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Articles published in PLoS One

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    January 2022
  1. ARANA C, Liang C, Brock M, Zhang B, et al
    A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome.
    PLoS One. 2022;17:e0261014.
    PubMed     Abstract available

  2. HUANG K, Wang C, Vagts C, Raguveer V, et al
    Long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 are differentially expressed in severe COVID-19 patients: An integrated single-cell analysis.
    PLoS One. 2022;17:e0261242.
    PubMed     Abstract available

  3. MIRANDA GHN, Alencar de Oliveira Lima L, Bittencourt LO, Dos Santos SM, et al
    Effects of long-term fluoride exposure are associated with oxidative biochemistry impairment and global proteomic modulation, but not genotoxicity, in parotid glands of mice.
    PLoS One. 2022;17:e0261252.
    PubMed     Abstract available

  4. DILMAGHANI S, Brust MR, Ribeiro CHC, Kieffer E, et al
    From communities to protein complexes: A local community detection algorithm on PPI networks.
    PLoS One. 2022;17:e0260484.
    PubMed     Abstract available

  5. PIERRE N, Wamalwa LN, Muiru WM, Simon B, et al
    Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses.
    PLoS One. 2022;17:e0256002.
    PubMed     Abstract available

  6. HAMMOND J, Klapwijk JE, Riedijk S, Lou S, et al
    Assessing women's preferences towards tests that may reveal uncertain results from prenatal genomic testing: Development of attributes for a discrete choice experiment, using a mixed-methods design.
    PLoS One. 2022;17:e0261898.
    PubMed     Abstract available

  7. IGATA T, Tanaka H, Etoh K, Hong S, et al
    Loss of the transcription repressor ZHX3 induces senescence-associated gene expression and mitochondrial-nucleolar activation.
    PLoS One. 2022;17:e0262488.
    PubMed     Abstract available

  8. COELHO DE SOUSA I, Nascimento M, de Castro Sant'anna I, Teixeira Caixeta E, et al
    Marker effects and heritability estimates using additive-dominance genomic architectures via artificial neural networks in Coffea canephora.
    PLoS One. 2022;17:e0262055.
    PubMed     Abstract available

  9. EL MOUZAN M, Assiri A, Al Sarkhy A, Alasmi M, et al
    Viral dysbiosis in children with new-onset celiac disease.
    PLoS One. 2022;17:e0262108.
    PubMed     Abstract available

  10. ELBEHIRY A, Aldubaib M, Al Rugaie O, Marzouk E, et al
    Proteomics-based screening and antibiotic resistance assessment of clinical and sub-clinical Brucella species: An evolution of brucellosis infection control.
    PLoS One. 2022;17:e0262551.
    PubMed     Abstract available

  11. KAPINOS A, Aghamalian P, Capehart E, Alag A, et al
    Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages.
    PLoS One. 2022;17:e0262556.
    PubMed     Abstract available

  12. BENNETT NE, Mirabal Torres SE, Gray PB
    Exploratory content analysis of direct-to-consumer pet genomics: What is being marketed and what are consumers saying?
    PLoS One. 2022;17:e0261694.
    PubMed     Abstract available

  13. KIM SS, Kycia I, Karski M, Ma RK, et al
    DNAJB1-PRKACA in HEK293T cells induces LINC00473 overexpression that depends on PKA signaling.
    PLoS One. 2022;17:e0263829.
    PubMed     Abstract available

  14. PADMANABHAN H, Hassan NT, Wong SW, Lee YQ, et al
    Psychosocial outcome and health behaviour intent of breast cancer patients with BRCA1/2 and PALB2 pathogenic variants unselected by a priori risk.
    PLoS One. 2022;17:e0263675.
    PubMed     Abstract available

  15. CONTE F, Sibilio P, Grimaldi AM, Salvatore M, et al
    In silico recognition of a prognostic signature in basal-like breast cancer patients.
    PLoS One. 2022;17:e0264024.
    PubMed     Abstract available

  16. KARADZOVSKA-KOTEVSKA M, Brunnstrom H, Kosieradzki J, Ek L, et al
    Feasibility of EBUS-TBNA for histopathological and molecular diagnostics of NSCLC-A retrospective single-center experience.
    PLoS One. 2022;17:e0263342.
    PubMed     Abstract available

  17. BORBA RS, Hoover SE, Currie RW, Giovenazzo P, et al
    Phenomic analysis of the honey bee pathogen-web and its dynamics on colony productivity, health and social immunity behaviors.
    PLoS One. 2022;17:e0263273.
    PubMed     Abstract available

  18. WARD SJ, McMahan CD, Khakurel B, Wright AM, et al
    Genomic data support the taxonomic validity of Middle American livebearers Poeciliopsis gracilis and Poeciliopsis pleurospilus (Cyprinodontiformes: Poeciliidae).
    PLoS One. 2022;17:e0262687.
    PubMed     Abstract available

    Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data.
    PLoS One. 2022;17:e0263344.
    PubMed     Abstract available

