Tag: bioRxiv

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…

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Genomic insights into Plasmodium vivax population structure and diversity in central Africa | Malaria Journal

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

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Causality-enriched epigenetic age uncouples damage and adaptation

Gladyshev, V. N. et al. Molecular damage in aging. Nat. Aging 1, 1096–1106 (2021). Article  PubMed  PubMed Central  Google Scholar  Sziráki, A., Tyshkovskiy, A. & Gladyshev, V. N. Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction. Aging Cell 17, e12738 (2018). Article  PubMed …

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The Biostar Herald for Tuesday, December 19, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, and was edited…

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A super-pangenome of the North American wild grape species | Genome Biology

Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar  Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…

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Startup can now screen IVF embryos for 1000+ diseases

Reproductive tech startup Orchid is now offering whole genome sequencing for embryos, giving prospective parents and their doctors information that could lead to healthier and more successful pregnancies — but not everyone is convinced it’s worth the cost. The challenge: Infertility is incredibly common, affecting 1 in 6 people worldwide,…

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Arsenic is a potent co-mutagen of ultraviolet light

Barnes, J. L., Zubair, M., John, K., Poirier, M. C. & Martin, F. L. Carcinogens and DNA damage. Biochem. Soc. Trans. 46, 1213–1224 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Ames, B. N., Durston, W. E., Yamasaki, E. & Lee, F. D. Carcinogens are mutagens: a simple test system…

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Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution

Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…

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Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles

Rignot, E., Jacobs, S., Mouginot, J. & Scheuchl, B. Ice-shelf melting around antarctica. Science (80-) 341, 266–270 (2013). Article  ADS  CAS  Google Scholar  Wadham, J. L. et al. Ice sheets matter for the global carbon cycle. Nat. Commun. 10, 1–17 (2019). Google Scholar  Adusumilli, S., Fricker, H. A., Medley, B.,…

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Scientists sequence genome for threatened Whitebark Pine

Pinus albicaulis pine cones on a tree in the Sierra Nevada Mountains.Getty Images Researchers have sequenced the whitebark pine genome, presenting new opportunities to help the threatened, high-altitude tree endure environmental challenges. “Sequencing the whitebark pine reference genome is an important scientific contribution,” said project lead David Neale, professor emeritus…

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Topological structures and syntenic conservation in sea anemone genomes

Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article  ADS  CAS  PubMed  Google Scholar  Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Srivastava, M….

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Kinnex launch promises to revolutionize RNA research

RNA sequencing (RNA-seq) has become an indispensable tool for analyzing transcriptomes across all domains of life that can reveal insights about biology and disease. While the genome remains relatively constant for most species over brief time scales, the transcriptome –the sum total of expressed messenger RNA (mRNA) transcripts – varies…

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The Biostar Herald for Monday, December 11, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, cmdcolin, and was edited by…

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FGFR2 point mutation in 2 cases of pleomorphic adenoma progressing to myoepithelial carcinoma

1. Carlson ER, Schlieve T. Salivary gland malignancies. Oral Maxillofac Surg Clin North Am 2019; 31: 125-144. 2. Seethala RR. Salivary gland tumors: current concepts and controversies. Surg Pathol Clin 2017; 10: 155-176. 3. Bradley PJ, McGurk M. Incidence of salivary gland neoplasms in a defined UK population….

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Validation Of Cell-free Protein Synthesis Aboard The International Space Station

Cell-free Protein Synthesis Aboard ISS — biorxiv.org Cell-free protein synthesis (CFPS) is a rapidly maturing in vitro gene expression platform that can be used to transcribe and translate nucleic acids at the point of need, enabling on-demand synthesis of peptide-based vaccines and biotherapeutics, as well as the development of diagnostic…

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The world’s largest proteins? These mega-molecules turn bacteria into predators

A structure prediction for a massive protein discovered by computational biologist Jacob West-Roberts and his colleagues.Credit: West-Roberts, J. et al./bioRxiv Jacob West-Roberts, a computational biologist at the University of California (UC) Berkeley, was scouring microbial DNA sequences for giant genes and discovered what he thought was a whopper: a gene…

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Building tools for zebra mussel genetic biocontrol

December 7, 2023 Lindsey O’Brien and Victor Hernandez Elizarraga, UMGC Innovation Lab scientists Zebra mussels are a damaging invasive species that are spreading throughout the lakes and rivers of Minnesota and beyond. The UMGC Innovation Lab is building on previous work sequencing the zebra mussel genome and working to develop…

