Draft Genome Sequences of 48 Vancomycin-Resistant Enterococcus faecium Strains Isolated from Inpatients with Bacteremia and Urinary Tract Infection
Zulema Udaondo
Thidathip Wongsurawat
Piroon Jenjaroenpun
Courtney Anderson
James Lopez
Meera Mohan
Ruslana Tytarenko
Brian Walker
Intawat Nookaew
David Ussery
Atul Kothari
Se-Ran Jun
David A. Baltrus
Microbiology resource announcements, 2019-4-11
Brian Walker
Walker Brian
/ Brian A Walker
ORCID: 0000-0002-8615-6254
Characterization of IGH locus breakpoints in multiple myeloma indicates a subset of translocations appear to occur in pregerminal center B cells
10.1182/blood-2012-12-471888
Intraclonal heterogeneity and distinct molecular mechanisms characterize the development of t(4;14) and t(11;14) myeloma
10.1182/blood-2012-03-412981
The genetic architecture of multiple myeloma
10.1038/nrc3257
Common variation at 3p22.1 and 7p15.3 influences multiple myeloma risk
10.1038/ng.993
A modified method for whole exome resequencing from minimal amounts of starting DNA
10.1371/journal.pone.0032617
The reconstruction of transcriptional networks reveals critical genes with implications for clinical outcome of multiple myeloma
10.1158/1078-0432.CCR-11-0596
Mapping of chromosome 1p deletions in myeloma identifies FAM46C at 1p12 and CDKN2C at 1p32.3 as being genes in regions associated with adverse survival
10.1158/1078-0432.CCR-11-1791
The clinical impact and molecular biology of del(17p) in multiple myeloma treated with conventional or thalidomide-based therapy
10.1002/gcc.20899
A gene expression-based predictor for myeloma patients at high risk of developing bone disease on bisphosphonate treatment
10.1158/1078-0432.CCR-11-0994
Gender disparities in the tumor genetics and clinical outcome of multiple myeloma
10.1158/1055-9965.EPI-11-0157
The dominantly expressed class I molecule of the chicken MHC is explained by coevolution with the polymorphic peptide transporter (TAP) genes
10.1073/pnas.1019496108
Could DNA methylation become a useful measure for multiple myeloma prognoses?
10.1586/ehm.11.7
Genetic factors underlying the risk of thalidomide-related neuropathy in patients with multiple myeloma
10.1200/JCO.2010.28.0792
Aberrant global methylation patterns affect the molecular pathogenesis and prognosis of multiple myeloma
10.1182/blood-2010-04-279539
High expression levels of the mammalian target of rapamycin inhibitor DEPTOR are predictive of response to thalidomide in myeloma
10.3109/10428194.2010.509893
A compendium of myeloma-associated chromosomal copy number abnormalities and their prognostic value
10.1182/blood-2010-04-279596
XBP1s levels are implicated in the biology and outcome of myeloma mediating different clinical outcomes to thalidomide-based treatments
10.1182/blood-2010-01-263236
Homozygous deletion mapping in myeloma samples identifies genes and an expression signature relevant to pathogenesis and outcome
10.1158/1078-0432.CCR-09-2831
Aminopeptidase inhibition as a targeted treatment strategy in myeloma
10.1158/1535-7163.MCT-08-0735
MMSET deregulation affects cell cycle progression and adhesion regulons in t(4;14) myeloma plasma cells
10.3324/haematol.13426
Deletions of CDKN2C in multiple myeloma: Biological and clinical implications
10.1158/1078-0432.CCR-08-0347
Gene mapping and expression analysis of 16q loss of heterozygosity identifies WWOX and CYLD as being important in determining clinical outcome in multiple myeloma
10.1182/blood-2007-02-075069
Integration of global SNP-based mapping and expression arrays reveals key regions, mechanisms, and genes important in the pathogenesis of multiple myeloma
10.1182/blood-2006-02-005496
The 7p15.3 (rs4487645) association for multiple myeloma shows strong allele-specific regulation of the myc-interacting gene cdca7l in malignant plasma cells
10.3324/haematol.2014.118786
Coexistent hyperdiploidy does not abrogate poor prognosis in myeloma with adverse cytogenetics and may precede IGH translocations
10.1182/blood-2014-07-584268
A molecular diagnostic approach able to detect the recurrent genetic prognostic factors typical of presenting myeloma
10.1002/gcc.22222
Cancer-Selective Targeting of the Nf-ΚB Survival Pathway With Gadd45Β/Mkk7 Inhibitors
10.1016/j.ccr.2014.07.027
Biology and treatment of myeloma
10.1016/j.clml.2014.06.011
A gene expression based predictor for high risk myeloma treated with intensive therapy and autologous stem cell rescue
10.3109/10428194.2014.911863
A novel functional role for MMSET in RNA processing based on the link between the REIIBP isoform and its interaction with the SMN complex
10.1371/journal.pone.0099493
Inherited genetic susceptibility to monoclonal gammopathy of unknown significance
10.1182/blood-2013-10-532283
Common variation at 3q26.2, 6p21.33, 17p11.2 and 22q13.1 influences multiple myeloma risk
10.1038/ng.2733
Intraclonal heterogeneity is a critical early event in the development of myeloma and precedes the development of clinical symptoms
10.1038/leu.2013.199
Identification of a novel t(7;14) translocation in multiple myeloma resulting in overexpression of EGFR
10.1002/gcc.22077
Improved risk stratification in myeloma using a microRNA-based classifier
10.1111/bjh.12394
Global methylation analysis identifies prognostically important epigenetically inactivated tumor suppressor genes in multiple myeloma
10.1182/blood-2013-03-487884
The CCND1 c.870G>A polymorphism is a risk factor for t(11;14)(q13;q32) multiple myeloma.
