Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture.

abstract：BACKGROUND:DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting. Recent studies have demonstrated the sequence b...

journal_title：Genome biology

authors： Karabacak Calviello A,Hirsekorn A,Wurmus R,Yusuf D,Ohler U

更新日期：2019-02-21 00:00:00

abstract：BACKGROUND:Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with t...

journal_title：Genome biology

authors： Rohmer L,Fong C,Abmayr S,Wasnick M,Larson Freeman TJ,Radey M,Guina T,Svensson K,Hayden HS,Jacobs M,Gallagher LA,Manoil C,Ernst RK,Drees B,Buckley D,Haugen E,Bovee D,Zhou Y,Chang J,Levy R,Lim R,Gillett W,Guenth

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an important opportunistic human pathogen. Generally, the acquisition of genes in the form of pathogenicity islands distinguishes pathogenic isolates from nonpathogens. We therefore sequenced a highly virulent strain of P. aeruginosa, PA14, a...

journal_title：Genome biology

authors： Lee DG,Urbach JM,Wu G,Liberati NT,Feinbaum RL,Miyata S,Diggins LT,He J,Saucier M,Déziel E,Friedman L,Li L,Grills G,Montgomery K,Kucherlapati R,Rahme LG,Ausubel FM

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotype...

journal_title：Genome biology

authors： Dueck H,Khaladkar M,Kim TK,Spaethling JM,Francis C,Suresh S,Fisher SA,Seale P,Beck SG,Bartfai T,Kuhn B,Eberwine J,Kim J

更新日期：2015-06-09 00:00:00

abstract：BACKGROUND:Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Tw...

journal_title：Genome biology

authors： Dudoit S,Fridlyand J

更新日期：2002-06-25 00:00:00

abstract：:A recent study has used serial analysis of gene expression to compare mouse forelimb and hindlimb gene-expression profiles. The method successfully identified known regulators of limb identity and has generated a candidate set of differentially expressed genes that may regulate limb identity. ...

journal_title：Genome biology

authors： Logan M

更新日期：2002-01-01 00:00:00

abstract：:Transcription factor binding sites compete for a limited pool of bioavailable transcription factor molecules to fine tune gene expression. ...

journal_title：Genome biology

authors： Karreth FA,Tay Y,Pandolfi PP

更新日期：2014-04-28 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level....

journal_title：Genome biology

authors： Arora A,Simpson DA

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype...

journal_title：Genome biology

authors： Badouin H,Velt A,Gindraud F,Flutre T,Dumas V,Vautrin S,Marande W,Corbi J,Sallet E,Ganofsky J,Santoni S,Guyot D,Ricciardelli E,Jepsen K,Käfer J,Berges H,Duchêne E,Picard F,Hugueney P,Tavares R,Bacilieri R,Rustenh

更新日期：2020-09-07 00:00:00

abstract：:An intriguing recent study examines the role of miR-1202, a glutamate receptor regulating microRNA, in regulating major depressive disorder. ...

journal_title：Genome biology

authors： Rucker JJ,McGuffin P

更新日期：2014-07-26 00:00:00

abstract：:We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identificati...

journal_title：Genome biology

authors： Rasmussen M,Sundström M,Göransson Kultima H,Botling J,Micke P,Birgisson H,Glimelius B,Isaksson A

更新日期：2011-10-24 00:00:00

abstract：BACKGROUND:Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. RESULTS:We previously described two mut...

journal_title：Genome biology

authors： Herman JD,Rice DP,Ribacke U,Silterra J,Deik AA,Moss EL,Broadbent KM,Neafsey DE,Desai MM,Clish CB,Mazitschek R,Wirth DF

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequenc...

journal_title：Genome biology

authors： Mendum TA,Newcombe J,Mannan AA,Kierzek AM,McFadden J

更新日期：2011-12-30 00:00:00

abstract：BACKGROUND:The cellular mechanisms that underlie metal toxicity and detoxification are rather variegated and incompletely understood. Genomic phenotyping was used to assess the roles played by all nonessential Saccharomyces cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel, and other me...

journal_title：Genome biology

authors： Ruotolo R,Marchini G,Ottonello S

更新日期：2008-04-07 00:00:00

abstract：BACKGROUND:Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune m...

journal_title：Genome biology

authors： Accomando WP,Wiencke JK,Houseman EA,Nelson HH,Kelsey KT

更新日期：2014-03-05 00:00:00

abstract：:A report on the Cold Spring Harbor Laboratory meeting on the Evolution of Developmental Diversity, Cold Spring Harbor, NY, USA, 17-21 April 2002. ...