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Metagenome-based microbial community analysis of urine-derived fertilizer

%PDF-1.4 % 60 0 obj <> endobj 77 0 obj <>stream PyPDF2 application/pdf Metagenome-based microbial community analysis of urine-derived fertilizer 2023-12-07T08:58:22-08:00 2023-12-07T08:58:22-08:00 2023-12-07T08:58:22-08:00 uuid:1d1cb7eb-1dd2-11b2-0a00-4e09278d5b00 uuid:1d1cb7ee-1dd2-11b2-0a00-1e0000000000 endstream endobj 1 0 obj <> endobj 2 0 obj <>/MediaBox[0 0 595.29999 841.90002]/Parent 1 0 R/Resources<>/ProcSet[/PDF/Text]>>/Type/Page>> endobj 3 0 obj <>/MediaBox[0 0 595.29999 841.90002]/Parent 1…

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Addgene: CAGGS-AsCpf1-2A-GFP-U6-AAVS1-MAFB-sgRNA

These plasmids were created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the plasmids were described, and include Addgene in the Materials and Methods of your future publications. For your Materials & Methods section: CAGGS-AsCpf1-2A-GFP-U6-AAVS1-MAFB-sgRNA was a gift from Rudolf Jaenisch (Addgene plasmid # 194725…

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Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet’s whelk [PeerJ]

Introduction Rapidly advancing next generation sequencing technologies such as whole genome sequencing, genotyping-in-thousands by sequencing (GT-seq), and restriction-site-associated DNA sequencing (RAD-seq), are becoming more available and affordable for non-model organisms (Park & Kim, 2016; Ellegren, 2014; Van Wyngaarden et al., 2017; Bootsma et al., 2020). However, applying these technologies to…

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Preprint peer review gains momentum with new

4 December 2023 – Review Commons, a platform dedicated to the peer review of preprints, announces the expansion of its family of affiliate journals to include publications from three additional organizations. Affiliate journals accept the transfer of peer-reviewed preprints directly from the Review Commons online portal into their editorial workflow, where they are assessed…

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Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces

Batinovic, S. et al. Bacteriophages in natural and artificial environments. Pathogens 8, 100. doi.org/10.3390/pathogens8030100 (2019). Article  PubMed  PubMed Central  Google Scholar  Mushegian, A. R. Are there 10^31 virus particles on earth, or more, or fewer?. J. Bacteriol. 202(9), 2020. doi.org/10.1128/JB.00052-20 (2020). Article  Google Scholar  Kutter, E. & Sulakvelidze, A. Bacteriophages:…

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Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes

Yang J, Liu X, Cao S, Dong X, Rao S, Cai K. Understanding esophageal cancer: the challenges and opportunities for the next decade. Front Oncol. 2020;10:1727. Article  PubMed  PubMed Central  Google Scholar  Li J, Xu J, Zheng Y, Gao Y, He S, Li H, et al. Esophageal cancer: epidemiology, risk…

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Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis

Centers for Disease Control and Prevention (U.S.). Antibiotic Resistance Threats in the United States, 2019. doi.org/10.15620/cdc:82532 (2019). Centers for Disease Control and Prevention. COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022. doi.org/10.15620/CDC:117915 (2022). Fricks-Lima, J. et al. Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from…

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Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Honegger, R. The lichen symbiosis: What is so spectacular about it?. Lichenologist 30, 193–212 (1998). Article  Google Scholar  Grube, M. & Berg, G. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fung. Biol. Rev. 23, 72–85 (2009). Article  Google Scholar  Spribille, T. et al. Basidiomycete yeasts…

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Mitophagy in human health, ageing and disease

Palikaras, K., Lionaki, E. & Tavernarakis, N. Mechanisms of mitophagy in cellular homeostasis, physiology and pathology. Nat. Cell Biol. 20, 1013–1022 (2018). Article  CAS  PubMed  Google Scholar  Palikaras, K., Lionaki, E. & Tavernarakis, N. Coordination of mitophagy and mitochondrial biogenesis during ageing in C. elegans. Nature 521, 525–528 (2015). Article …

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Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

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“PaperPlayer biorxiv bioinformatics” Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index (Podcast Episode 2020) – News

It looks like we don’t have any news for this title yet. IMDb.com, Inc. takes no responsibility for the content or accuracy of the above news articles, Tweets, or blog posts. This content is published for the entertainment of our users only. The news articles, Tweets, and blog posts do…

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Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability

Szekanecz, Z. et al. Autoinflammation and autoimmunity across rheumatic and musculoskeletal diseases. Nat. Rev. Rheumatol. 17, 585–595 (2021). Article  CAS  PubMed  Google Scholar  Rosenblum, M. D., Remedios, K. A. & Abbas, A. K. Mechanisms of human autoimmunity. J. Clin. Invest. 125, 2228–2233 (2015). Article  PubMed  PubMed Central  Google Scholar  Wang,…

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Bacteriophage-host Interactions In Microgravity Onboard The International Space Station

Deep Mutational Scanning profiles beneficial substitutions in the RBP tip domain (A-B) Heatmaps showing normalized functional scores (FN) of all substitutions (red gradient) and wildtype amino acids (FN=1 and black dot upper left) at every position after incubation with E. coli BL21 in (A) microgravity and (B) after terrestrial incubation….

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Hot Springs Viruses At Yellowstone National Park Have Ancient Origins And Are Adapted To Their Thermophilic Hosts

Taxonomic classification consensus of virus operational taxonomic units (vOTUs). — biorxiv Geothermal springs in areas such as Yellowstone National Park (YNP), USA house unicellular red algae that dominate the microbial biomass. Little is known about the viruses that infect the biota. Here we used metagenomics to characterize the multi-kingdom infecting…

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Longitudinal detection of circulating tumor DNA

Analysis of Roche KAPA Target Enrichment kit experimental data obtained on an Illumina sequencing system is most frequently performed using a variety of publicly available, open-source analysis tools. The typical variant calling analysis workflow consists of sequencing read quality assessment, read filtering, mapping against the reference genome, duplicate removal, coverage…

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Germline PTEN genotype-dependent phenotypic divergence during the early neural developmental process of forebrain organoids

American Psychiatric Association Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5). Arlington, VA: American Psychiatric Publishing; 2013. Lewis MH, Bodfish JW. Repetitive behavior disorders in autism. Ment Retard Dev D R. 1998;4:80–9. Article  Google Scholar  Bodfish JW, Symons FJ, Parker DE, Lewis MH. Varieties of repetitive behavior in…

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Transformer-based tool recommendation system in Galaxy | BMC Bioinformatics

Kumar A, Rasche H, Grüning B, Backofen R. Tool recommender system in Galaxy using deep learning. GigaScience. 2021. doi.org/10.1093/gigascience/giaa152. Article  PubMed  PubMed Central  Google Scholar  The galaxy community: the galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res 50(W1):W345-W35104 2022. (2022). doi.org/10.1093/nar/gkac247 Gil Y, Ratnakar…

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Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy | Molecular Cancer

Rowe RG, Daley GQ. Induced pluripotent stem cells in disease modelling and drug discovery. Nat Rev Genet. 2019;20:377–88. Article  CAS  PubMed  PubMed Central  Google Scholar  Li L, Papadopoulos V. Advances in stem cell research for the treatment of primary hypogonadism. Nat Rev Urol. 2021;18:487–507. Article  CAS  PubMed  Google Scholar  Lawrence…

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Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar  Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article  CAS  PubMed  Google…

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Tricorder Tech: Sequencing DNA in Space

NASA is not often known for making the best use of existing COTS (commercial off the shelf technology) aboard the ISS. Then again, sometimes they are. This is an example of when the agency really grabs cutting edge biotech and sends it into space. There’s usually quite a lag time….

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Analyzing somatic mutations by single-cell whole-genome sequencing

Failla, G. The aging process and cancerogenesis. Ann. N. Y. Acad. Sci. 71, 1124–1140 (1958). Article  CAS  PubMed  Google Scholar  Szilard, L. On the nature of the aging process. Proc. Natl Acad. Sci. USA 45, 30–45 (1959). Article  CAS  PubMed  PubMed Central  Google Scholar  Vijg, J. & Dong, X. Pathogenic…

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Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

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The Biostar Herald for Monday, November 20, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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Morphological evolution of bird wings follows a mechanical sensitivity gradient determined by the aerodynamics of flapping flight

Claramunt, S., Derryberry, E. P., Brumfield, R. T. & Remsen, J. V. Ecological Opportunity and Diversification in a Continental Radiation of Birds: Climbing Adaptations and Cladogenesis in the Furnariidae. Am. Naturalist 179, 649–666 (2012). Article  Google Scholar  Derryberry, E. P. et al. Lineage diversification and morphological evolution in a large-scale…