10.1038/ng.2583
Genes with a spike expression are clustered in chromosome (sub)bands and spike (sub)bands have a powerful prognostic value in patients with multiple myeloma.
10.3324/haematol.2011.046821
Chicken TAP genes differ from their human orthologues in locus organisation, size, sequence features and polymorphism
10.1007/s00251-005-0786-2
Use of Single Nucleotide Polymorphism–Based Mapping Arrays to Detect Copy Number Changes and Loss of Heterozygosity in Multiple Myeloma
10.3816/clm.2006.n.057
Translocations at 8q24 juxtapose MYC with genes that harbor superenhancers resulting in overexpression and poor prognosis in myeloma patients
10.1038/bcj.2014.13
APOBEC family mutational signatures are associated with poor prognosis translocations in multiple myeloma
10.1038/ncomms7997
Single-cell genetic analysis reveals the composition of initiating clones and phylogenetic patterns of branching and parallel evolution in myeloma
10.1038/leu.2014.13
MMSET is the key molecular target in t(4;14) myeloma
10.1038/bcj.2013.9
A TC classification-based predictor for multiple myeloma using multiplexed real-time quantitative PCR
10.1038/leu.2013.12
A novel prognostic model in myeloma based on co-segregating adverse FISH lesions and the ISS: Analysis of patients treated in the MRC Myeloma IX trial
10.1038/leu.2011.204
Impact of genes highly correlated with MMSET myeloma on the survival of non-MMSET myeloma patients
10.1158/1078-0432.CCR-15-2366
High-resolution genomic profiling in hairy cell leukemia-variant compared with typical hairy cell leukemia
10.1038/leu.2011.47
Genomewide profiling of copy-number alteration in monoclonal gammopathy of undetermined significance
10.1111/ejh.12774
Mutational spectrum, copy number changes, and outcome: Results of a sequencing study of patients with newly diagnosed myeloma
10.1200/JCO.2014.59.1503
Understanding next generation sequencing in oncology: A guide for oncologists
10.1016/j.critrevonc.2015.06.007
Cancer-Selective Targeting of the NF-κB Survival Pathway with GADD45β/MKK7 Inhibitors
10.1016/j.ccell.2014.11.021
The chicken B locus is a minimal essential major histocompatibility complex
10.1038/44856
Genome-wide association study identifies multiple susceptibility loci for multiple myeloma
10.1038/ncomms12050
Prediction of outcome in newly diagnosed myeloma: a meta-analysis of the molecular profiles of 1905 trial patients
10.1038/leu.2017.179
The level of deletion 17p and bi-allelic inactivation of TP53 has a significant impact on clinical outcome in multiple myeloma
10.3324/haematol.2017.168872
Somatic mutation spectrum in monoclonal gammopathy of undetermined significance indicates a less complex genomic landscape compared to multiple myeloma.
10.3324/haematol.2017.163766
The prognostic value of the depth of response in multiple myeloma depends on the time of assessment, risk status and molecular subtype
10.3324/haematol.2017.165217
Low expression of hexokinase-2 is associated with false-negative FDG–positron emission tomography in multiple myeloma
10.1182/blood-2017-03-774422
Molecular profiling of colorectal pulmonary metastases and primary tumours: Implications for targeted treatment
10.18632/oncotarget.17048
Overexpression of EZH2 in multiple myeloma is associated with poor prognosis and dysregulation of cell cycle control
10.1038/bcj.2017.27
Search for rare protein altering variants influencing susceptibility to multiple myeloma.