  20. GOLJAN E, Abouelhoda M, ElKalioby MM, Jabaan A, et al
    Identification of pharmacogenetic variants from large scale next generation sequencing data in the Saudi population.
    PLoS One. 2022;17:e0263137.
    PubMed     Abstract available

  21. SHAHDADI A, von Wyschetzki K, Liu HC, Chu KH, et al
    Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific.
    PLoS One. 2022;17:e0262122.
    PubMed     Abstract available

  22. PECANKOVA K, Pecherkova P, Gasova Z, Sovova Z, et al
    Proteome changes of plasma-derived extracellular vesicles in patients with myelodysplastic syndrome.
    PLoS One. 2022;17:e0262484.
    PubMed     Abstract available

  23. MILLER JK, Elenberg K, Dubrawski A
    Forecasting emergence of COVID-19 variants of concern.
    PLoS One. 2022;17:e0264198.
    PubMed     Abstract available

  24. WANKAEW N, Chariyavilaskul P, Chamnanphon M, Assawapitaksakul A, et al
    Genotypic and phenotypic landscapes of 51 pharmacogenes derived from whole-genome sequencing in a Thai population.
    PLoS One. 2022;17:e0263621.
    PubMed     Abstract available

  25. CAIRO A, Iorio MV, Spena S, Tagliabue E, et al
    Worldwide SARS-CoV-2 haplotype distribution in early pandemic.
    PLoS One. 2022;17:e0263705.
    PubMed     Abstract available

  26. BISCHOF EA, Schluter N, Lehmann J
    Geometric morphometric analysis of morphologic disparity, intraspecific variation and ontogenetic allometry of beyrichitine ammonoids.
    PLoS One. 2022;17:e0263524.
    PubMed     Abstract available

  27. JESKE M, Vasquez E, Fullerton SM, Saperstein A, et al
    Beyond inclusion: Enacting team equity in precision medicine research.
    PLoS One. 2022;17:e0263750.
    PubMed     Abstract available

  28. HONG S, Park KH, Lee YE, Lee JE, et al
    Antibody microarray analysis of amniotic fluid proteomes in women with cervical insufficiency and short cervix, and their association with pregnancy latency length.
    PLoS One. 2022;17:e0263586.
    PubMed     Abstract available

  29. WU Y, Zhu Y, Xie N, Wang H, et al
    A network pharmacology approach to explore active compounds and pharmacological mechanisms of a patented Chinese herbal medicine in the treatment of endometriosis.
    PLoS One. 2022;17:e0263614.
    PubMed     Abstract available

  30. CONRAD MS, Gardner ML, Miguel C, Freitas MA, et al
    Proteomic analysis of the umbilical cord in fetal growth restriction and preeclampsia.
    PLoS One. 2022;17:e0262041.
    PubMed     Abstract available

  31. GARDINER LJ, Carrieri AP, Bingham K, Macluskie G, et al
    Combining explainable machine learning, demographic and multi-omic data to inform precision medicine strategies for inflammatory bowel disease.
    PLoS One. 2022;17:e0263248.
    PubMed     Abstract available

  32. HARTMANN K, Seweryn M, Sadee W
    Interpreting coronary artery disease GWAS results: A functional genomics approach assessing biological significance.
    PLoS One. 2022;17:e0244904.
    PubMed     Abstract available

  33. CHEN Y, Kaplan Lease N, Gin JW, Ogorzalek TL, et al
    Modular automated bottom-up proteomic sample preparation for high-throughput applications.
    PLoS One. 2022;17:e0264467.
    PubMed     Abstract available

  34. PIE MR, Caron FS
    Geographical range overlap networks and the macroecology of species co-occurrence.
    PLoS One. 2022;17:e0266275.
    PubMed     Abstract available

  35. LI J, Xu H, McIndoe RA
    A novel network based linear model for prioritization of synergistic drug combinations.
    PLoS One. 2022;17:e0266382.
    PubMed     Abstract available

  36. PFENNINGER M, Doria HB, Nickel J, Thielsch A, et al
    Spontaneous rate of clonal single nucleotide mutations in Daphnia galeata.
    PLoS One. 2022;17:e0265632.
    PubMed     Abstract available

  37. WEISS L, Gaelings L, Reiner T, Mergner J, et al
    Posttranslational modification of the RHO of plants protein RACB by phosphorylation and cross-kingdom conserved ubiquitination.
    PLoS One. 2022;17:e0258924.
    PubMed     Abstract available

  38. SHU J, Ma X, Ma H, Huang Q, et al
    Transcriptomic, proteomic, metabolomic, and functional genomic approaches of Brassica napus L. during salt stress.
    PLoS One. 2022;17:e0262587.
    PubMed     Abstract available

  39. SUNDERHAUS A, Imran R, Enoh E, Adedeji A, et al
    Comparative expression of soluble, active human kinases in specialized bacterial strains.
    PLoS One. 2022;17:e0267226.
    PubMed     Abstract available

