Tag: bioRxiv

NEW YORK – Since its introduction in 2018, DeepMind’s AlphaFold program has become a key tool in biological research, allowing scientists to predict protein structures with high accuracy based on their amino acid sequences. More recently, researchers have begun using AlphaFold and its newer iteration, AlphaFold2, for protein-protein interaction (PPI)…

Awasthi MK, Singh E, Binod P, Sindhu R, Sarsaiya S, Kumar A, et al. Biotechnological strategies for bio-transforming biosolid into resources toward circular bio-economy: a review. Renew Sustain Energy Rev. 2022;156:111987. Article  CAS  Google Scholar  Diamantis V, Eftaxias A, Stamatelatou K, Noutsopoulos C, Vlachokostas C, Aivasidis A. Bioenergy in the…

Avise J (2008) Clonality: the genetics, ecology, and evolution of sexual abstinence in vertebrate animals. Oxford University Press, USA Book  Google Scholar  Avise JC (2015) Evolutionary perspectives on clonal reproduction in vertebrate animals. Proc Natl Acad Sci USA 112(29):8867–8873 Article  CAS  PubMed  PubMed Central  Google Scholar  Andrews S (2010) FastQC:…

Flaxman JP, Smith DW, Mackenzie JS, Fraser JRE, Bass SP, Hueston L, et al. A comparison of the diseases caused by Ross River virus and Barmah Forest virus. Med J Aust. 1998;169:159–63. Article  Google Scholar  El-Hage CM, Bamford NJ, Gilkerson JR, Lynch SE. Ross River virus infection of horses: appraisal…

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…

Hingorani M, Hanson I, van Heyningen V. Aniridia. Eur J Hum Genet. 2012;20:1011–7. Article  CAS  PubMed  PubMed Central  Google Scholar  Lima Cunha D, Arno G, Corton M, Moosajee M. The spectrum of PAX6 mutations and genotype-phenotype correlations in the eye. Genes. 2019;10:1050. Article  PubMed  PubMed Central  Google Scholar  Cvekl A,…

Johnson, W. E. Endogenous retroviruses in the genomics era. Annu. Rev. Virol. 2, 135–159 (2015). Article  CAS  PubMed  Google Scholar  Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol. 17, 355–370 (2019). Article  CAS  PubMed  Google Scholar  Johnson, W. E. Endless forms most viral. PLoS…

Vaswani, A. et al. Attention is all you need. Preprint at doi.org/10.48550/arXiv.1706.03762 (2017). Devlin, J., Chang, M. W., Lee, K. & Toutanova, K. BERT: pre-training of deep bidirectional transformers for language understanding. In Proc. 2019 Conference North American Chapter of the Association for Computational Linguistics: Human Language Technologies Vol. 1…

Hampoelz, B., Andres-Pons, A., Kastritis, P. & Beck, M. Structure and assembly of the nuclear pore complex. Annu. Rev. Biophys. 48, 515–536 (2019). Article  CAS  PubMed  Google Scholar  Lin, D. H. & Hoelz, A. The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725–783 (2019). Article …

Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA. Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev. 2015;39:203–21. Article  CAS  PubMed  Google Scholar  Pointing SB, Belnap J. Microbial colonization and controls in dryland systems. Nat Rev Microbiol. 2012;10:551–62. Article  CAS  PubMed  Google Scholar  Ji M,…

Cho, N. H. et al. IDF Diabetes Atlas: global estimates of diabetes prevalence for 2017 and projections for 2045. Diabetes Res. Clin. Pract. 138, 271–281 (2018). Article  CAS  PubMed  Google Scholar  Lu, Y. et al. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk. Nat….

GBD 2016 Disease Injury Incidence Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet. 2017;390:1211–59. Article  Google Scholar  Kato T. Current understanding of bipolar disorder:…

Kingwell, K. T cell receptor therapeutics hit the immuno-oncology stage. Nat. reviews. Drug Discov. www.nature.com/articles/d41573-022-00073-7 (2022). Kaplon, H., Chenoweth, A., Crescioli, S. & Reichert, J. M. Antibodies to watch in 2022. mAbs 14, 2014296 (2022). Article  PubMed  PubMed Central  Google Scholar  Lu, R.-M. et al. Development of therapeutic antibodies for…

Origin & Evolution of Life Status Report biorxiv.org May 28, 2023 Stochastic simulation of a population of water-in-oil droplets containing strands. Heatmaps for A: average fraction of replicase ribozymes per droplet; B: fraction of droplets containing both replicase (R) and replicase encoding DNA template (TdR); C: average reaction propensity of…