10.18632/oncotarget.15874
The varied distribution and impact of RAS codon and other key DNA alterations across the translocation cyclin D subgroups in multiple myeloma
10.18632/oncotarget.15718
Bi-allelic inactivation is more prevalent at relapse in multiple myeloma, identifying RB1 as an independent prognostic marker
10.1038/bcj.2017.12
Comprehensive translocation and clonality detection in lymphoproliferative disorders by next-generation sequencing
10.3324/haematol.2016.155424
Clonal selection and double-hit events involving tumor suppressor genes underlie relapse in myeloma
10.1182/blood-2016-06-723007
The Spectrum and Clinical Impact of Epigenetic Modifier Mutations in Myeloma.
10.1158/1078-0432.ccr-15-1790
Loss of heterozygosity as a marker of homologous repair deficiency in multiple myeloma: a role for PARP inhibition?
10.1038/s41375-018-0017-0
Identification of novel mutational drivers reveals oncogene dependencies in multiple myeloma
10.1182/blood-2018-03-840132
The presence of large focal lesions is a strong independent prognostic factor in multiple myeloma
10.1182/blood-2018-04-842880
Kinase domain activation through gene rearrangement in multiple myeloma
10.1038/s41375-018-0108-y
Treatment to suppression of focal lesions on positron emission tomography-computed tomography is a therapeutic goal in newly diagnosed multiple myeloma
10.3324/haematol.2017.177139
A rapid and robust protocol for reduced representation bisulfite sequencing in multiple myeloma
10.1007/978-1-4939-7865-6_13
Whole exome sequencing in multiple myeloma to identify somatic single nucleotide variants and key translocations involving immunoglobulin loci and MYC
10.1007/978-1-4939-7865-6_6
Development of a targeted sequencing approach to identify prognostic, predictive and diagnostic markers in paediatric solid tumours
10.18632/oncotarget.23000
Neutral tumor evolution in myeloma is associated with poor prognosis
10.1182/blood-2016-11-750612
Spatial genomic heterogeneity in multiple myeloma revealed by multi-region sequencing
10.1038/s41467-017-00296-y
A high-risk, Double-Hit, group of newly diagnosed myeloma identified by genomic analysis
10.1038/s41375-018-0196-8
Knick-knack PADIMAC
10.1182/blood-2018-10-875138
An acquired high-risk chromosome instability phenotype in multiple myeloma: Jumping 1q Syndrome
10.1038/s41408-019-0226-4
Long-term outcomes after autologous stem cell transplantation for multiple myeloma
10.1182/bloodadvances.2019000524
Epigenomic translocation of H3K4me3 broad domains following super-enhancer hijacking
10.1101/2020.02.12.938563
Investigating the feasibility of tumour molecular profiling in gastrointestinal malignancies in routine clinical practice
10.1093/annonc/mdx631
Erratum: Identification of novel mutational drivers reveals oncogene dependencies in multiple myeloma (Blood (2018) 132:6 (587-597) DOI : 10.1182/blood-2018-03-840132)
10.1182/blood-2018-08-870022
Genetic correlation between multiple myeloma and chronic lymphocytic leukaemia provides evidence for shared aetiology
10.1038/s41408-018-0162-8
The genomic landscape of plasma cells in systemic light chain amyloidosis
10.1182/blood-2018-08-872226
Inactivating NF1 Mutations Are Enriched in Advanced Breast Cancer and Contribute to Endocrine Therapy Resistance
10.1158/1078-0432.CCR-18-4044
Transcriptome-wide association study of multiple myeloma identifies candidate susceptibility genes
10.1186/s40246-019-0231-5
Combination of flow cytometry and functional imaging for monitoring of residual disease in myeloma
10.1038/s41375-018-0329-0
MAFb protein confers intrinsic resistance to proteasome inhibitors in multiple myeloma
10.1186/s12885-018-4602-4
Assessing the effect of obesity-related traits on multiple myeloma using a Mendelian randomisation approach
10.1038/bcj.2017.48
Draft genome sequences of 48 vancomycin-resistant enterococcus faecium strains isolated from inpatients with bacteremia and urinary tract infection
10.1128/MRA.00222-19
A tailored molecular profiling programme for children with cancer to identify clinically actionable genetic alterations
10.1016/j.ejca.2019.07.027
A multiple myeloma classification system that associates normal B-cell subset phenotypes with prognosis
10.1182/bloodadvances.2018018564
Erratum: Correction to: A Rapid and Robust Protocol for Reduced Representation Bisulfite Sequencing in Multiple Myeloma (Methods in molecular biology (Clifton, N.J.) (2018) 1792 (179-191))