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11-100test | EpCAM antibody [VU-1D9] (PerCP-Cy5.5) Clinisciences

Application Note *Optimal dilutions/concentrations should be determined by the researcher. Application Recommended Dilution FACS 4 μl reagent / 100 μl of whole blood or 10⁶ cells in a suspension Not tested in other applications. Calculated MW 35 kDa. ( Note ) Product Note This antibody recognizes an epitope within EGF-like…

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Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations

Adams, R. H. & Eichmann, A. Axon guidance molecules in vascular patterning. Cold Spring Harb. Perspect. Biol. 2, a001875 (2010). Article  PubMed  PubMed Central  Google Scholar  Fish, J. E. & Wythe, J. D. The molecular regulation of arteriovenous specification and maintenance. Dev. Dyn. 244, 391–409 (2015). Article  CAS  PubMed  Google…

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The Bread Wheat Reference Genome Sequence

Adams MD, Celnicke SE, Holt RA, Evans CA et al (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195. doi.org/10.1126/science.287.5461.2185 CrossRef  PubMed  Google Scholar  Alonge M, Shumata A, Pulu D, Zimin AV, Salzberg SL (2020) Chromosome-scale assembly of the bread wheat genome reveals thousands of additional gene copies. Genetics 216:599–608….

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Genetic manipulation of giant viruses and their host, Acanthamoeba castellanii

Rayamajhee, B., Willcox, M. D., Henriquez, F. L., Petsoglou, C. & Carnt, N. Acanthamoeba keratitis: an increasingly common infectious disease of the cornea. Lancet Microbe 2, e345–e346 (2021). PubMed  Google Scholar  Guimaraes, A. J., Gomes, K. X., Cortines, J. R., Peralta, J. M. & Peralta, R. H. Acanthamoeba spp. as…

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Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article  CAS  PubMed  Google Scholar  Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…

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Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques

Victora CG, Bahl R, Barros AJD, França GVA, Horton S, Krasevec J, et al. Breastfeeding in the 21st century: Epidemiology, mechanisms, and lifelong effect. Lancet. 2016;387:475–90. Article  PubMed  Google Scholar  Bardanzellu F, Fanos V, Strigini FAL, Artini PG, Peroni DG. Human breast milk: Exploring the linking ring among emerging components….

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Characterization of intrinsic and effective fitness changes caused by temporarily fixed mutations in the SARS-CoV-2 spike E484 epitope and identification of an epistatic precondition for the evolution of E484A in variant Omicron | Virology Journal

Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021;593(7857):142–6. Article  CAS  PubMed  PubMed Central  Google Scholar  Planas D, Bruel T, Grzelak L, Guivel-Benhassine F, Staropoli I, Porrot F, et al. Sensitivity of infectious SARS-CoV-2…

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Chromosome-level genomes of three key Allium crops and their trait evolution

Chase, M. W. et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016). Article  Google Scholar  Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot….

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Coenzyme-Protein Interactions Since Early Life

Origin & Evolution of Life Status Report biorxiv November 6, 2023 Workflow of this study. All available coenzymes in the PDB were identified according to the CoFactor database (Fischer et al., 2010). The PDB entries of structures bound to coenzymes were downloaded programmatically through the PDBe REST API (pdbe.org/api), including…

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Phage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection

Shreiner, A. B., Kao, J. Y. & Young, V. B. The gut microbiome in health and in disease. Curr. Opin. Gastroenterol. 31, 69–75. doi.org/10.1097/Mog.0000000000000139 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  Selber-Hnatiw, S. et al. Human gut microbiota: Toward an ecology of disease. Front. Microbiol. 8, 1265. doi.org/10.3389/fmicb.2017.017E5 (2017)….

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Using easyPubMed and scholar package to get all citations of your paper

This is a tutorial on downloading all the citations for the articles present in any Google Scholar Profile. Use Case You might want to do it for your CV or help a friend. Update your lab website with the latest publication list. You might want to add all your published…

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Artificial surface labelling of Escherichia coli with StrepTagII antigen to study how monoclonal antibodies drive complement-mediated killing

Delcour, A. H. Outer membrane permeability and antibiotic resistance. Biochim. Biophys. Acta 1794, 808 (2009). Article  CAS  PubMed  Google Scholar  Silhavy, T. J., Kahne, D. & Walker, S. The bacterial cell envelope. Cold Spring Harb. Perspect. Biol. 2, a000414 (2010). Article  PubMed  PubMed Central  Google Scholar  Lu, L. L., Suscovich,…