  40. AKBARI ROKN ABADI S, Mohammadi A, Koohi S
    WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs.
    PLoS One. 2022;17:e0267106.
    PubMed     Abstract available

  41. LYALINA S, Stepanauskas R, Wu F, Sanjabi S, et al
    Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community.
    PLoS One. 2022;17:e0261795.
    PubMed     Abstract available

  42. MUSHTAQ S, Shafiq M, Ashraf T, Haider MS, et al
    Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique.
    PLoS One. 2022;17:e0263144.
    PubMed     Abstract available

  43. MILBURY CA, Creeden J, Yip WK, Smith DL, et al
    Clinical and analytical validation of FoundationOne(R)CDx, a comprehensive genomic profiling assay for solid tumors.
    PLoS One. 2022;17:e0264138.
    PubMed     Abstract available

  44. CASSELBRANT A, Fedorowski A, Frantz S, Engstrom G, et al
    Common physiologic and proteomic biomarkers in pulmonary and coronary artery disease.
    PLoS One. 2022;17:e0264376.
    PubMed     Abstract available

  45. MORADI S, Kamal A, Aboulkheyr Es H, Farhadi F, et al
    Pan-cancer analysis of microRNA expression profiles highlights microRNAs enriched in normal body cells as effective suppressors of multiple tumor types: A study based on TCGA database.
    PLoS One. 2022;17:e0267291.
    PubMed     Abstract available

  46. DUTTMANN C, Flores B, Sheleby-Elias J, Castillo G, et al
    Africanized honeybee population (Apis mellifera L.) in Nicaragua: Forewing length and mitotype lineages.
    PLoS One. 2022;17:e0267600.
    PubMed     Abstract available

  47. LIPMAN D, Safo SE, Chekouo T
    Multi-omic analysis reveals enriched pathways associated with COVID-19 and COVID-19 severity.
    PLoS One. 2022;17:e0267047.
    PubMed     Abstract available

  48. NOURANI L, Abouie Mehrizi A, Zakeri S, Djadid ND, et al
    Untangling population structure and genetic diversity of reticulocyte binding protein 2b (PvRBP2b) erythrocytic stage vaccine candidate in worldwide Plasmodium vivax isolates.
    PLoS One. 2022;17:e0266067.
    PubMed     Abstract available

  49. CAPPA EP, Klutsch JG, Sebastian-Azcona J, Ratcliffe B, et al
    Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program.
    PLoS One. 2022;17:e0264549.
    PubMed     Abstract available

  50. ZHOU Z, Tang J, Cao Q, Li Z, et al
    Differential response of physiology and metabolic response to drought stress in different sweetpotato cultivars.
    PLoS One. 2022;17:e0264847.
    PubMed     Abstract available

  51. MUKHOPADHYAY S, Saha S, Chakraborty S, Prasad P, et al
    Differential colitis susceptibility of Th1- and Th2-biased mice: A multi-omics approach.
    PLoS One. 2022;17:e0264400.
    PubMed     Abstract available

  52. MAGHRADZE N, Jugheli L, Borrell S, Tukvadze N, et al
    Developing customized stepwise MIRU-VNTR typing for tuberculosis surveillance in Georgia.
    PLoS One. 2022;17:e0264472.
    PubMed     Abstract available

  53. LI S, Counter CM
    Non-canonical genomic driver mutations of urethane carcinogenesis.
    PLoS One. 2022;17:e0267147.
    PubMed     Abstract available

  54. DIEYE Y, Hull DM, Wane AA, Harden L, et al
    Genomics of human and chicken Salmonella isolates in Senegal: Broilers as a source of antimicrobial resistance and potentially invasive nontyphoidal salmonellosis infections.
    PLoS One. 2022;17:e0266025.
    PubMed     Abstract available

  55. ANTHONYSAMY WJB, Dreslik MJ, Baker SJ, Davis MA, et al
    Limited gene flow and pronounced population genetic structure of Eastern Massasauga (Sistrurus catenatus) in a Midwestern prairie remnant.
    PLoS One. 2022;17:e0265666.
    PubMed     Abstract available

  56. YASUDA T, Tahara K, Sawada T
    Detection of salivary citrullinated cytokeratin 13 in healthy individuals and patients with rheumatoid arthritis by proteomics analysis.
    PLoS One. 2022;17:e0265687.
    PubMed     Abstract available

  57. DIEKI R, Nsi Emvo E, Akue JP
    Comparison of six methods for Loa loa genomic DNA extraction.
    PLoS One. 2022;17:e0265582.
    PubMed     Abstract available

  58. GUO YH, Halasan LC, Wang HY, Lin HC, et al
    High migratory propensity constitutes a single stock of an exploited cutlassfish species in the Northwest Pacific: A microsatellite approach.
    PLoS One. 2022;17:e0265548.
    PubMed     Abstract available

  59. DAVIK J, Roen D, Lysoe E, Buti M, et al
    A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.).
    PLoS One. 2022;17:e0265096.
    PubMed     Abstract available

