Next Generation Sequencing Citations

Featured Publications

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Rutgers scientists have revealed a key signaling pathway for cell differentiation in the intestinal lining. The new study published in Nature Genetics used GENEWIZ’s Single-Cell RNA-Seq service.

doi:10.1038/s41588-019-0384-0

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USDA researchers show that Honeycrisp apple trees sprayed with the plant hormone gibberellic acid develop seedless fruits without fertilization. RNA-Seq performed by GENEWIZ revealed the underlying gene expression changes.

doi:10.1038/s41438-019-0124-8

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A new study from Weill Cornell Medicine sheds light on the genetic and epigenetic causes of male infertility using a combination of whole genome, whole exome, and RNA sequencing performed at GENEWIZ.

doi:10.1371/journal.pone.0214275

RNA Sequencing

Onyema, O. O. et al. Eosinophils downregulate lung alloimmunity by decreasing TCR signal transduction. JCI Insight 4, (2019). doi:10.1172/jci.insight.128241

Blache, U. et al. Mesenchymal stromal cell activation by breast cancer secretomes in bioengineered 3D microenvironments. Life Science Alliance 2, e201900304 (2019). doi:10.26508/lsa.201900304

McNamara-Bordewick, N. K., McKinstry, M. & Snow, J. W. Robust Transcriptional Response to Heat Shock Impacting Diverse Cellular Processes despite Lack of Heat Shock Factor in Microsporidia. mSphere 4, (2019). doi:10.1128/mSphere.00219-19

Koyama, T. et al. A SNP in a Steroidogenic Enzyme Is Associated with Phenotypic Sex in Seriola Fishes. Current Biology (2019). doi:10.1016/j.cub.2019.04.069

Pennerman, K. K. et al. Volatile 1-octen-3-ol increases patulin production by Penicillium expansum on a patulin-suppressing medium. Mycotoxin Research (2019). doi:10.1007/s12550-019-00348-w

Castrejón-Godínez, M. L. et al. Transcriptional analysis reveals the metabolic state of Burkholderia zhejiangensis CEIB S4-3 during methyl parathion degradation. PeerJ 7, e6822 (2019). doi:10.7717/peerj.6822

Chen, L. et al. A reinforcing HNF4–SMAD4 feed-forward module stabilizes enterocyte identity. Nature Genetics (2019). doi:10.1038/s41588-019-0384-0 **Single-Cell RNA-Seq**

Li, S. et al. Transcriptional regulation of autophagy-lysosomal function in BRAF-driven melanoma progression and chemoresistance. Nature Communications 10, (2019). doi:10.1038/s41467-019-09634-8

Fan, Y. et al. Optimal translational fidelity is critical for Salmonella virulence and host interactions. Nucleic Acids Research (2019). doi:10.1093/nar/gkz229

Galimba, K. D., Bullock, D. G., Dardick, C., Liu, Z. & Callahan, A. M. Gibberellic acid induced parthenocarpic “Honeycrisp” apples (Malus domestica) exhibit reduced ovary width and lower acidity. Horticulture Research 6, (2019). doi:10.1038/s41438-019-0124-8

Deng, X. et al. Analysis of coronavirus temperature-sensitive mutants reveals an interplay between the macrodomain and papain-like protease impacting replication and pathogenesis. Journal of Virology (2019). doi:10.1128/jvi.02140-18

Cheung, S., Parrella, A., Rosenwaks, Z. & Palermo, G. D. Genetic and epigenetic profiling of the infertile male. PLOS ONE 14, e0214275 (2019). doi:10.1371/journal.pone.0214275

Al Nabhani, Z. et al. A Weaning Reaction to Microbiota Is Required for Resistance to Immunopathologies in the Adult. Immunity 50, 1-13 (2019). doi:10.1016/j.immuni.2019.02.014

da Cruz, R. S. et al. Parental obesity programs pancreatic cancer development in offspring. Endocrine-Related Cancer (2019). doi:10.1530/erc-19-0016

Rayman, J. B., Hijazi, J., Li, X., Kedersha, N., Anderson, P. J. & Kandel, E. R. Genetic Perturbation of TIA1 Reveals a Physiological Role in Fear Memory. Cell Reports 26, 2970-2983 (2019). doi:10.1016/j.celrep.2019.02.048