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Tom Terwilliger Publishes Work on AlphaFold Predictions

Tom Terwilliger Publishes Work on AlphaFold Predictions Tom Terwilliger, a New Mexico Consortium Senior Research Scientist and Los Alamos National Laboratory Scientist, recently published his work, AlphaFold predictions are valuable hypotheses, and accelerate but do not replace experimental structure determination, in bioRxiv, The Preprint Server for Biology. Artificial Intelligence (AI)-based…

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Unraveling the Mystery of Zombie Genes

Gulnaz Javan is a forensic scientist at Alabama State University who studies the practical applications of zombie genes. Gulnaz Javan Life begins and ends in low oxygen. Mammalian embryos are submerged in a hypoxic environment before the cardiovascular system and placenta develop. In this low oxygen state, embryonic stem cells…

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Proteins in ancient skeletons could provide key insights into human evolution

Credit: Andrea Piacquadio from Pexels Humankind’s genetic links to long-extinct relatives are being mapped in a rapidly expanding research field called paleoproteomics. They are a fixture of almost every novelty T-shirt shop: humorous pictorials of human evolution, five figures in silhouette—from ape to human—usually with the last replaced by a…

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epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data | GigaScience

Abstract Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5–8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new…

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MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing | Genome Biology

Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang C-Z, Wala J, Mermel CH. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013;45:1134–40. Article  CAS  PubMed  PubMed Central  Google Scholar  Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı…

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Element Biosciences’ NGS Tech, App Stories to Be Featured at ASHG

Element Biosciences, the developer of the AVITI benchtop sequencer, will be sharing details about its technology and discussing customer stories at the annual meeting of the American Society of Human Genetics (ASHG) annual meeting. Element is a silver sponsor of the meeting, which will be held November 1–5 in Washington,…

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A new tool for protein designers

Proteins are important molecules—but they aren’t the only molecules in a cell, and they don’t operate alone. In a new preprint, the team behind the protein structure prediction software RoseTTAFold has announced a tool that expands the types of chemistry that protein designers using deep learning will be able to…

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Strain-level diversity of symbiont communities between individuals and populations of a bioluminescent fish

Sachs JL, Ehinger MO, Simms EL. Origins of cheating and loss of symbiosis in wild Bradyrhizobium. J Evol Biol. 2010;23:1075-89. Carrow HC, Batachari LE, Chu H. Strain diversity in the microbiome: Lessons from Bacteroides fragilis. PLoS Pathog. 2020;16:e1009056. Article  CAS  PubMed  PubMed Central  Google Scholar  Martinez J, Tolosana I, Ok…

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Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium

Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH, Lee P-H, et al. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome. 2020;8:111. Article  CAS  PubMed  PubMed Central  Google Scholar  Conrad R. Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic…

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Genomic signatures of convergent shifts to plunge-diving behavior in birds

Wyles, J. S., Kunkel, J. G. & Wilson, A. C. Birds, behavior, and anatomical evolution. Proc. Natl Acad. Sci. 80, 4394–4397 (1983). Article  CAS  PubMed  PubMed Central  Google Scholar  Lapiedra, O., Sol, D., Carranza, S. & Beaulieu, J. M. Behavioural changes and the adaptive diversification of pigeons and doves. Proc….

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That New Nanopore Protein Sequencing Paper

There’s a new nanopore protein sequencing BioRxiv out! It’s well worth a read. But here are my high level thoughts… They design a bunch of synthetic proteins with a bit on the end which the ClpX unfoldase can attach to. This allows them to use ClpX to ratchet the protein…

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Dutch bluetongue virus type is unique

Phylogenetic trees obtained with the Maximum Likelihood method showing (A) the obtained segment 2 sequence with reference strains from each of the 24 notifiable BTV serotypes and in detail (B) selected field strains of closely related BTV-3 sequences. Unrooted trees with UFBoot2 bootstrap values indicated at the nodes, GenBank accession…

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Genome sequences of 36,000- to 37,000-year-old modern humans at Buran-Kaya III in Crimea

Hajdinjak, M. et al. Initial upper palaeolithic humans in europe had recent neanderthal ancestry. Nature 592, 253–257 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Slimak, L. et al. Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France. Sci. Adv. 8, eabj9496 (2022). Article  CAS  PubMed  PubMed…

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Genomics for monitoring and understanding species responses to global climate change