  60. JI G, Chang H, Yang M, Chen H, et al
    The mitochondrial proteomic changes of rat hippocampus induced by 28-day simulated microgravity.
    PLoS One. 2022;17:e0265108.
    PubMed     Abstract available

  61. HARFORD TJ, Rezaee F, Dye BR, Fan J, et al
    RSV-induced changes in a 3-dimensional organoid model of human fetal lungs.
    PLoS One. 2022;17:e0265094.
    PubMed     Abstract available

  62. CARLAND M, Pedersen H, Bose M, Novkovic B, et al
    EZTraits: A programmable tool to evaluate multi-site deterministic traits.
    PLoS One. 2022;17:e0259327.
    PubMed     Abstract available

  63. KHAN MN, Ahmed I, Ud Din I, Noureldeen A, et al
    Proteomic insight into soybean response to flooding stress reveals changes in energy metabolism and cell wall modifications.
    PLoS One. 2022;17:e0264453.
    PubMed     Abstract available

  64. LOVE TM, Anaya DA, Prime MS, Ardolino L, et al
    Development and validation of ACTE-MTB: A tool to systematically assess the maturity of molecular tumor boards.
    PLoS One. 2022;17:e0268477.
    PubMed     Abstract available

  65. HOLM M, Saraswat M, Joenvaara S, Seppo A, et al
    Quantitative glycoproteomics of human milk and association with atopic disease.
    PLoS One. 2022;17:e0267967.
    PubMed     Abstract available

    An ancestral genomic sequence that serves as a nucleation site for de novo gene birth.
    PLoS One. 2022;17:e0267864.
    PubMed     Abstract available

  67. VOLYNKINA A, Lisitskaya Y, Kolosov A, Shaposhnikova L, et al
    Molecular epidemiology of Crimean-Congo hemorrhagic fever virus in Russia.
    PLoS One. 2022;17:e0266177.
    PubMed     Abstract available

  68. VENTRESCA MILLER AR, Wilkin S, Hendy J, Turbat T, et al
    The spread of herds and horses into the Altai: How livestock and dairying drove social complexity in Mongolia.
    PLoS One. 2022;17:e0265775.
    PubMed     Abstract available

  69. LANG J
    MAECI: A pipeline for generating consensus sequence with nanopore sequencing long-read assembly and error correction.
    PLoS One. 2022;17:e0267066.
    PubMed     Abstract available

  70. GENISH I, Gabay B, Ruban A, Goldshmit Y, et al
    Electroporation-based proteome sampling ex vivo enables the detection of brain melanoma protein signatures in a location proximate to visible tumor margins.
    PLoS One. 2022;17:e0265866.
    PubMed     Abstract available

  71. ARORA D, Park JE, Lim D, Cho IC, et al
    Multi-omics approaches for comprehensive analysis and understanding of the immune response in the miniature pig breed.
    PLoS One. 2022;17:e0263035.
    PubMed     Abstract available

  72. COLLER HA, Beggs S, Andrews S, Maloy J, et al
    Bruins-in-Genomics: Evaluation of the impact of a UCLA undergraduate summer program in computational biology on participating students.
    PLoS One. 2022;17:e0268861.
    PubMed     Abstract available

  73. PAUDEL D, Kuramitsu Y, Uehara O, Morikawa T, et al
    Proteomic and microbiota analyses of the oral cavity during psychological stress.
    PLoS One. 2022;17:e0268155.
    PubMed     Abstract available

  74. HUANG RDL, Nguyen XT, Peloso GM, Trinder M, et al
    Genome-wide and phenome-wide analysis of ideal cardiovascular health in the VA Million Veteran Program.
    PLoS One. 2022;17:e0267900.
    PubMed     Abstract available

  75. ANDREEV VP, Helmuth ME, Liu G, Smith AR, et al
    Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study.
    PLoS One. 2022;17:e0268547.
    PubMed     Abstract available

  76. BLAGEC K, Swen JJ, Koopmann R, Cheung KC, et al
    Pharmacogenomics decision support in the U-PGx project: Results and advice from clinical implementation across seven European countries.
    PLoS One. 2022;17:e0268534.
    PubMed     Abstract available

  77. AUTERI GG, Marchan-Rivadeneira MR, Olson DH, Knowles LL, et al
    Landscape connectivity among coastal giant salamander (Dicamptodon tenebrosus) populations shows no association with land use, fire frequency, or river drainage but exhibits genetic signatures of potential conservation concern.
    PLoS One. 2022;17:e0268882.
    PubMed     Abstract available

  78. FROMMLET F, Szulc P, Konig F, Bogdan M, et al
    Selecting predictive biomarkers from genomic data.
    PLoS One. 2022;17:e0269369.
    PubMed     Abstract available

  79. MARBUN VMG, Erlina L, Lalisang TJM
    Genomic landscape of pathogenic mutation of APC, KRAS, TP53, PIK3CA, and MLH1 in Indonesian colorectal cancer.
    PLoS One. 2022;17:e0267090.
    PubMed     Abstract available