Genomelink’s global ancestry (New): Uses the XGMix algorithm for deeper DNA analysis (at the Chromosome level) that shows how the ancestry breaks down at the chromosome level and also shows the overalls ethnicity estimate. Backed by Carlos D. Bustamante, Alexander Ioanidis, Razib Khan. see:genomelink.io/product/global…try-dna-reportwww.biorxiv.org/content/10.1…876v1.full.pdf My overall ethnicity: chromosome level (examples…

Bessant, D. A., Ali, R. R. & Bhattacharya, S. S. Molecular genetics and prospects for therapy of the inherited retinal dystrophies. Curr. Opin. Genet. Dev. 11, 307–316 (2001). Article  CAS  PubMed  Google Scholar  Berger, W., Kloeckener-Gruissem, B. & Neidhardt, J. The molecular basis of human retinal and vitreoretinal diseases. Prog….

Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article  PubMed  PubMed Central  Google Scholar  Bankevich A, Nurk S,…

Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, et al. The population biology of invasive species. Annu Rev Ecol Syst. 2001;32:305–32. Article  Google Scholar  Allendorf FW, Lundquist LL. Introduction: population biology, evolution, and control of invasive species. Conserv Biol. 2003;17:24–30. Article  Google Scholar  Erickson AB. The…

Single-cycle vaccine concept and viral characterization. Credit: bioRxiv (2023). DOI: 10.1101/2023.05.17.541127 Researchers at the University of Basel have developed a new approach for a vaccine against COVID-19. This vaccine is based on a modified coronavirus that can enter body cells and trigger an effective immune response but cannot multiply in…

Tarr, P. I., Gordon, C. A. & Chandler, W. L. Shiga toxin-producing Escherichia coli and haemolytic uremic syndrome. Lancet 365, 1073–1086 (2006). Google Scholar  Koudelka, G. B., Arnold, J. W. & Chkraborty, D. Evolution of STEC virulence: Insights from the antipredator activities of shiga toxing-producing E. coli. Int. J. Med….

Dubilier N, Bergin C, Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol. 2008;6:725–40. Article  CAS  PubMed  Google Scholar  Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the dark: phylogenetic and physiological diversity of chemosynthetic symbioses. Annu Rev Microbiol. 2021;75:695–718….

Summary The Jiang laboratory in the Departments of Neuroscience at Baylor College of Medicine is seeking applicants for postdoc associate positions. The specific goal of the postdoc fellows for these positions is to use a multi-disciplinary approach, including single-cell transcriptomics, Patch-seq, multi-patch clamp recording, machine learning, and complicated genetic tools…

LOS ANGELES — That the honor of opening the Presidential Symposium of the American Society of Gene and Cell Therapy (ASGCT) conference should fall to 2020 Nobel laureate Jennifer Doudna, PhD, the CRISPR genome editing pioneer, was no surprise. But the topic of Doudna’s presentation—new research in the arena of…

Ryan, J. F. et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342, 1242592 (2013). Article  PubMed  PubMed Central  Google Scholar  Halanych, K. M. The ctenophore lineage is older than sponges? That cannot be right! Or can it? J. Exp. Biol. 218,…

Elmore, S. Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495–516 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  Shi, Y. Caspase activation, inhibition, and reactivation: A mechanistic view. Protein Sci. 13, 1979–1987 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  Alberts, B., Johnson, A. & Lewis, J….

Bergmann, O. et al. Evidence for cardiomyocyte renewal in humans. Science 324, 98–102 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  Senyo, S. E. et al. Mammalian heart renewal by pre-existing cardiomyocytes. Nature 493, 433–436 (2013). Article  CAS  PubMed  Google Scholar  Bergmann, O. et al. Dynamics of cell generation and…

A recent study posted to the bioRxiv*preprint server described rapid mutagenesis and rescue of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants without cloning, using a novel reverse genetics strategy. Study: Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. Image Credit: kentoh/Shutterstock.com *Important notice: bioRxiv publishes preliminary…

Abubucker, Sahar, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, and Curtis Huttenhower. 2012. Metabolic reconstruction for metagenomic data and its application to the…

Chazot, N. et al. Priors and posteriors in Bayesian timing of divergence analyses: the age of butterflies revisited. Syst. Biol. 68, 797–813 (2019). Article  PubMed  PubMed Central  Google Scholar  Allio, R. et al. Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution. Syst. Biol. 69, 38–60…

Cerejeira, J., Lagarto, L. & Mukaetova-Ladinska, E. B. Behavioral and psychological symptoms of dementia. Front. Neurol. 3, 73 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Murphy, M. P. & LeVine, H. III Alzheimer’s disease and the amyloid-beta peptide. J. Alzheimers Dis. 19, 311–323 (2010). Article  PubMed  PubMed Central  Google…

Cawthon, R. M. et al. A major segment of the neurofibromatosis type 1 gene: cDNA sequence, genomic structure, and point mutations. Cell 62, 193–201 (1990). Article  CAS  PubMed  Google Scholar  Buske, A. et al. Recurrent NF1 gene mutation in a patient with oligosymptomatic neurofibromatosis type 1 (NF1). Am. J. Med….