Aho, E. R. et al. Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity. Cell Reports 26, 2916-2928 (2019). doi:10.1016/j.celrep.2019.02.047

Stratmann, J., Ekman, H. & Thor, S. Branching gene regulatory network dictating different aspects of a neuronal cell identity. Development (2019). doi:10.1242/dev.174300

Mascia, T., Labarile, R., Doohan, F. & Gallitelli, D. Tobacco mosaic virus infection triggers an RNAi-based response in Phytophthora infestans. Scientific Reports 9, (2019). doi:10.1038/s41598-019-39162-w

Kitada, M., Murakami, T., Wakao, S., Li, G. & Dezawa, M. Direct conversion of adult human skin fibroblasts into functional Schwann cells that achieve robust recovery of the severed peripheral nerve in rats. Glia (2019). doi:10.1002/glia.23582

Boumart, Z. et al. Safety and immunogenicity of a live attenuated Rift Valley Fever recombinant arMP-12DNSm21/384 vaccine candidate for sheep, goats and calves. Vaccine (2019). doi:10.1016/j.vaccine.2019.01.067

Cheng, D. et al. Moringa Isothiocyanate Activates Nrf2: Potential Role in Diabetic Nephropathy. The AAPS Journal 21, (2019). doi:10.1208/s12248-019-0301-6

Nowicki, M. et al. Development and Characterization of Genic Microsatellites for the Ornamental Plant Green and Gold (Chrysogonum virginianum). HortScience 54, 395–400 (2019). doi:10.21273/HORTSCI13739-18

Crava, C. M., Sassù, F., Tait, G., Becher, P. G. & Anfora, G. Functional transcriptome analyses of Drosophila suzukii antennae reveal mating-dependent olfaction plasticity in females. Insect Biochemistry and Molecular Biology 105, 51–59 (2019). doi:10.1016/j.ibmb.2018.12.012

Hogan, S. E. et al. Mesenchymal Stromal Cell-Derived Exosomes Improve Mitochondrial Health in Pulmonary Arterial Hypertension. American Journal of Physiology-Lung Cellular and Molecular Physiology (2019). doi:10.1152/ajplung.00058.2018

Puri, A. W. et al. Interspecies chemical signaling in a methane-oxidizing bacterial community. Applied and Environmental Microbiology (2019). doi:10.1128/aem.02702-18

Tjitro, R. et al. Modeling the Function of TATA Box Binding Protein in Transcriptional Changes Induced by HIV-1 Tat in Innate Immune Cells and the Effect of Methamphetamine Exposure. Frontiers in Immunology 9, (2019). doi:10.3389/fimmu.2018.03110

Li, Z. T. et al. Exposure in vitro to an Environmentally Isolated Strain TC09 of Cladosporium sphaerospermum Triggers Plant Growth Promotion, Early Flowering, and Fruit Yield Increase. Frontiers in Plant Science 9, (2019). doi:10.3389/fpls.2018.01959

Nguyen, M. B. et al. Dissection of Merkel cell formation in hairy and glabrous skin reveals a common requirement for FGFR2-mediated signaling. Experimental Dermatology (2019). doi:10.1111/exd.13901

Li, Z. et al. Loss of the FAT1 Tumor Suppressor Promotes Resistance to CDK4/6 Inhibitors via the Hippo Pathway. Cancer Cell 34, 893–905.e8 (2018). doi:10.1016/j.ccell.2018.11.006

Vogt, S. L. et al. Characterization of the Citrobacter rodentium Cpx regulon and its role in host infection. Molecular Microbiology (2018). doi:10.1111/mmi.14182

Szádeczky-Kardoss, I. et al. The nonstop decay and the RNA silencing systems operate cooperatively in plants. Nucleic Acids Research 46, 4632–4648 (2018). doi:10.1093/nar/gky279

Yao, W. et al. Transcriptome Analysis of Poplar Under Salt Stress and Over-Expression of Transcription Factor NAC57 Gene Confers Salt Tolerance in Transgenic Arabidopsis. Frontiers in Plant Science 9, (2018). doi:10.3389/fpls.2018.01121

Cao, Z. et al. NagRBt Is a Pleiotropic and Dual Transcriptional Regulator in Bacillus thuringiensis. Frontiers in Microbiology 9, (2018). doi:10.3389/fmicb.2018.01899