Smith, T. B. & Bernatchez, L. Evolutionary change in human-altered environments. Mol. Ecol. 17, 1–8 (2008). Article  PubMed  Google Scholar  Bellard, C., Bertelsmeier, C., Leadley, P., Thuiller, W. & Courchamp, F. Impacts of climate change on the future of biodiversity. Ecol. Lett. 15, 365–377 (2012). Article  PubMed  PubMed Central  Google…

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Systematic differences in discovery of genetic effects on gene expression and complex traits

Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179–189 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Gusev, A. et…

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Tauopathy Transcriptomes Tell Tantalizing Tales

18 Oct 2023 Fibrillar tau accumulates in several neurodegenerative diseases. Are the same molecular mechanisms responsible, or does each tauopathy follow distinct pathways? Some of both, according to a preprint posted to bioRxiv on September 30. Researchers led by Jessica Rexach and Daniel Geschwind at the University of California, Los…

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Distinct non-synonymous mutations in cytochrome b highly correlate with decoquinate resistance in apicomplexan parasite Eimeria tenella | Parasites & Vectors

Chapman HD, Rathinam T. Focused review: the role of drug combinations for the control of coccidiosis in commercially reared chickens. Int J Parasitol Drugs Drug Resist. 2022;18:32–42. PubMed  PubMed Central  Google Scholar  Peek HW, Landman WJM. Coccidiosis in poultry: anticoccidial products, vaccines and other prevention strategies. Vet Q. 2011;31:143–61. CAS …

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Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps

de Jonge, P. A., Nobrega, F. L., Brouns, S. J. J. & Dutilh, B. E. Molecular and evolutionary determinants of bacteriophage host range. Trends Microbiol. 27, 51–63 (2019). Article  PubMed  Google Scholar  Cambillau, C. Bacteriophage module reshuffling results in adaptive host range as exemplified by the baseplate model of listerial…

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Bioconductor – DepInfeR (development version)

DOI: 10.18129/B9.bioc.DepInfeR   This is the development version of DepInfeR; for the stable release version, see DepInfeR. Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling Bioconductor version: Development (3.18) DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines…

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Behold, the Human Brain Like Never Seen Before

12 Oct 2023 Understanding the human brain has entered a new era with the birth of a comprehensive cell atlas. Scientists used single-cell RNA sequencing, epigenetic analyses, and spatial mapping to study millions of brain cells from 100 brain regions, distinguishing 3,300 cell types. Researchers compared cell types to one…

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Generation of quality-controled SARS-CoV-2 variant stocks

World Health Organization. WHO Coronavirus (COVID-19) Dashboard. Available at covid19.who.int/ (2023). de Vries, M. et al. A comparative analysis of SARS-CoV-2 antivirals characterizes 3CLpro inhibitor PF-00835231 as a potential new treatment for COVID-19. J. Virol. 95, e01819-20 (2021). Article  PubMed  PubMed Central  Google Scholar  FDA. Emergency Use Authorization (Eua) of…

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Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease | Genome Biology

Zhang L, Wang F, Wang L, Wang W, Liu B, Liu J, Chen M, He Q, Liao Y, Yu X, et al. Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet. 2012;379:815–22. Article  PubMed  Google Scholar  Collaboration GBDCKD. Global, regional, and national burden of chronic kidney disease, 1990–2017:…

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Multi-faceted attributes of salivary cell-free DNA as liquid biopsy biomarkers for gastric cancer detection | Biomarker Research

Nonaka T, Wong DTW. Saliva Diagnostics. Annual Rev Anal Chem. 2022;15(1):107–21. Article  Google Scholar  Gardner A, Carpenter G, So PW. Salivary metabolomics: from Diagnostic Biomarker Discovery to investigating biological function. Metabolites 2020, 10(2). Koopaie M, Ghafourian M, Manifar S, Younespour S, Davoudi M, Kolahdooz S, Shirkhoda M. Evaluation of CSTB…

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How AlphaFold and other AI tools could help us prepare for the next pandemic

The rare Langya virus (computer-generated image) is related to some deadly pathogens.Credit: Kateryna Kon/Science Photo Library In the third year of the COVID-19 pandemic, researchers reported another worrying virus. Identified in 35 people in eastern China since 2018, Langya henipavirus causes breathing problems, fever and other troubling symptoms. Langya hasn’t…

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Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Anderson, P. K. et al. Emerging infectious diseases of plants: Pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19, 535–544. doi.org/10.1016/j.tree.2004.07.021 (2004). Article  PubMed  Google Scholar  Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012). Article  ADS  CAS  PubMed …