10.1007/978-1-4939-7865-6_17
Poor overall survival in hyperhaploid multiple myeloma is defined by double-hit bi-allelic inactivation of TP53
10.18632/oncotarget.26589
Daratumumab and dexamethasone is safe and effective for triple refractory myeloma patients: final results of the IFM 2014-04 (Etoile du Nord) trial
10.1111/bjh.16059
Clonal evolution in myeloma: The impact of maintenance lenalidomide and depth of response on the genetics and sub-clonal structure of relapsed disease in uniformly treated newly diagnosed patients
10.3324/haematol.2018.202200
The Chromosome 13 Conundrum in Multiple Myeloma
10.1158/2643-3249.BCD-20-0081
High-resolution simulations of chromatin folding at genomic rearrangements in malignant B-cells provide mechanistic insights on proto-oncogene deregulation
10.1101/2021.03.12.434963
Improving prognostic assignment in older adults with multiple myeloma using acquired genetic features, clonal hemopoiesis and telomere length
10.1038/s41375-021-01320-3
Mutations in CRBN and other cereblon pathway genes are infrequently associated with acquired resistance to immunomodulatory drugs
10.1038/s41375-021-01373-4
David Ussery
Ussery David
ORCID: 0000-0003-3632-5512
Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104
10.1128/AEM.03821-15
Vibrio chromosome-specific families
10.3389/fmicb.2014.00073
Comparative Genomics
10.1007/978-3-642-30194-0_11
Physical Maps of Chromosomes
10.1002/9780470015902.a0001425
Bayesian prediction of microbial oxygen requirement
10.12688/f1000research.2-184.v1
Is the pan-genome also a pan-selectome?
10.12688/f1000research.1-16.v1
Computing for Comparative Microbial Genomics
10.1007/978-1-84800-255-5
Microbial Communities: Core and Pan-Genomics
10.1007/978-1-84800-255-5_12
Methods to Compare Genomes The First Examples
10.1007/978-1-84800-255-5_6
Bioinformatics for Microbiologists: An Introduction
10.1007/978-1-84800-255-5_2
Faculty of 1000 evaluation for Transposable elements re-wire and fine-tune the transcriptome.
10.3410/f.717973393.793470113
DNA Structure: A-, B- and Z-DNA Helix Families
10.1038/npg.els.0003122
A domain sequence approach to pangenomics: applications to Escherichia coli
10.12688/f1000research.1-19.v2
A domain sequence approach to pangenomics: applications to Escherichia coli
10.3410/f1000research.1-19.v1
Is the pan-genome also a pan-selectome?
10.3410/f1000research.1-16.v1
A domain sequence approach to pangenomics: applications to Escherichia coli
10.12688/f1000research.1-19.v1
Transcriptomics: Translated and Untranslated RNA
10.1007/978-1-84800-255-5_9
Expression of Genes and Proteins
10.1007/978-1-84800-255-5_10
Genomic Properties: Length, Base Composition and DNA Structures
10.1007/978-1-84800-255-5_7
Word Frequencies and Repeats
10.1007/978-1-84800-255-5_8
The Challenges of Programming: A Brief Introduction
10.1007/978-1-84800-255-5_5
Of Proteins, Genomes, and Proteomes
10.1007/978-1-84800-255-5_11
Metagenomics of Microbial Communities
10.1007/978-1-84800-255-5_13
Evolution of Microbial Communities; or, On the Origins of Bacterial Species
10.1007/978-1-84800-255-5_14
Sigma factors in a thousand E. coli genomes
10.1111/1462-2920.12236
Three views of microbial genomes
10.1016/s0923-2508(99)00116-3
Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
10.1371/annotation/45b4b21a-d0d1-40d2-8efd-c30b28baf1eb
Microbial Genome Sequences: A New Era in Microbiology
10.1007/978-1-84800-255-5_3
An Overview of Genome Databases
10.1007/978-1-84800-255-5_4
Comparative Genomics ofPseudomonas
10.1002/9783527622009.ch1
Design of an Enterobacteriaceae Pan-Genome Microarray Chip
10.1007/978-3-642-16750-8_15
DNA Bendability and Nucleosome Positioning in Transcriptional Regulation
10.1007/0-387-29148-2_14
Genome Atlases, Potential Applications in Study of Metagenomes
10.1007/978-1-4614-6418-1_686-1
Standard operating procedure for computing pangenome trees
10.4056/sigs.38923
Comparison of 61 Sequenced Escherichia coli Genomes
10.1007/s00248-010-9717-3
PanFunPro: PAN-genome analysis based on FUNctional PROfiles
10.12688/f1000research.2-265.v1
Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
10.1371/journal.pcbi.1000057
Comparative genomics of green sulfur bacteria
10.1007/s11120-009-9515-2
Extracytoplasmic function sigma factors in Pseudomonas syringae
10.1016/j.tim.2005.10.005
Faculty of 1000 evaluation for Finished bacterial genomes from shotgun sequence data.