Shin, B. et al. Effector CD4 T cells with progenitor potential mediate chronic intestinal inflammation. The Journal of Experimental Medicine jem.20172335 (2018). doi:10.1084/jem.20172335

He, Q. et al. Oleaginicity of the yeast strain Saccharomyces cerevisiae D5A. Biotechnology for Biofuels 11, (2018). doi:10.1186/s13068-018-1256-z

Nowicki, M. et al. Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars. PLOS ONE 13, e0205407 (2018). doi:10.1371/journal.pone.0205407

Liu, X. et al. Cyanidin Curtails Renal Cell Carcinoma Tumorigenesis. Cellular Physiology and Biochemistry 46, 2517–2531 (2018). doi:10.1159/000489658

Onishi, M., Pecani, K., Jones, T., IV, Pringle, J. R. & Cross, F. R. F-actin homeostasis through transcriptional regulation and proteasome-mediated proteolysis. Proceedings of the National Academy of Sciences 115, E6487–E6496 (2018). doi:10.1073/pnas.1721935115

Nunez, J. C. B., Elyanow, R. G., Ferranti, D. A. & Rand, D. M. Population Genomics and Biogeography of the Northern Acorn Barnacle (Semibalanus balanoides) Using Pooled Sequencing Approaches. in Population Genomics (Springer International Publishing, 2018). doi:10.1007/13836_2018_58

Monge, E. C., Tuveng, T. R., Vaaje-Kolstad, G., Eijsink, V. G. H. & Gardner, J. G. Systems analysis of the glycoside hydrolase family 18 enzymes from Cellvibrio japonicus characterizes essential chitin degradation functions. Journal of Biological Chemistry 293, 3849–3859 (2018). doi:10.1074/jbc.RA117.000849

Dey, K. K., Leite, M., Hu, J. S., Jordan, R. & Melzer, M. J. Detection of Jasmine virus H and characterization of a second pelarspovirus infecting star jasmine (Jasminum multiflorum) and angelwing jasmine (J. nitidum) plants displaying virus-like symptoms. Archives of Virology 163, 3051–3058 (2018). doi:10.1007/s00705-018-3947-y

Nourinejhad Zarghani, S. et al. Grapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data. PLOS ONE 13, e0206010 (2018). doi:10.1371/journal.pone.0206010

Banaszak, L. G. et al. Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing. Blood Cells, Molecules, and Diseases 69, 10–22 (2018). doi:10.1016/j.bcmd.2017.12.002

Zepecki, J. P. et al. Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor. Oncogene (2018). doi:10.1038/s41388-018-0546-z

Xu, B., Santos, S. A. A. & Hinton, B. T. Protein tyrosine kinase 7 regulates extracellular matrix integrity and mesenchymal intracellular RAC1 and myosin II activities during Wolffian duct morphogenesis. Developmental Biology 438, 33–43 (2018). doi:10.1016/j.ydbio.2018.03.011

Burl, R. B. et al. Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling. Cell Metabolism 28, 300–309.e4 (2018). doi:10.1016/j.cmet.2018.05.025

Xiao, J., Khan, M. M., Vemula, S., Tian, J. & LeDoux, M. S. Consequences of Cre-mediated deletion of Ciz1 exon 5 in mice. FEBS Letters 592, 3101–3110 (2018). doi:10.1002/1873-3468.13221

Dnyansagar, R. et al. Dispersal and speciation: The cross Atlantic relationship of two parasitic cnidarians. Molecular Phylogenetics and Evolution 126, 346–355 (2018). doi:10.1016/j.ympev.2018.04.035

Shaw, C. H., Gao, G. & Wiens, G. D. Differential expression and evolution of three tandem, interleukin-1 receptor-like 1 genes in rainbow trout (Oncorhynchus mykiss). Developmental & Comparative Immunology 87, 193–203 (2018). doi:10.1016/j.dci.2018.06.003

Gonzalez, T. J. et al. Fluorescent light exposure incites acute and prolonged immune responses in zebrafish (Danio rerio) skin. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 208, 87–95 (2018). doi:10.1016/j.cbpc.2017.09.009

Black, K. L. et al. Aberrant splicing in B-cell acute lymphoblastic leukemia. Nucleic Acids Research (2018). doi:10.1093/nar/gky946

