interfering influenza virus RNAs: time to reevaluate their clinical potential as broad- spectrum antivirals? |
| cord-022128-r8el8nqm | Pnemocystis genetic variability: cryptic biological species or clonal near- clades? |
| cord-022128-r8el8nqm | Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population Replication slippage involves DNA polymerase pausing and dissociation Genome instability: a conserved mechanism of ageing? |
| cord-022128-r8el8nqm | Ribavirin resistance in hepatitis C virus replicon- containing cell lines conferred by changes in the cell line or mutations in the replicon RNA Altering the intracellular environment increases the frequency of tandem repeat deletion during Moloney murine leukemia virus reverse transcription Transfection- mediated generation of functionally competent Tula hantavirus with recombinant S RNA segment Low- fidelity polymerases of alphaviruses recombine at higher rates to overproduce defective interfering particles Mechanisms of retroviral mutation Reproductive clonality in protozoan pathogens ─ truth or artefact? |
| cord-022128-r8el8nqm | reveals the dynamic nature of viral genome evolution Molecular Basis of Virus Evolution Functional and genetic plasticities of the poliovirus genome: quasi- infectious RNAs modified in the 5'-untranslated region yield a variety of pseudorevertants Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? |
| cord-320005-i30t7cvr | How can we define the limits between what is permitted and what is prohibited, or between privacy and responsibility towards third parties? |
| cord-320005-i30t7cvr | How will it influence medicine? |
| cord-320005-i30t7cvr | If only 1% to 2% of the bases in the human genome code for proteins, then what do the rest do? |
| cord-320005-i30t7cvr | What ethical problems does it pose? |
| cord-320005-i30t7cvr | What general lessons has it taught us so far? |
| cord-320005-i30t7cvr | What was the genesis of this project? |
| cord-320005-i30t7cvr | Why are there so many repetitive sequences in the human genome not found in the genomes of invertebrates? |
| cord-320005-i30t7cvr | has it given rise to? |
| cord-298136-mel9fxw8 | ( Office for Official Publications of the European Communities Re- examining the role of patents in appropriating the value of DNA sequences Bioinformatics-a patenting view Are you ready for the revolution? |
| cord-298136-mel9fxw8 | Are any special uses attributed to genomes that are not attributed to isolated fragments of DNA? |
| cord-298136-mel9fxw8 | But what is the difference between wholegenome patents and patents that have been issued on whole microorganisms? |
| cord-298136-mel9fxw8 | Evidence and Policies SARS genome patent: symptom or disease? |
| cord-298136-mel9fxw8 | Is the genome just a concept that is used to unite several nucleotide sequences into a single invention, or is it a causally efficacious phenomenon that does something more than an aggregation of genes can do? |
| cord-298136-mel9fxw8 | Is the genome just … used to unite several nucleotide sequences into a single invention, or … a causally efficacious phenomenon that does something more than an aggregation of genes can do?" |
| cord-298136-mel9fxw8 | Is the genome sequence the representative of the organism? |
| cord-298136-mel9fxw8 | The minimal gene complement of Mycoplasma genitalium Whole- genome random sequencing and assembly of Haemophilus influenzae Rd Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii Can patents deter innovation? |
| cord-298136-mel9fxw8 | What is the relationship between the utility of a part( a gene) and any utility associated with the whole( the genome)? |
| cord-304498-ty41xob0 | Does the ExoN mutator phenotype result in more rapid adaptation or attenuation associated with lethal mutational load and rapid extinction during infection in vivo? |
| cord-304498-ty41xob0 | Does the mutator phenotype increase susceptibility to mutagens for lethal mutagenesis? |
| cord-304498-ty41xob0 | How do CoVs maintain a large and complex genome over time while allowing sufficient mutation rates for adaptation and trans- species movement? |
| cord-304498-ty41xob0 | In this case the central unanswered research question remains: by what mechanism does nsp14 increase fidelity? |
| cord-304498-ty41xob0 | Is the fidelity of wt CoV replication fixed by highly selected interactions between the RdRp, ExoN and possibly other viral and cellular proteins or is it flexible in response to altered environmental conditions as has been shown for bacteria such as E. coli? |
| cord-304498-ty41xob0 | What are the limitations to CoV genome diversity in vitro and in vivo? |
| cord-304498-ty41xob0 | clues that the last universal common ancestor possessed an RNA genome? |
| cord-304498-ty41xob0 | subgenomic mouse hepatitis virus replicative intermediates function in RNA synthesis Nidovirus transcription: how to make sense …? |
| 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-022262-ck2lhojz | But what about receptor specificity of these viruses? |
| cord-022262-ck2lhojz | Do these considerations allow us to safely conclude that, after its global eradication, poliovirus will have no chance to re- emerge through enterovirus evolution? |
| cord-022262-ck2lhojz | Does the history of the polyprotein determine how picornaviruses may evolve in the future? |
| cord-022262-ck2lhojz | For example, the precursor 3CD pr~ can be cleaved into 3C pr~ and 3CD p~ by a( cis?) cleavage in which the 3C/3CD pr~ proteinase is involved. |
| cord-022262-ck2lhojz | Genetic analyses have indicated that template switching occurs( predominantly?) |
| cord-022262-ck2lhojz | How do the multiple mechanisms alluded to interlace to produce a specific picornavirus disease syndrome? |
| cord-022262-ck2lhojz | How it is Likely to Evolve in the Future? |
| cord-022262-ck2lhojz | Moreover, if the genome has to be translated for replication to occur, how can inhibition of translation promote RNA synthesis? |
| cord-022262-ck2lhojz | The mechanism of RNA recombination in poliovirus Primary structure, gene organization and polypeptide expression of poliovirus RNA The poliovirus receptor protein is produced both as membrane- bound and secreted forms Transgenic mice susceptible to poliovirus Q[3 replicase as repressor of Q[3 RNA- directed protein synthesis Evolution of RNA genomes: does the high mutation rate necessitate high rate of evolution of viral proteins? |
| cord-022262-ck2lhojz | We have discussed different aspects relevant to picornavirus evolution, but we did not address one crucial question: Are picornaviruses a successful family? |
| cord-022262-ck2lhojz | What are the mechanisms by which the picornaviruses and other RNA virus families have diversified? |
| cord-022262-ck2lhojz | What is the identity of picornaviruses? |
| cord-022262-ck2lhojz | What is the mechanism by which poliovirus may eliminate foreign sequences? |
| 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? |