10.3410/f.717963312.793465218
Faculty of 1000 evaluation for Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain.
10.3410/f.13960969.15418071
Faculty of 1000 evaluation for Population genomics of early events in the ecological differentiation of bacteria.
10.3410/f.14264956.15777401
Faculty of 1000 evaluation for Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.
10.3410/f.717497832.792902821
Faculty of 1000 evaluation for Bacterial species may exist, metagenomics reveal.
10.3410/f.717959594.793462923
Faculty of 1000 evaluation for The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli.
10.3410/f.13378960.14748059
Faculty of 1000 evaluation for IS30 elements are mediators of genetic diversity in Oenococcus oeni.
10.3410/f.717950467.793455723
Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
10.1371/annotation/4eb76620-9599-40f5-bb05-54f252e48f3b
Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
10.1371/annotation/27a4f12b-e6e6-4d19-bf53-09ce05dfe1b9
Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
10.1371/annotation/3785bc7c-4548-4554-8331-74cc68b8f356
Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
10.1371/annotation/91dc9016-fc1e-495e-8828-22608c3efe44
Comparative Genomics of Bifidobacterium, Lactobacillus and Related Probiotic Genera
10.1007/s00248-011-9948-y
Opening the pan-genomics box
10.1016/j.mib.2006.08.010
DNA: Structure and function
10.1016/s1067-5701(98)80019-3
Structural features of fungal genomes
10.1007/4735_112
Genome Atlases, Potential Applications in Study of Metagenomes
10.1007/978-1-4899-7478-5_686
GSC 11: Dave Ussery
10.4016/28633.01
Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics
10.1007/978-1-84800-255-5_1
Bias of purine stretches in sequenced chromosomes
10.1016/s0097-8485(02)00013-x
Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome
10.1111/j.1574-6968.2007.00916.x
A DNA structural atlas for Escherichia coli
10.1006/jmbi.2000.3787
A Classification of Possible Routes of Darwinian Evolution
10.1006/jtbi.2000.1070
Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes
10.1186/1471-2164-9-104
Comparative Genomics of Four Pseudomonas Species
10.1007/978-1-4419-9086-0_5
Faculty of 1000 evaluation for Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.
10.3410/f.718012890.793477220
Natural genetic engineering: intelligence & design in evolution?
10.1186/2042-5783-1-11
Genomic Analysis of Two-Component Signal Transduction Proteins in Basidiomycetes
10.1159/000277654
Stretches of alternating pyrimidine/purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes
10.1186/1471-2164-10-346
The Genome Atlas Resource
10.1007/978-3-642-16750-8_13
Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray
10.1186/gb-2007-8-12-r267
Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae
10.1186/1471-2164-8-397
Environmental influences on the in vivo level of intramolecular triplex DNA in Escherichia coli
10.1021/bi00075a013
Microbial comparative pan-genomics using binomial mixture models
10.1186/1471-2164-10-385
From essential to persistent genes: a functional approach to constructing synthetic life
10.1016/j.tig.2012.11.001
Origin of replication in circular prokaryotic chromosomes
10.1111/j.1462-2920.2005.00917.x
Analysis and prediction of gene splice sites in four Aspergillus genomes
10.1016/j.fgb.2008.09.010
Special Issue on Campylobacter and Helicobacter Genomics
10.1166/153730503322351890
LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium
10.1111/j.1365-2958.2012.08162.x
CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics
10.1371/journal.pone.0060120
Genome organisation and chromatin structure in Escherichia coli
10.1016/s0300-9084(00)01225-6
Strand misalignments lead to quasipalindrome correction
10.1016/s0168-9525(03)00136-7
Global features of the Alcanivorax borkumensis SK2 genome
10.1111/j.1462-2920.2007.01483.x
The genome BLASTatlas—a GeneWiz extension for visualization of whole-genome homology
10.1039/b717118h
Environmental Influences on DNA Curvature
10.1080/07391102.1999.10508294
Genomic variation in Salmonella enterica core genes for epidemiological typing
10.1186/1471-2164-13-88
Visualization and Significance of DNA Structural Motifs in the Campylobacter jejuni Genome
10.1166/gl.2002.004
Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina
10.1186/1471-2164-8-325
The genomic code: inferring Vibrionaceae niche specialization
10.1038/nrmicro1476
The Atlas visualization of genomewide information
10.1016/s0580-9517(02)33004-6
Systems biology: in the broadest sense of the word
10.1111/j.1462-2920.2005.803_12.x
A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut
10.1007/s00248-010-9796-1
Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?