Guo, X. et al. Pharmacodynamic biomarkers and differential effects of TNF- and GM-CSF-targeting biologics in rheumatoid arthritis. International Journal of Rheumatic Diseases (2018). doi:10.1111/1756-185x.13395

Arreola, A. et al. Von Hippel-Lindau mutations disrupt vascular patterning and maturation via Notch. JCI Insight 3, (2018). doi:10.1172%2Fjci.insight.92193

Banaszak, L. G. et al. Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing. Blood Cells, Molecules, and Diseases 69, 10–22 (2018). doi:10.1016/j.bcmd.2017.12.002

Boulain, H. et al. Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants. Genome Biology and Evolution 10, 1554–1572 (2018). doi:10.1093/gbe/evy097

Dnyansagar, R. et al. Dispersal and speciation: The cross Atlantic relationship of two parasitic cnidarians. Molecular Phylogenetics and Evolution 126, 346–355 (2018). doi:10.1016/j.ympev.2018.04.035

Endalur Gopinarayanan, V. & Nair, N. U. A semi-synthetic regulon enables rapid growth of yeast on xylose. Nature Communications 9, (2018). doi:10.1038/s41467-018-03645-7

Geisler, C. A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production. BMC Biotechnology 18, (2018). doi:10.1186/s12896-017-0412-z

Smith, H. K. et al. Metallothionein I as a direct link between therapeutic hematopoietic stem/progenitor cells and cerebral protection in stroke. The FASEB Journal 32, 2381–2394 (2018). doi:10.1096/fj.201700746R

Wu, Z.-J. et al. CRISPR/Cas9-mediated ASXL1 mutations in U937 cells disrupt myeloid differentiation. International Journal of Oncology (2018). doi:10.3892/ijo.2018.4290

Botta, D. et al. Dynamic regulation of T follicular regulatory cell responses by interleukin 2 during influenza infection. Nature Immunology 18, 1249–1260 (2017). doi:10.1038/ni.3837

Cahoon, A., Nauss, J., Stanley, C. & Qureshi, A. Deep Transcriptome Sequencing of Two Green Algae, Chara vulgaris and Chlamydomonas reinhardtii, Provides No Evidence of Organellar RNA Editing. Genes 8, 80 (2017). doi:10.3390/genes8020080

Carey, M. A. & Ho, E. S. A Transcriptome Study of Borrelia burgdorferi Infection in Murine Heart and Brain Tissues. Journal of Young Investigators (2017). doi:10.22186/jyi.33.1.28-41

Donohue, M. W., Carleton, K. L. & Cronin, T. W. Opsin Expression in the Central Nervous System of the Mantis Shrimp Neogonodactylus oerstedii. The Biological Bulletin 233, 58–69 (2017). doi:10.1086/694421

Gilman, A. et al. Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C. PeerJ 5, e3945 (2017). doi:10.7717/peerj.3945

Nguyen, N. M. et al. Maternal intake of high n-6 polyunsaturated fatty acid diet during pregnancy causes transgenerational increase in mammary cancer risk in mice. Breast Cancer Research 19, (2017). doi:10.1186/s13058-017-0866-x

Yang, L., Fang, J. & Chen, J. Tumor cell senescence response produces aggressive variants. Cell Death Discovery 3, 17049 (2017). doi:10.1038/cddiscovery.2017.49

 

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Whole Genome Sequencing

Hattori, A. et al. Transient multifocal genomic crisis creating chromothriptic and non-chromothriptic rearrangements in prezygotic testicular germ cells. BMC Medical Genomics 12, (2019). doi:10.1186/s12920-019-0526-3

Pereira, A., Xavier, R., Perera, A., Salvi, D. & Harris, D. J. DNA metabarcoding to assess diet partitioning and feeding strategies in generalist vertebrate predators: a case study on three syntopic lacertid lizards from Morocco. Biological Journal of the Linnean Society (2019). doi:10.1093/biolinnean/blz061

Massey, D. J., Kim, D., Brooks, K. E., Smolka, M. B. & Koren, A. Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing. Genes 10, 269 (2019). doi:10.3390/genes10040269

Cheung, S., Parrella, A., Rosenwaks, Z. & Palermo, G. D. Genetic and epigenetic profiling of the infertile male. PLOS ONE 14, e0214275 (2019). doi:10.1371/journal.pone.0214275