journal_title：Genome biology

authors： King N

更新日期：2002-07-15 00:00:00

abstract：:Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected...

journal_title：Genome biology

authors： Wu W,Ji P,Zhao F

更新日期：2020-04-28 00:00:00

abstract：:The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...

journal_title：Genome biology

authors： Liang S,Tippens ND,Zhou Y,Mort M,Stenson PD,Cooper DN,Yu H

更新日期：2017-01-18 00:00:00

abstract：BACKGROUND:Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. RESULTS:Here, we explore whether chromatin conformation can be used to classify human leu...

journal_title：Genome biology

authors： Rousseau M,Ferraiuolo MA,Crutchley JL,Wang XQ,Miura H,Blanchette M,Dostie J

更新日期：2014-04-30 00:00:00

abstract：BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...

journal_title：Genome biology

authors： Mitchell K,Brito JJ,Mandric I,Wu Q,Knyazev S,Chang S,Martin LS,Karlsberg A,Gerasimov E,Littman R,Hill BL,Wu NC,Yang HT,Hsieh K,Chen L,Littman E,Shabani T,Enik G,Yao D,Sun R,Schroeder J,Eskin E,Zelikovsky A,S

更新日期：2020-03-17 00:00:00

abstract：:The subcellular localization of the entire proteome of an organism, the yeast Saccharomyces cerevisiae, has been revealed for the first time. Comparison with less comprehensive studies of mammalian cells provides insights into the localization of the mammalian proteome. ...

journal_title：Genome biology

authors： Simpson JC,Pepperkok R

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of...

journal_title：Genome biology

authors： Liu Z,Ran Y,Tao C,Li S,Chen J,Yang E

更新日期：2019-05-20 00:00:00

abstract：:Following publication of the original article [1], the authors reported the following errors. ...

journal_title：Genome biology

authors： Lee H,McManus CJ,Cho DY,Eaton M,Renda F,Somma MP,Cherbas L,May G,Powell S,Zhang D,Zhan L,Resch A,Andrews J,Celniker SE,Cherbas P,Przytycka TM,Gatti M,Oliver B,Graveley B,MacAlpine D

更新日期：2019-03-11 00:00:00

abstract：BACKGROUND:The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient's tumor cells is a central task in the era of precision cancer medicine. Over the deca...

journal_title：Genome biology

authors： Chen H,Li J,Wang Y,Ng PK,Tsang YH,Shaw KR,Mills GB,Liang H

更新日期：2020-02-20 00:00:00

abstract：:Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies....

journal_title：Genome biology

authors： Gabaldón T

更新日期：2008-10-30 00:00:00

abstract：BACKGROUND:Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they origina...

journal_title：Genome biology

authors： Demeulemeester J,Kumar P,Møller EK,Nord S,Wedge DC,Peterson A,Mathiesen RR,Fjelldal R,Zamani Esteki M,Theunis K,Fernandez Gallardo E,Grundstad AJ,Borgen E,Baumbusch LO,Børresen-Dale AL,White KP,Kristensen VN,Van Loo P,

更新日期：2016-12-09 00:00:00

abstract：BACKGROUND:Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but th...

journal_title：Genome biology

authors： Frei dit Frey N,Garcia AV,Bigeard J,Zaag R,Bueso E,Garmier M,Pateyron S,de Tauzia-Moreau ML,Brunaud V,Balzergue S,Colcombet J,Aubourg S,Martin-Magniette ML,Hirt H

更新日期：2014-06-30 00:00:00

abstract：BACKGROUND:Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences integrated into the wasp genome. These particles are co-injected with eggs into caterp...

journal_title：Genome biology

authors： Desjardins CA,Gundersen-Rindal DE,Hostetler JB,Tallon LJ,Fadrosh DW,Fuester RW,Pedroni MJ,Haas BJ,Schatz MC,Jones KM,Crabtree J,Forberger H,Nene V

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Despite decades of research, the molecular mechanisms responsible for the evolution of morphological diversity remain poorly understood. While current models assume that species-specific morphologies are governed by differential use of conserved genetic regulatory circuits, it is debated whether non-conserve...

journal_title：Genome biology

authors： Milde S,Hemmrich G,Anton-Erxleben F,Khalturin K,Wittlieb J,Bosch TC

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene e...

journal_title：Genome biology

authors： Narsai R,Gouil Q,Secco D,Srivastava A,Karpievitch YV,Liew LC,Lister R,Lewsey MG,Whelan J

更新日期：2017-09-15 00:00:00