  80. ZHANG X, Takeuchi T, Takeda A, Mochizuki H, et al
    Comparison of serum and plasma as a source of blood extracellular vesicles: Increased levels of platelet-derived particles in serum extracellular vesicle fractions alter content profiles from plasma extracellular vesicle fractions.
    PLoS One. 2022;17:e0270634.
    PubMed     Abstract available

    January 2021
  81. BHOYAR RC, Jain A, Sehgal P, Divakar MK, et al
    High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.
    PLoS One. 2021;16:e0247115.
    PubMed     Abstract available

  82. DADOUSIS C, Cecchi F, Ablondi M, Fabbri MC, et al
    Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed.
    PLoS One. 2021;16:e0232436.
    PubMed     Abstract available

  83. ZHANG ML, Wang LQ, Qi Y, Wu Y, et al
    Comparative genomic analysis of three geographical isolates from China reveals high genetic stability of Plutella xylostella granulovirus.
    PLoS One. 2021;16:e0243143.
    PubMed     Abstract available

  84. HAN M, Yan H, Yang K, Fan B, et al
    Identification of biomarkers and construction of a microRNAmRNA regulatory network for clear cell renal cell carcinoma using integrated bioinformatics analysis.
    PLoS One. 2021;16:e0244394.
    PubMed     Abstract available

  85. MI W, Liu Z, Jin J, Dong X, et al
    Comparative proteomics analysis reveals the molecular mechanism of enhanced cold tolerance through ROS scavenging in winter rapeseed (Brassica napus L.).
    PLoS One. 2021;16:e0243292.
    PubMed     Abstract available

  86. EPELBOIN Y, Wang L, Giai Gianetto Q, Choumet V, et al
    CYP450 core involvement in multiple resistance strains of Aedes aegypti from French Guiana highlighted by proteomics, molecular and biochemical studies.
    PLoS One. 2021;16:e0243992.
    PubMed     Abstract available

  87. MAROSO F, Gkagkavouzis K, De Innocentiis S, Hillen J, et al
    Genome-wide analysis clarifies the population genetic structure of wild gilthead sea bream (Sparus aurata).
    PLoS One. 2021;16:e0236230.
    PubMed     Abstract available

  88. TAMAR K, Els J, Kornilios P, Soorae P, et al
    The demise of a wonder: Evolutionary history and conservation assessments of the Wonder Gecko Teratoscincus keyserlingii (Gekkota, Sphaerodactylidae) in Arabia.
    PLoS One. 2021;16:e0244150.
    PubMed     Abstract available

  89. MORIBE F, Nishikori M, Takashima T, Taniyama D, et al
    Epigenetic suppression of SLFN11 in germinal center B-cells during B-cell development.
    PLoS One. 2021;16:e0237554.
    PubMed     Abstract available

  90. SCIABOLA S, Xi H, Cruz D, Cao Q, et al
    PFRED: A computational platform for siRNA and antisense oligonucleotides design.
    PLoS One. 2021;16:e0238753.
    PubMed     Abstract available

  91. GUEVARRA RB, Magez S, Peeters E, Chung MS, et al
    Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen.
    PLoS One. 2021;16:e0239792.
    PubMed     Abstract available

  92. EGFJORD AF, Margaryan A, Fischer A, Sjogren KG, et al
    Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark.
    PLoS One. 2021;16:e0244872.
    PubMed     Abstract available

  93. MACHER JN, Prazeres M, Taudien S, Jompa J, et al
    Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia.
    PLoS One. 2021;16:e0244616.
    PubMed     Abstract available

  94. COELHO AC, Pires R, Schutz G, Santa C, et al
    Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: A long-term proteomics approach.
    PLoS One. 2021;16:e0245148.
    PubMed     Abstract available

  95. SOUTO BM, de Araujo ACB, Hamann PRV, Bastos AR, et al
    Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 beta-xylosidase.
    PLoS One. 2021;16:e0245118.
    PubMed     Abstract available

  96. MAGUIRE M, Kase JA, Roberson D, Muruvanda T, et al
    Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water.
    PLoS One. 2021;16:e0245172.
    PubMed     Abstract available

  97. ELMASSRY MM, Kim S, Busby B
    Predicting drug-metagenome interactions: Variation in the microbial beta-glucuronidase level in the human gut metagenomes.
    PLoS One. 2021;16:e0244876.
    PubMed     Abstract available

  98. MUTURI SM, Muthui LW, Njogu PM, Onguso JM, et al
    Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya.
    PLoS One. 2021;16:e0244755.
    PubMed     Abstract available

  99. MADDUPPA H, Martaulina R, Zairion Z, Renjani RM, et al
    Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: Implication to sustainable fishery.
    PLoS One. 2021;16:e0240951.
    PubMed     Abstract available

  100. FAZZI-GOMES P, Aguiar J, Cabral GF, Marques D, et al
    Genomic approach for conservation and the sustainable management of endangered species of the Amazon.
    PLoS One. 2021;16:e0240002.
    PubMed     Abstract available