Zhang, H. et al. Development of a goosegrass (Eleusine indica ) draft genome and application to weed science research. Pest Management Science (2019). doi:10.1002/ps.5389

Meurs, K. et al. A QIL1 Variant Associated with Ventricular Arrhythmias and Sudden Cardiac Death in the Juvenile Rhodesian Ridgeback Dog. Genes 10, 168 (2019). doi:10.3390/genes10020168

Zhivagui, M. et al. Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans. Genome Research (2019). doi:10.1101/gr.242453.118

Dunphy, L. J., Yen, P. & Papin, J. A. Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa. Cell Systems 8, 3–14.e3 (2019). doi:10.1016/j.cels.2018.12.002

Yost, O., Friedenberg, S. G., Jesty, S. A., Olby, N. J. & Meurs, K. M. The R9H phospholamban mutation is associated with highly penetrant dilated cardiomyopathy and sudden death in a spontaneous canine model. Gene (2019). doi:10.1016/j.gene.2019.02.022

Yang, S., Li, S. & Li, X.-J. Shortening the Half-Life of Cas9 Maintains Its Gene Editing Ability and Reduces Neuronal Toxicity. Cell Reports 25, 2653–2659.e3 (2018). doi:10.1016/j.celrep.2018.11.019

Meurs, K. M. et al. Evaluation of genes associated with human myxomatous mitral valve disease in dogs with familial myxomatous mitral valve degeneration. The Veterinary Journal 232, 16–19 (2018). doi:10.1016/j.tvjl.2017.12.002

Chen, C.-T. et al. Synthetic methanol auxotrophy of Escherichia coli for methanol-dependent growth and production. Metabolic Engineering 49, 257–266 (2018). doi:10.1016/j.ymben.2018.08.010

Gao, R. et al. Complete chloroplast genome sequence of Dryopteris fragrans (L.) Schott and the repeat structures against the thermal environment. Scientific Reports 8, (2018). doi:10.1038/s41598-018-35061-8

Crowell, R. M., Nienow, J. A. & Bruce Cahoon, A. The complete chloroplast and mitochondrial genomes of the diatom Nitzschia palea (Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotom Durinskia baltica. Journal of Phycology (2018). doi:10.1111/jpy.12824

Deng, S., Pomraning, K. R., Bohutskyi, P. & Magnuson, J. K. Draft Genome Sequence of Aspergillus oryzae ATCC 12892 . Genome Announcements 6, (2018). doi:10.1128/genomeA.00251-18

Friedenberg, S. G. et al. A de novo mutation in the EXT2 gene associated with osteochondromatosis in a litter of American Staffordshire Terriers. Journal of Veterinary Internal Medicine 32, 986–992 (2018). doi:10.1111/jvim.15073

Geisler, C. A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production. BMC Biotechnology 18, (2018). doi:10.1186/s12896-017-0412-z

Guevar, J., Olby, N. J., Meurs, K. M., Yost, O. & Friedenberg, S. G. Deafness and vestibular dysfunction in a Doberman Pinscher puppy associated with a mutation in the PTPRQ gene. Journal of Veterinary Internal Medicine 32, 665–669 (2018). doi:10.1111/jvim.15060

Oliver, A., Kay, M. & Cooper, K. K. Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC Genomics 19, (2018). doi:10.1186/s12864-018-4635-8

Iyer, R., Iken, B., Damania, A. & Krieger, J. Whole genome analysis of six organophosphate-degrading rhizobacteria reveals putative agrochemical degradation enzymes with broad substrate specificity. Environmental Science and Pollution Research 25, 13660–13675 (2018). doi:10.1007/s11356-018-1435-2 

Margres, M. J. et al. The genomic basis of tumor regression in Tasmanian devils (Sarcophilus harrisii). Genome Biology and Evolution (2018). doi:10.1093/gbe/evy229

Adams, H. M., Joyce, L. R., Guan, Z., Akins, R. L. & Palmer, K. L. Streptococcus mitis and S. oralis Lack a Requirement for CdsA, the Enzyme Required for Synthesis of Major Membrane Phospholipids in Bacteria. Antimicrobial Agents and Chemotherapy 61, (2017). doi:10.1128/AAC.02552-16.