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Set to Join the NGS Race, Ultima Genomics Offers a Peek under the Hood

By Julianna LeMieux, PhD Ultima Genomics has been quiet since the June 2022 Advances in Genome Biology and Technology (AGBT) conference, where the company boldly entered the next-generation sequencing (NGS) world by introducing the UG 100 sequencing instrument. At that AGBT meeting, the UG 100, which was ensconced in Ultima’s…

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The effect of vitrification on blastocyst mitochondrial DNA dynamics and gene expression profiles

Bosch E, De Vos M, Humaidan P. The future of cryopreservation in assisted reproductive technologies. Front Endocrinol (Lausanne). 2020;11:1–15. Article  Google Scholar  De Geyter C, Calhaz-Jorge C, Kupka MS, Wyns C, Mocanu E, Motrenko T, et al. ART in Europe, 2015: results generated from European registries by ESHRE†. Hum Reprod…

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Life history strategies of soil bacterial communities across global terrestrial biomes

Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017). Article  CAS  PubMed  Google Scholar  Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018). Article  CAS  PubMed  Google Scholar  Delgado-Baquerizo, M. et al. A global…

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Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes

Li QS, Shabalin AA, DiBlasi E, Gopal S, Canuso CM, FinnGen ISGC, et al. Genome-wide association study meta-analysis of suicide death and suicidal behavior. Mol. Psychiatry 2023;28:891–900. McGuffin P, Marusic A, Farmer A. What can psychiatric genetics offer suicidology? Crisis. 2001;22:61–65. Article  CAS  PubMed  Google Scholar  Pedersen NL, Fiske A….

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Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience

Lo MT, Kauppi K, Fan CC, Sanyal N, Reas ET, Sundar VS, Lee WC, Desikan RS, McEvoy LK, Chen CH, Alzheimer’s Disease Genetics, C. Identification of genetic heterogeneity of Alzheimer’s disease across age. Neurobiol Aging. 2019;84(243):e241-243. doi.org/10.1016/j.neurobiolaging.2019.02.022. Article  Google Scholar  Nacmias B, Bagnoli S, Piaceri I, Sorbi S. Genetic heterogeneity…

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Bioinformatics short paper journal resource [software/webapps/database]

I wrote a short paper recently regarding a web application I developed, but had a hard time in finding a list of journals which would publish short tool and software, web-application, database articles except Bioinformatics Applications Note (2-3 pages). I would like to create a resource for that here at…

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OpenFold Drug Discovery AI Research Consortium Announces Funding of Large-Scale Protein Data Collection at Prof. Gabriel Rocklin’s Laboratory at Northwestern University

New first-in-class datasets will improve the capabilities of state of the art protein AI models to create new biologic drugs DAVIS, Calif., October 02, 2023–(BUSINESS WIRE)–The OpenFold group, a non-profit artificial intelligence (AI) research consortium of biotech and tech firms whose goal is to develop free and open-source software tools…

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Synechococcus nitrogen gene loss in iron-limited ocean regions

Richardson TL, Jackson GA. Small phytoplankton and carbon export from the surface ocean. Science. 2007;315:838–40. Article  CAS  PubMed  Google Scholar  Flombaum P, Gallegos JL, Gordillo RA, Rincón J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci…

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Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule

Murchison, E. P. Clonally transmissible cancers in dogs and Tasmanian devils. Oncogene 27, S19–S30 (2009). Article  Google Scholar  Metzger, M. J. & Goff, S. P. A sixth modality of infectious disease: contagious cancer from devils to clams and beyond. PLoS Pathog. 12, e1005904 (2016). Article  PubMed  PubMed Central  Google Scholar …

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NanoLAS: a Comprehensive Nanobody Database with Data Integration, Consolidation, and Application,bioRxiv – Bioinformatics

NanoLAS: a Comprehensive Nanobody Database with Data Integration, Consolidation, and Application bioRxiv – Bioinformatics Pub Date : 2023-09-29 , DOI: 10.1101/2023.09.27.559691 Shuchang Xiong, Zhengwen Liu, Xin Yi, Kai Liu,…

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Predicting tumour content of liquid biopsies from cell-free DNA | BMC Bioinformatics

Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DWY, Kaper F, et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med. 2012;4(136):136ra68. Article  PubMed  Google Scholar  Newman AM, Bratman SV, To J, Wynne JF, Eclov NCW, Modlin LA, et al….

