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
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 10.1006/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