  101. BARRETT DE, Bartholomew JL
    A tale of two fish: Comparative transcriptomics of resistant and susceptible steelhead following exposure to Ceratonova shasta highlights differences in parasite recognition.
    PLoS One. 2021;16:e0234837.
    PubMed     Abstract available

  102. HARDMEIER I, Aeberhard N, Qi W, Schoenbaechler K, et al
    Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses.
    PLoS One. 2021;16:e0252534.
    PubMed     Abstract available

  103. SEYYEDSALEHI SF, Soleymani M, Rabiee HR, Mofrad MRK, et al
    PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks.
    PLoS One. 2021;16:e0244430.
    PubMed     Abstract available

  104. RICHTER J, Fanis P, Tryfonos C, Koptides D, et al
    Molecular epidemiology of SARS-CoV-2 in Cyprus.
    PLoS One. 2021;16:e0248792.
    PubMed     Abstract available

  105. LI Q, Yu X, Chen L, Zhao G, et al
    Genome-wide identification and expression analysis of the NCED family in cotton (Gossypium hirsutum L.).
    PLoS One. 2021;16:e0246021.
    PubMed     Abstract available

  106. MENDOZA N, Rivas E, Rodriguez-Roisin R, Garcia T, et al
    Liver epigenome changes in patients with hepatopulmonary syndrome: A pilot study.
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    Mitocondrial COI and 16S rDNA sequences support morphological identification and biogeography of deep-sea red crabs of the genus Chaceon (Crustacea, Decapoda, Geryonidae) in the Eastern Central and South Atlantic Ocean.
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    PubMed     Abstract available

  744. ZHAO Y, Pan B, Zhang M
    Phylogeography and conservation genetics of the endangered Tugarinovia mongolica (Asteraceae) from Inner Mongolia, Northwest China.
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  745. BERGERON MJ, Feau N, Stewart D, Tanguay P, et al
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    Avian haemosporidians in the cattle egret (Bubulcus ibis) from central-western and southern Africa: High diversity and prevalence.
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    Rectifying long-standing misconceptions about the rho statistic for molecular dating.
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    PubMed     Abstract available

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    PubMed     Abstract available

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    The first isolation of Clostridium difficile RT078/ST11 from pigs in China.
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    Proteomic analyses reveal misregulation of LIN28 expression and delayed timing of glial differentiation in human iPS cells with MECP2 loss-of-function.
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    Pathology and molecular epidemiology of Mycobacterium pinnipedii tuberculosis in native New Zealand marine mammals.
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    Analyzing bioactive effects of the minor hop compound xanthohumol C on human breast cancer cells using quantitative proteomics.
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    Advanced approach to analyzing calcareous protists for present and past pelagic ecology: Comprehensive analysis of 3D-morphology, stable isotopes, and genes of planktic foraminifers.
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    PubMed     Abstract available

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    Viral infection detection using metagenomics technology in six poultry farms of eastern China.
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  775. IQBAL N, Liu X, Yang T, Huang Z, et al
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    PubMed     Abstract available

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    PubMed     Abstract available

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    Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye.
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    PubMed     Abstract available

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    Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection.
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    PubMed     Abstract available

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    Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development.
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    Unassigned diversity of planktonic foraminifera from environmental sequencing revealed as known but neglected species.
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    Comparative proteomic study reveals the enhanced immune response with the blockade of interleukin 10 with anti-IL-10 and anti-IL-10 receptor antibodies in human U937 cells.
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    PubMed     Abstract available

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    PubMed     Abstract available

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    PubMed     Abstract available

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    PubMed     Abstract available

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    Functional genomics analysis of Phelan-McDermid syndrome 22q13 region during human neurodevelopment.
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    PubMed     Abstract available

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    Opportunities for genomic selection in American mink: A simulation study.
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    PubMed     Abstract available

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    Expansion of the known distribution of the coastal tailed frog, Ascaphus truei, in British Columbia, Canada, using robust eDNA detection methods.
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    PubMed     Abstract available

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    A common genomic code for chromatin architecture and recombination landscape.
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    PubMed     Abstract available

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    Molecular epidemiology survey and characterization of human influenza A viruses circulating among Palestinians in East Jerusalem and the West Bank in 2015.
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    PubMed     Abstract available