Banla, I. L. et al. Modulators of Enterococcus faecalis Cell Envelope Integrity and Antimicrobial Resistance Influence Stable Colonization of the Mammalian Gastrointestinal Tract . Infection and Immunity 86, (2017). doi:10.1128/iai.00381-17

Iyer, R., Damania, A. & Iken, B. Whole genome sequencing of Microbacterium sp. AISO3 from polluted San Jacinto River sediment reveals high bacterial mobility, metabolic versatility and heavy metal resistance. Genomics Data 14, 10–13 (2017). doi:10.1016/j.gdata.2017.07.009

Iyer, R., Iken, B. & Damania, A. Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants. Genomics Data 14, 40–43 (2017). doi:10.1016/j.gdata.2017.07.011

Mayer-Blackwell, K. et al. 1,2-Dichloroethane Exposure Alters the Population Structure, Metabolism, and Kinetics of a Trichloroethene-Dechlorinating Dehalococcoides mccartyi Consortium. Environmental Science & Technology 50, 12187–12196 (2016). doi:10.1021/acs.est.6b02957 

Gu, J. et al. Therapeutic effect of Pseudomonas aeruginosa phage YH30 on mink hemorrhagic pneumonia. Veterinary Microbiology 190, 5–11 (2016). doi:10.1016/j.vetmic.2016.03.016

Hilton, L. K. et al. A Forward Genetic Screen and Whole Genome Sequencing Identify Deflagellation Defective Mutants in Chlamydomonas, Including Assignment of ADF1 as a TRP Channel. G3: Genes|Genomes|Genetics (2016). doi:10.1534/g3.116.034264

Hu, B. et al. Comprehensive molecular characterization of Methylobacterium extorquens AM1 adapted for 1-butanol tolerance. Biotechnology for Biofuels 9, (2016). doi:10.1186/s13068-016-0497-y

Jiao, Y. et al. A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. The Plant Cell (2016). doi:10.1105/tpc.16.00373

Li, L. et al. Characterization of Pseudomonas aeruginosaphage K5 genome and identification of its receptor related genes. Journal of Basic Microbiology 56, 1344–1353 (2016). doi:10.1002/jobm.201600116

Martínez, T., Ropelewski, A. J., González-Mendez, R., Vázquez, G. J. & Robledo, I. E. Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Sequence Type 2 Isolate from Puerto Rico . Genome Announcements 4, (2016). doi:10.1128/genomeA.00758-16 

Sturmberger, L. et al. Refined Pichia pastoris reference genome sequence. Journal of Biotechnology 235, 121–131 (2016). doi:10.1016/j.jbiotec.2016.04.023

Xiong, Y. et al. An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry. Analytical Chemistry 88, 2784–2791 (2016). doi:10.1021/acs.analchem.5b04417

 

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Exome Sequencing

Quentmeier, H. et al. The LL-100 panel: 100 cell lines for blood cancer studies. Scientific Reports 9, (2019). doi:10.1038/s41598-019-44491-x

Peter, B. et al. Exome Sequencing of Two Siblings with Sporadic Autism Spectrum Disorder and Severe Speech Sound Disorder Suggests Pleiotropic and Complex Effects. Behavior Genetics (2019). doi:10.1007/s10519-019-09957-8

Cheung, S., Parrella, A., Rosenwaks, Z. & Palermo, G. D. Genetic and epigenetic profiling of the infertile male. PLOS ONE 14, e0214275 (2019). doi:10.1371/journal.pone.0214275

Urreizti, R. et al. DPH1 syndrome: two novel variants and structural and functional analyses of seven missense variants identified in syndromic patients. European Journal of Human Genetics (2019). doi:10.1038/s41431-019-0374-9

Cheung, S., Schlegel, P. N., Rosenwaks, Z. & Palermo, G. D. Revisiting aneuploidy profile of surgically retrieved spermatozoa by whole exome sequencing molecular karyotype. PLOS ONE 14, e0210079 (2019). doi:10.1371/journal.pone.0210079

Xu, G., Zheng, H. & Li, J. Y. Next-generation whole exome sequencing of glioblastoma with a primitive neuronal component. Brain Tumor Pathology (2019). doi:10.1007/s10014-019-00334-1

Kinney, N. et al. Whole-exome sequencing reveals microsatellite DNA markers for response to dofetilide initiation in patients with persistent atrial fibrillation: A pilot study. Clinical Cardiology 41, 849–854 (2018). doi:10.1002/clc.22969