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Genomic insights into Bacillus subtilis MBB3B9 mediated aluminium stress mitigation for enhanced rice growth

Bian, M. et al. Development of gene-specific markers for acid soil/aluminium tolerance in barley (Hordeum vulgare L.). Mol. Breed. 32, 155–164 (2013). Article  CAS  Google Scholar  Kochian, L. V., Piñeros, M. A., Liu, J. & Magalhaes, J. V. Plant adaptation to acid soils: The molecular basis for crop aluminum resistance….

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Innovative strategies of reprograming immune system cells

Introduction Cancer is well characterized by genomic instability resulting in structural alterations that build up with tumor progression.1,2 A subpopulation of undifferentiated cancer cells, known as cancer stem cells (CSCs) are found within the tumor bulk. These cells are responsible for cancer initiation, recurrence and show therapeutic resistance and these…

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Unmapped Reads in Kallisto

Unmapped Reads in Kallisto 1 Hi, I’m using kallisto and bustools for single cell RNA-seq, in a similar way to what is done in the Pall Melsted et. al. paper here: www.biorxiv.org/content/10.1101/673285v1 I’m trying to get an idea of what information is in the reads that aren’t aligned to anything,…

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The Biostar Herald for Tuesday, September 26, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, Shred, and was edited by…

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Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast

Rubin, S., Parr, T., Da Costa, L. & Friston, K. Future climates: Markov blankets and active inference in the biosphere. J. R. Soc. Interface 17, 20200503 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Cantonati, M. et al. Characteristics, main impacts, and stewardship of natural and artificial freshwater environments: Consequences…

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Fast and sensitive validation of fusion transcripts in whole-genome sequencing data | BMC Bioinformatics

Al-Salama ZT, Keam SJ. Entrectinib: first global approval. Drugs. 2019;79(13):1477–83. Article  PubMed  Google Scholar  Drilon A, Laetsch TW, Kummar S, DuBois SG, Lassen UN, Demetri GD, Nathenson M, Doebele RC, Farago AF, Pappo AS, et al. Efficacy of larotrectinib in TRK fusion-positive cancers in adults and children. N Engl J…

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Genome-Based Prediction of Bacterial Antibiotic Resistance

Abdelbary M, Basset P, Blanc D et al (2017) In: Tibayrenc M (ed) Genetics and evolution of infectious diseases: the evolution and dynamics of methicillin-resistant Staphylococcus aureus, 2nd edn. Elsevier, pp 553–572. ISBN: 9780127999425 CrossRef  Google Scholar  Allard MW, Stevens EL, Brown EW (2019) All for one and one for…

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More than a decade of genetic research on the Denisovans

Stoneking, M. An Introduction to Molecular Anthropology (Wiley, 2017). Fuhlrott, J. C. & Schaaffhausen, H. Über die Knochenfunde aus dem Neandertal bei Mettmann. Verhandlungen naturwissenschaftlicher-historischer Ver. preussisch Rheinl. Westfal. Correspondenz-Bl. 14, 50–52 (1857). Google Scholar  Meyer, M. et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos…

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Bayesian Maximum Entropy Ensemble Refinement,bioRxiv – Bioinformatics

Bayesian Maximum Entropy Ensemble Refinement bioRxiv – Bioinformatics Pub Date : 2023-09-15 , DOI: 10.1101/2023.09.12.557310 Benjamin Eltzner, Julian Hofstadler, Daniel Rudolf, Michael Habeck, Bert de Groot …

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Paired ATAC- and RNA-seq offer insight into the impact of HIV on alveolar macrophages: a pilot study

Fitzpatrick, M. E., Kunisaki, K. M. & Morris, A. Pulmonary disease in HIV-infected adults in the era of antiretroviral therapy. AIDS 32, 277–292. doi.org/10.1097/qad.0000000000001712 (2018). Article  PubMed  Google Scholar  Brown, J. & Lipman, M. Community-acquired pneumonia in HIV-Infected individuals. Curr. Infect. Dis. Rep. 16, 397. doi.org/10.1007/s11908-014-0397-x (2014). Article  PubMed  PubMed…

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Community-developed checklists for publishing images and image analyses

North, A. J. Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition. J. Cell Biol. 172, 9–18 (2006). Article  CAS  PubMed  PubMed Central  Google Scholar  Brown, C. M. Fluorescence microscopy—avoiding the pitfalls. J. Cell Sci. 120, 1703–1705 (2007). Article  CAS  PubMed  Google Scholar  Senft, R. A. et…

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