10.1007/s00248-011-9914-8
The Salmonella enterica Pan-genome
10.1007/s00248-011-9880-1
On the Origins of a Vibrio Species
10.1007/s00248-009-9596-7
Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972
10.1007/s00438-008-0330-9
Amino Acid Usage Is Asymmetrically Biased in AT- and GC-Rich Microbial Genomes
10.1371/journal.pone.0069878
Design and construction of a circular intensity differential scattering instrument
10.1063/1.1137612
[13] Probing DNA structure with psoralen in vitro
10.1016/0076-6879(92)12015-i
Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering
10.1186/1471-2164-10-487
The σ 54 regulon (sigmulon) of Pseudomonas putida
10.1111/j.1462-2920.2003.00528.x
Appendix Estimation of superhelical density in Vivo from analysis of the level of cruciforms existing in living cells
10.1016/0022-2836(91)80209-d
Microbial taxonomy in the post-genomic era: Rebuilding from scratch?
10.1007/s00203-014-1071-2
Insights from 20 years of bacterial genome sequencing
10.1007/s10142-015-0433-4
GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes
10.4056/sigs.28608
Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
10.1186/1471-2164-13-66
GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes
10.4056/sigs.28177
The Importance of Virulence Prediction and Gene Networks in Microbial Risk Assessment
10.1080/10807030701226855
Genomic taxonomy of vibrios
10.1186/1471-2148-9-258
Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli
10.1186/2042-5783-2-8
Studies on Monitoring and Tracking Genetic Resources: An Executive Summary
10.4056/sigs.1491
Comparative Genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440: Orthologs, Codon Usage, Repetitive Extragenic Palindromic Elements, and Oligonucleotide Motif Signatures
10.1166/gl.2002.021
Analysis of intra-genomic GC content homogeneity within prokaryotes
10.1186/1471-2164-11-464
Review and phylogenetic analysis of qac genes that reduce susceptibility to quaternary ammonium compounds in Staphylococcus species
10.1556/eujmi-d-14-00038
Quality scores for 32,000 genomes
10.1186/1944-3277-9-20
The Complete Genome Sequence and Analysis of the Epsilonproteobacterium Arcobacter butzleri
10.1371/journal.pone.0001358
Veillonella, Firmicutes: Microbes disguised as Gram negatives
10.4056/sigs.2981345
Genomic Characterization of Campylobacter jejuni Strain M1
10.1371/journal.pone.0012253
RpoD Promoters in Campylobacter jejuni Exhibit a Strong Periodic Signal Instead of a −35 Box
10.1016/s0022-2836(03)00034-2
Ebolavirus comparative genomics
10.1093/femsre/fuv031
Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains)
10.1186/2042-5783-2-7
Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes
10.1186/1471-2164-13-577
Bayesian prediction of bacterial growth temperature range based on genome sequences
10.1186/1471-2164-13-s7-s3
Differences in two-component signal transduction proteins among the genus Brucella: Implications for host preference and pathogenesis
10.1016/j.vetmic.2010.01.007
The TNFα receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in cystic fibrosis
10.1007/s00439-006-0140-2
Comparative Genomics to Delineate Pathogenic Potential in Non-O157 Shiga Toxin-Producing Escherichia coli (STEC) from Patients with and without Haemolytic Uremic Syndrome (HUS) in Norway
10.1371/journal.pone.0111788
[18] Analysis of DNA structure in vivo using psoralen photobinding: Measurement of supercoiling, topological domains, and DNA-protein interactions
10.1016/0076-6879(92)12020-q
Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus
10.1186/1471-2180-8-110
Genome Update: promoter profiles
10.1099/mic.0.27504-0
Databases, Sequenced Genomes
10.1006/rwgn.2001.0313
DNA Denaturation
10.1016/b978-0-12-374984-0.00418-6
DNA Denaturation
10.1006/rwgn.2001.0353
The Genomic Standards Consortium
10.1371/journal.pbio.1001088
Campylobacter fetus subspecies: Comparative genomics and prediction of potential virulence targets
10.1016/j.gene.2012.07.070
The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571
10.1186/1471-2164-9-271
Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis
10.1128/aem.02612-15
Pan-Genome Analysis of Human Gastric PathogenH. pylori: Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets
10.1155/2015/139580
Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
10.1186/1471-2148-10-249
Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene
10.1046/j.0014-2956.2001.02679.x
Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment
10.3389/fmicb.2015.01118
Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)
10.1186/s40793-016-0134-1
Genome Update: DNA repeats in bacterial genomes
10.1099/mic.0.27628-0
Genome Update: rRNAs in sequenced microbial genomes
10.1099/mic.0.27173-0