Adam, L. et al. DNA Sequencing of Small Bowel Adenocarcinomas Identifies Targetable Recurrent Mutations in the ERBB2 Signaling Pathway. Clinical Cancer Research 25, 641–651 (2018). doi:10.1158/1078-0432.CCR-18-1480

 

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Amplicon Sequencing

Tao, L. et al. Sulfated glycosaminoglycans and low-density lipoprotein receptor contribute to Clostridium difficile toxin A entry into cells. Nature Microbiology (2019). doi:10.1038/s41564-019-0464-z

Pereira, A., Xavier, R., Perera, A., Salvi, D. & Harris, D. J. DNA metabarcoding to assess diet partitioning and feeding strategies in generalist vertebrate predators: a case study on three syntopic lacertid lizards from Morocco. Biological Journal of the Linnean Society (2019). doi:10.1093/biolinnean/blz061

François, S. et al. A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations. Viruses 11, 233 (2019). doi:10.3390/v11030233

Wolfe, A. D., Arnold, D. B. & Chen, X. Comparison of RNA Editing Activity of APOBEC1-A1CF and APOBEC1-RBM47 Complexes Reconstituted in HEK293T Cells. Journal of Molecular Biology (2019). doi:10.1016/j.jmb.2019.02.025

VanLith, C. J. et al. Ex Vivo Hepatocyte Reprograming Promotes Homology-Directed DNA Repair to Correct Metabolic Disease in Mice After Transplantation. Hepatology Communications (2019). doi:10.1002/hep4.1315

Arunsan, P. et al. Programmed knockout mutation of liver fluke granulin attenuates virulence of infection-induced hepatobiliary morbidity. eLife 8, (2019). doi:10.7554/eLife.41463

Wollacott, A. M. et al. Structural prediction of antibody-APRIL complexes by computational docking constrained by antigen saturation mutagenesis library data. Journal of Molecular Recognition e2778 (2019). doi:10.1002/jmr.2778

Lemmel, F., Maunoury-Danger, F., Fanesi, A., Leyval, C. & Cébron, A. Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient. Microbial Ecology (2018). doi:10.1007/s00248-018-1297-7

Cortes-Tolalpa, L., Norder, J., van Elsas, J. D. & Falcao Salles, J. Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate. Applied Microbiology and Biotechnology 102, 2913–2927 (2018). doi:10.1007/s00253-017-8714-6

Tian, S. et al. Genome-wide CRISPR screens for Shiga toxins and ricin reveal Golgi proteins critical for glycosylation. PLOS Biology 16, e2006951 (2018). doi:10.1371/journal.pbio.2006951

Phillips, J. N., Berlow, M. & Derryberry, E. P. The Effects of Landscape Urbanization on the Gut Microbiome: An Exploration Into the Gut of Urban and Rural White-Crowned Sparrows. Frontiers in Ecology and Evolution 6, (2018). doi:10.3389/fevo.2018.00148

Yukilevich, R., Maroja, L. S., Nguyen, K., Hussain, S. & Kumaran, P. Rapid sexual and genomic isolation in sympatric Drosophila without reproductive character displacement. Ecology and Evolution 8, 2852–2867 (2018). doi:10.1002/ece3.3893

Mas-Carrió, E., Dini-Andreote, F., Brossi, M. J. de L., Salles, J. F. & Olff, H. Organic Amendment Under Increasing Agricultural Intensification: Effects on Soil Bacterial Communities and Plant Productivity. Frontiers in Microbiology 9, (2018). doi:10.3389/fmicb.2018.02612

Stoeckle, M. Y., Das Mishu, M. & Charlop-Powers, Z. GoFish: A versatile nested PCR strategy for environmental DNA assays for marine vertebrates. PLOS ONE 13, e0198717 (2018). doi:10.1371/journal.pone.0198717

Cahoon, A. B., Huffman, A. G., Krager, M. M. & Crowell, R. M. A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA. Metabarcoding and Metagenomics 2, (2018). doi:10.3897/mbmg.2.26939

Gainey, D. P., Kim, J. Y. & Maroja, L. S. Mapping reduced introgression loci to the X chromosome of the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus. PLOS ONE 13, e0208498 (2018). doi:10.1371/journal.pone.0208498