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    Assessing the role of transmission chains in the spread of HIV-1 among men who have sex with men in Quebec, Canada.
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    GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization.
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    Molecular characterization of Histomonas meleagridis exoproteome with emphasis on protease secretion and parasite-bacteria interaction.
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    Epistasis detectably alters correlations between genomic sites in a narrow parameter window.
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    Alleles associated with physical activity levels are estimated to be older than anatomically modern humans.
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    Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data.
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    RNA-sequencing analysis reveals betalains metabolism in the leaf of Amaranthus tricolor L.
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    Phylogeographic structure and ecological niche modelling reveal signals of isolation and postglacial colonisation in the European stag beetle.
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    Population genetic differentiation of the hydrothermal vent crab Austinograea alayseae (Crustacea: Bythograeidae) in the Southwest Pacific Ocean.
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    Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics.
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    Identifying suitable habitat and corridors for Indian Grey Wolf (Canis lupus pallipes) in Chotta Nagpur Plateau and Lower Gangetic Planes: A species with differential management needs.
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    Building the drug-GO function network to screen significant candidate drugs for myasthenia gravis.
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    Estimation of physiological genomic estimated breeding values (PGEBV) combining full hyperspectral and marker data across environments for grain yield under combined heat and drought stress in tropical maize (Zea mays L.).
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    Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia.
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    PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production.
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    The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages.
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    Fecal microbiota dysbiosis in macaques and humans within a shared environment.
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    Cryptic diversity and limited connectivity in octopuses: Recommendations for fisheries management.
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    Uncovering population structure in the Humboldt penguin (Spheniscus humboldti) along the Pacific coast at South America.
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    Hypothalamic transcriptome analysis reveals the neuroendocrine mechanisms in controlling broodiness of Muscovy duck (Cairina moschata).
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    DNA methylome of human neonatal umbilical cord: Enrichment of differentially methylated regions compared to umbilical cord blood DNA at transcription factor genes involved in body patterning and effects of maternal folate deficiency or children's sex.
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    Protein expression profiling of plasma and lungs at different stages of metastatic development in a human triple negative breast cancer xenograft model.
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    Using the Plasmodium mitochondrial genome for classifying mixed-species infections and inferring the geographical origin of P. falciparum parasites imported to the U.S.
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    Discovering cryptic species in the Aspiciliella intermutans complex (Megasporaceae, Ascomycota) - First results using gene concatenation and coalescent-based species tree approaches.
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    Phylogeography of Borrelia spirochetes in Ixodes pacificus and Ixodes spinipalpis ticks highlights differential acarological risk of tick-borne disease transmission in northern versus southern California.
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    Model-free feature screening for categorical outcomes: Nonlinear effect detection and false discovery rate control.
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    HIV-1 genetic diversity and demographic characteristics in Bulgaria.
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    PubMed     Abstract available

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    From genomic to LC-MS/MS evidence: Analysis of PfEMP1 in Benin malaria cases.
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    Genome-wide comparative analysis of RNA-binding Glycine-rich protein family genes between Gossypium arboreum and Gossypium raimondii.
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    Habitat suitability and the genetic structure of human populations during the Last Glacial Maximum (LGM) in Western Europe.
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    Maize responsiveness to Azospirillum brasilense: Insights into genetic control, heterosis and genomic prediction.
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    Comprehensive transcriptome analysis reveals genes potentially involved in isoflavone biosynthesis in Pueraria thomsonii Benth.
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  862. NEWTON R, Wernisch L
    A meta-analysis of multiple matched aCGH/expression cancer datasets reveals regulatory relationships and pathway enrichment of potential oncogenes.
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    Molecular prognosticators in clinically and pathologically distinct cohorts of head and neck squamous cell carcinoma-A meta-analysis approach.
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    Hybrid gene misregulation in multiple developing tissues within a recent adaptive radiation of Cyprinodon pupfishes.
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    Comparative transcriptome analysis of pigeonpea, Cajanus cajan (L.) and one of its wild relatives Cajanus platycarpus (Benth.) Maesen.
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    PubMed     Abstract available

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    Closing target trimming and CTTdocker programs for discovering hidden superfamily loci in genomes.
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    Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. var durum) collection.
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    Enhanced trypsin on a budget: Stabilization, purification and high-temperature application of inexpensive commercial trypsin for proteomics applications.
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    The antipsychotic medication, risperidone, causes global immunosuppression in healthy mice.
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    The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis.
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    Phylogeography, genetic diversity, and connectivity of brown bear populations in Central Asia.
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    PubMed     Abstract available

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    The genomic landscape of estrogen receptor alpha binding sites in mouse mammary gland.
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    Metagenomic analysis of the effects of toll-like receptors on bacterial infection in the peritoneal cavity following cecum ligation and puncture in mice.
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    Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns.
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    Gaining ecological insight on dietary allocation among horseshoe bats through molecular primer combination.
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    Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing.
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    Predicting drug activity against cancer cells by random forest models based on minimal genomic information and chemical properties.
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    PubMed     Abstract available

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    Genomic surveillance of invasive meningococcal disease in the Czech Republic, 2015-2017.
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    Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin.
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    The proteome of extracellular vesicles released by clastic cells differs based on their substrate.
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    PubMed     Abstract available