Genome Update: tRNAs in sequenced microbial genomes
10.1099/mic.0.27260-0
Genome Update: annotation quality in sequenced microbial genomes
10.1099/mic.0.27338-0
Genome Update: alignment of bacterial chromosomes
10.1099/mic.0.27416-0
Genome Update: 161 prokaryotic genomes sequenced, and counting
10.1099/mic.0.26984-0
Genome Update: length distributions of sequenced prokaryotic genomes
10.1099/mic.0.27032-0
Genome Update: AT content in sequenced prokaryotic genomes
10.1099/mic.0.27103-0
Genome Comparison of Bacterial Pathogens
10.1159/000235759
Tools for Comparison of Bacterial Genomes
10.1007/978-3-540-77587-4_337
Genome update: the 1000th genome - a cautionary tale
10.1099/mic.0.038257-0
Two novel methods for using genome sequences to infer taxonomy
10.1099/mic.0.059816-0
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data
10.1093/bioinformatics/bth423
Design of a Seven-Genome Escherichia coli Microarray for Comparative Genomic Profiling
10.1128/jb.01043-06
The Genus Burkholderia: Analysis of 56 Genomic Sequences
10.1159/000235768
The chromatin-associated protein H-NS
10.1016/0300-9084(94)90022-1
On the total number of genes and their length distribution in complete microbial genomes
10.1016/s0168-9525(01)02372-1
DNA microarray analysis of fim mutations in Escherichia coli
10.1007/s00438-002-0705-2
Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis
10.1007/s00438-004-1046-0
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
10.1093/nar/gkm160
Genome Sequences of Two Stress-Tolerant Campylobacter jejuni Poultry Strains, 305 and DFVF1099
10.1128/jb.05753-11
Formation of a Combined H-DNA/Open TATA Box Structure in the Promoter Sequence of the Human Na,K-ATPase alpha 2 Gene
10.1074/jbc.271.23.13441
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
10.1038/nbt1282
Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792
10.1099/mic.0.000141
Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse
10.4056/sigs.1313504
Complete Genome Sequence of the Commensal Enterococcus faecalis 62, Isolated from a Healthy Norwegian Infant
10.1128/jb.00183-11
17 The TNFα receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in Cystic Fibrosis
10.1016/s1569-1993(06)80018-4
Benchmarking of Methods for Genomic Taxonomy
10.1128/jcm.02981-13
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
10.1128/jcm.06094-11
Polyclonality of Concurrent Natural Populations of Alteromonas macleodii
10.1093/gbe/evs112
Genome Sequencing Identifies Two Nearly Unchanged Strains of Persistent Listeria monocytogenes Isolated at Two Different Fish Processing Plants Sampled 6 Years Apart
10.1128/aem.03715-12
Non-O1 Vibrio cholerae unlinked to cholera in Haiti
10.1073/pnas.1212443109
Toward a Standards-Compliant Genomic and Metagenomic Publication Record
10.1089/omi.2008.a2b2
Genomic Standards Consortium Projects
10.4056/sigs.5559680
Genomic Standards Consortium Projects
10.4056/sigs.5559608
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium
10.1073/pnas.1201061109
Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA
10.1128/genomeA.00555-17
Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D
10.1093/nar/gky014
Genome Sequences of Zika Virus Strains Recovered from Amniotic Fluid, Placenta, and Fetal Brain of a Microcephaly Patient in Thailand, 2017
10.1128/MRA.01020-18
Complete Genome and Plasmid Sequences of Escherichia coli Type Strain ATCC 11775
10.1128/MRA.00046-19
Draft Genome Sequences of 48 Vancomycin-Resistant Enterococcus faecium Strains Isolated from Inpatients with Bacteremia and Urinary Tract Infection
10.1128/MRA.00222-19
What can we learn from over 100,000 Escherichia coli genomes?
10.1101/708131
Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species
10.1002/mbo3.973
Complete Genome Sequences of Four Isolates of Vancomycin-Resistant Enterococcus faecium with the vanA Gene and Two Daptomycin Resistance Mutations, Obtained from Two Inpatients with Prolonged Bacteremia
10.1128/MRA.01380-19
Two Cases of Vancomycin-Resistant Enterococcus faecium Bacteremia With Development of Daptomycin-Resistant Phenotype and its Detection Using Oxford Nanopore Sequencing
10.1093/ofid/ofaa180
16S rRNA Gene Amplicon Profiling of Baby and Adult Captive Elephants in Thailand
10.1128/MRA.00248-20
Machine Learning Methods in Drug Discovery
10.3390/molecules25225277
Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing
10.1128/MRA.01109-20
Assessment of Bacterial Load in Polyethylene Terephthalate (PET) Bottled Water Marketed in Kathmandu Valley, Nepal
10.1155/2021/6681249
Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups
10.1038/s42003-020-01626-5
Zulema Udaondo
Udaondo Zulema
ORCID: 0000-0003-3445-6842
Interspecies cross-talk between co-cultured Pseudomonas putida and Escherichia coli.