Hadigol, M. & Khiabanian, H. MERIT reveals the impact of genomic context on sequencing error rate in ultra-deep applications. BMC Bioinformatics 19, (2018). doi:10.1186/s12859-018-2223-1

Rabadan, R. et al. On Statistical Modeling of Sequencing Noise in High Depth Data to Assess Tumor Evolution. Journal of Statistical Physics 172, 143–155 (2017). doi:10.1007/s10955-017-1945-1

Veeravalli, K. et al. Strain engineering to reduce acetate accumulation during microaerobic growth conditions in Escherichia coli. Biotechnology Progress 34, 303–314 (2017). doi:10.1002/btpr.2592 

 

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Metagenomics

Tarnecki, A. M., Wafapoor, M., Phillips, R. N. & Rhody, N. R. Benefits of a Bacillus probiotic to larval fish survival and transport stress resistance. Scientific Reports 9, (2019). doi:10.1038/s41598-019-39316-w

Mahalingam, S., Dharumadurai, D. & Archunan, G. Vaginal microbiome analysis of buffalo (Bubalus bubalis) during estrous cycle using high-throughput amplicon sequence of 16S rRNA gene. Symbiosis (2019). doi:10.1007/s13199-018-00595-y

Ruiz-Moreno, H. A., López-Tamayo, A. N., Caro-Quintero, A., Husserl, J. & González Barrios, A. F. Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water. Ecological Modelling 399, 1-12 (2019). doi:10.1016/j.ecolmodel.2019.02.001

Chen, G. et al. Rapid reformation of larger aerobic granular sludge in an internal-circulation membrane bioreactor after long-term operation: Effect of short-time aeration. Bioresource Technology 273, 462–467 (2019). doi:10.1016/j.biortech.2018.11.029

Brand, V. R., Crosby, L. D. & Criddle, C. S. Niche Differentiation among Three Closely Related Competibacteraceae Clades at a Full-Scale Activated Sludge Wastewater Treatment Plant and Putative Linkages to Process Performance. Applied and Environmental Microbiology 85, (2018). doi:10.1128/AEM.02301-18

Pratscher, J., Vollmers, J., Wiegand, S., Dumont, M. G. & Kaster, A.-K. Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane-Oxidizing Upland Soil Cluster α. Environmental Microbiology 20, 1016–1029 (2018). doi:10.1111/1462-2920.14036

Barreto, C. R., Morrissey, E. M., Wykoff, D. D. & Chapman, S. K. Co-occurring Mangroves and Salt Marshes Differ in Microbial Community Composition. Wetlands 38, 497–508 (2018). doi:10.1007/s13157-018-0994-9

Sapp, M., Ploch, S., Fiore-Donno, A. M., Bonkowski, M. & Rose, L. E. Protists are an integral part of the Arabidopsis thaliana microbiome. Environmental Microbiology 20, 30–43 (2017). doi:10.1111/1462-2920.13941

 

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Epigenomics

Weissmiller, A. M., Wang, J., Lorey, S. L., Howard, G. C., Martinez, E., Liu, Q., & Tansey, W. P. (2019). Inhibition of MYC by the SMARCB1 tumor suppressor. Nature Communications, 10(1). doi:10.1038/s41467-019-10022-5

Mack, S. C. et al. Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma. The Journal of Experimental Medicine jem.20190196 (2019). doi:10.1084/jem.20190196

Wheeler, M. A. et al. Environmental Control of Astrocyte Pathogenic Activities in CNS Inflammation. Cell 176, 581–596.e18 (2019). doi:10.1016/j.cell.2018.12.012

Wang, B. et al. Integrated RNA-seq and ChIP-seq analysis reveals a feed-forward loop regulating H3K9ac and key labor drivers in human placenta. Placenta 76, 40–50 (2019). doi:10.1016/j.placenta.2019.01.010

Hopcraft, S. E. et al. Chromatin remodeling controls Kaposi’s sarcoma-associated herpesvirus reactivation from latency. PLOS Pathogens 14, e1007267 (2018). doi:10.1371/journal.ppat.1007267

Wang, B. et al. Vitamin D stimulates multiple microRNAs to inhibit CRH and other pro-labor genes in human placenta. Endocrine Connections 1380–1388 (2018). doi:10.1530/ec-18-0345

 

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