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    Sequence and phylogenetic analysis of novel porcine parvovirus 7 isolates from pigs in Guangxi, China.
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    Examining population structure of a bertha armyworm, Mamestra configurata (Lepidoptera: Noctuidae), outbreak in western North America: Implications for gene flow and dispersal.
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    Genetic analysis of Ghanaian G1P[8] and G9P[8] rotavirus A strains reveals the impact of P[8] VP4 gene polymorphism on P-genotyping.
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    Phylogeographic evidence for the inter- and intracontinental dissemination of avian influenza viruses via migration flyways.
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    Metagenomic analyses reveal previously unrecognized variation in the diets of sympatric Old World monkey species.
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    The prediction of early preeclampsia: Results from a longitudinal proteomics study.
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    Genetic diversity and population structure of four Chinese rabbit breeds.
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    False-negative errors in next-generation sequencing contribute substantially to inconsistency of mutation databases.
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    Genomic characterization of the complete terpene synthase gene family from Cannabis sativa.
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    Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans.
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    Polysaccharide-based liquid storage and transport media for non-refrigerated preservation of bacterial pathogens.
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    A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes.
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    Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally.
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    Comparative multi-omics systems analysis reveal the glycolysis / gluconeogenesis signal pathway play an important role in virulence attenuation in fish-derived GBS YM001.
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    A comparative proteomic study of plasma in Colombian childhood acute lymphoblastic leukemia.
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    Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome.
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    Proteomic analysis of gametophytic sex expression in the fern Ceratopteris thalictroides.
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    Evaluation of sodium deoxycholate as solubilization buffer for oil palm proteomics analysis.
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    PubMed     Abstract available

  908. GONZALEZ C, Gallagher AJ, Caballero S
    Conservation genetics of the bonnethead shark Sphyrna tiburo in Bocas del Toro, Panama: Preliminary evidence of a unique stock.
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    Advances in gene ontology utilization improve statistical power of annotation enrichment.
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    Population genetic data of the 21 autosomal STRs included in GlobalFiler kit of a population sample from the Kingdom of Bahrain.
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    Population structuring of the invasive mosquito Aedes albopictus (Diptera: Culicidae) on a microgeographic scale.
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    Enteric and non-enteric adenoviruses associated with acute gastroenteritis in pediatric patients in Thailand, 2011 to 2017.
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    NHBA is processed by kallikrein from human saliva.
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    Lessons for conservation management: Monitoring temporal changes in genetic diversity of Cape mountain zebra (Equus zebra zebra).
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    Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics.
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    Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: A preliminary computational analysis of the COSMIC Cancer Gene Census.
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    Transcriptional regulation of abscisic acid biosynthesis and signal transduction, and anthocyanin biosynthesis in 'Bluecrop' highbush blueberry fruit during ripening.
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    Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes.
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    Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae.
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    A comprehensive expression analysis of the expansin gene family in potato (Solanum tuberosum) discloses stress-responsive expansin-like B genes for drought and heat tolerances.
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    A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.).
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    Xanthomonas citri subsp. citri and Xanthomonas arboricola pv. pruni: Comparative analysis of two pathogens producing similar symptoms in different host plants.
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    Salivary proteomics of canine oral tumors using MALDI-TOF mass spectrometry and LC-tandem mass spectrometry.
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    Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus.
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    From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers.
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    Transcriptomic profiling and analysis of differentially expressed genes in asparagus bean (Vigna unguiculata ssp. sesquipedalis) under salt stress.
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    Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy.
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    The genome of the migratory nematode, Radopholus similis, reveals signatures of close association to the sedentary cyst nematodes.
    PLoS One. 2019;14:e0224391.
    PubMed     Abstract available

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    Functional models in genome-wide selection.
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    Amphibian skin-associated Pigmentiphaga: Genome sequence and occurrence across geography and hosts.
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    Proteomic analysis of Escherichia coli detergent-resistant membranes (DRM).
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    A super-SILAC based proteomics analysis of diffuse large B-cell lymphoma-NOS patient samples to identify new proteins that discriminate GCB and non-GCB lymphomas.
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    Clustering of the structures by using "snakes-&-dragons" approach, or correlation matrix as a signal.
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    Take one step backward to move forward: Assessment of genetic diversity and population structure of captive Asian woolly-necked storks (Ciconia episcopus).
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    A proteomic clock for malignant gliomas: The role of the environment in tumorigenesis at the presymptomatic stage.
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    Comparison of transcriptomes of an orthotospovirus vector and non-vector thrips species.
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    Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains.
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    Nutrigenomic effect of conjugated linoleic acid on growth and meat quality indices of growing rabbit.
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    Spread of domestic animals across Neolithic western Anatolia: New stable isotope evidence from Ugurlu Hoyuk, the island of Gokceada, Turkey.
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    Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach.
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    Reconstructing the population history of the sandy beach amphipod Haustorioides japonicus using the calibration of demographic transition (CDT) approach.
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    Suppression treatment differentially influences the microbial community and the occurrence of broad host range plasmids in the rhizosphere of the model cover crop Avena sativa L.
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    Inter-individual genomic heterogeneity within European population isolates.
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    Method comparison for N-glycan profiling: Towards the standardization of glycoanalytical technologies for cell line analysis.
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    Sugar transporters in Fabaceae, featuring SUT MST and SWEET families of the model plant Medicago truncatula and the agricultural crop Pisum sativum.
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    Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids.
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