10.1111/1758-2229.12553
The pangenome of the genus Clostridium.
10.1111/1462-2920.13732
Genome Sequence of Serratia marcescens MSU97, a Plant-Associated Bacterium That Makes Multiple Antibiotics.
10.1128/genomea.01752-16
Iron Uptake Analysis in a Set of Clinical Isolates of Pseudomonas putida.
10.3389/fmicb.2016.02100
Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene.
10.1111/1462-2920.13585
Pseudomonas putida as a platform for the synthesis of aromatic compounds.
10.1099/mic.0.000333
Specific Gene Loci of Clinical Pseudomonas putida Isolates.
10.1371/journal.pone.0147478
Genome Sequence of Serratia plymuthica A153, a Model Rhizobacterium for the Investigation of the Synthesis and Regulation of Haterumalides, Zeamine, and Andrimid.
10.1128/genomea.00373-16
First- and second-generation biochemicals from sugars: biosynthesis of itaconic acid.
10.1111/1751-7915.12333
Draft Genome Sequence of Pseudomonas putida JLR11, a Facultative Anaerobic 2,4,6-Trinitrotoluene Biotransforming Bacterium.
10.1128/genomea.00904-15
Analysis of the core genome and pangenome of Pseudomonas putida.
10.1111/1462-2920.13015
Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features.
10.1016/j.syapm.2015.07.002
Efflux pump-deficient mutants as a platform to search for microbes that produce antibiotics.
10.1111/1751-7915.12295
Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida.
10.1093/femsre/fuv006
Differential transcriptional response to antibiotics by Pseudomonas putida DOT-T1E.
10.1111/1462-2920.12775
Draft whole-genome sequence of the antibiotic-producing soil isolate Pseudomonas sp. strain 250J.
10.1111/1758-2229.12245
Synergic role of the two ars operons in arsenic tolerance in Pseudomonas putida KT2440.
10.1111/1758-2229.12167
Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital.
10.1371/journal.pone.0081604
Complete Genome Sequence of a Pseudomonas putida Clinical Isolate, Strain H8234.
10.1128/genomea.00496-13
Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome.
10.1111/1751-7915.12061
Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1.
10.1111/1462-2920.12037
Genes for carbon metabolism and the ToxA virulence factor in Pseudomonas aeruginosa are regulated through molecular interactions of PtxR and PtxS.
10.1371/journal.pone.0039390
Evolution of antibiotic resistance, catabolic pathways and niche colonization.
10.1111/j.1751-7915.2012.00335.x
Analysis of solvent tolerance in Pseudomonas putida DOT-T1E based on its genome sequence and a collection of mutants.
10.1016/j.febslet.2012.07.031
Mining for novel antibiotics in the age of antimicrobial resistance.
10.1111/1751-7915.13662
Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries.
10.1111/1462-2920.15138
Two Cases of Vancomycin-Resistant Enterococcus faecium Bacteremia With Development of Daptomycin-Resistant Phenotype and its Detection Using Oxford Nanopore Sequencing.
10.1093/ofid/ofaa180
Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide.
10.3389/fmicb.2020.00202
Complete Genome Sequences of Four Isolates of Vancomycin-Resistant Enterococcus faecium with the vanA Gene and Two Daptomycin Resistance Mutations, Obtained from Two Inpatients with Prolonged Bacteremia.
10.1128/mra.01380-19
Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016.
10.1016/j.meegid.2019.103965
Microbiomes as the new keystone for life sciences development.
10.1111/1751-7915.13424
Draft Genome Sequences of 48 Vancomycin-Resistant Enterococcus faecium Strains Isolated from Inpatients with Bacteremia and Urinary Tract Infection.
10.1128/mra.00222-19
Towards a better metabolic engineering reference: the microbial chassis.
10.1111/1751-7915.13363
Genome Sequence of the Oocydin A-Producing Rhizobacterium Serratia plymuthica 4Rx5.
10.1128/mra.00997-18
Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production.
10.1111/1751-7915.13269
Regulation of carbohydrate degradation pathways in Pseudomonas involves a versatile set of transcriptional regulators.
10.1111/1751-7915.13263
Fighting the enemy: one health approach against microbial resistance
10.1111/1751-7915.13587
Plasma Metabolomics in a Nonhuman Primate Model of Abdominal Radiation Exposure
10.3390/metabo11080540
Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon
10.3390/life11080862