This is a relatively well-known story. About 4,000 years ago, a band of Bantu speakers left West Africa and moved to colonise half of Africa. They pushed through the Congo rainforest spreading to southern and eastern Africa. Some eventually settled in what is modern-day Kenya. They migrated further from Kenya…

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…

Laurenti, E. & Gottgens, B. From haematopoietic stem cells to complex differentiation landscapes. Nature (London) 553, 418–426 (2018). ADS  CAS  PubMed  Google Scholar  Miller, I. J. & Bieker, J. J. A novel, erythroid cell-specific murine transcription factor that binds to the CACCC element and is related to the Krüppel family…

Pan genome based assembly 1 Hi, I have some queries related to Pangenome. I have 8 genome assemblies of single eukaryotic species, could I make a pan-genome from this? Should I follow the Denovo approach method? Resequencing data is not available. ngs assembly Pangenome denovo • 69 views bioinfo –…

Dekker, J. & Mirny, L. The 3D genome as moderator of chromosomal communication. Cell 164, 1110–1121 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Oudelaar, A. M. et al. The relationship between genome structure and function. Nat. Rev. Genet. 22, 154–168 (2021). Article  CAS  PubMed  Google Scholar  Lieberman-Aiden, E. et…

Brown, T. B. et al. In Adv. Neural Inf. Process. Syst. 33 (eds Larochelle, H. et al.) 1877–1901 (Curran Associates, 2020). Open AI. Preprint at arXiv doi.org/10.48550/arXiv.2303.08774 (2023). Nguyen, N. & Nadi, S. In Proc. 19th Intl Conf. Mining Software Repositories 1–5 (Association for Computing Machinery, 2022); doi.org/10.1145/3524842.3528470 Nan, Y….

Liu, J. et al. Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification. Mol. Ecol. Resour. 18, 1115–1131 (2018). Article  CAS  Google Scholar  Parveen, I., Singh, H. K., Raghuvanshi, S., Pradhan, U. C. & Babbar, S. B. DNA barcoding of endangered…

– Record revenue of $60.2M in 2QFY23; up 25% over $48.1M in 2QFY22 – – Orders increased to $64.2M in 2QFY23; up 17% over 2QFY22 – – Decisive Actions to Accelerate Path to Profitability – SOUTH SAN FRANCISCO, Calif., May 05, 2023–(BUSINESS WIRE)–Twist Bioscience Corporation (NASDAQ: TWST), a company enabling…

Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014). Article  PubMed  Google Scholar  Prüfer, K. et…

Model overview. Credit: Nature Computational Science (2023). DOI: 10.1038/s43588-023-00440-3 Researchers at the University of Toronto have developed an artificial intelligence system that can create proteins not found in nature using generative diffusion, the same technology behind popular image-creation platforms such as DALL-E and Midjourney. The system will help advance the…

Alkooranee JT, Liu S, Aledan TR, Yin Y, Li M (2015) First report of powdery mildew caused by erysiphe cruciferarum on brassica napus in China. Plant Dis 99(11):1651 CrossRef  Google Scholar  Al-Lami HFD, You MP, Barbetti MJ (2019a) Incidence, pathogenicity and diversity of Alternaria spp. associated with alternaria leaf spot…

Igbokwe, I. O. Evolving anti-disease strategies from biochemical pathogenesis of African trypanosomiasis. Adv. Cytol. Pathol. 3(2), 33–39 (2018). Google Scholar  Njiru, Z. K., Constantine, C. C., Gitonga, P. K., Thompson, R. C. & Reid, S. A. Genetic variability of Trypanosoma evansi isolates detected by inter-simple sequence repeat anchored-PCR and microsatellite….

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…

DiMasi, J. A., Grabowski, H. G. & Hansen, R. W. Innovation in the pharmaceutical industry: new estimates of R&D costs. J. Health Econ. 47, 20–33 (2016). Article  PubMed  Google Scholar  Wouters, O. J., McKee, M. & Luyten, J. Estimated research and development investment needed to bring a new medicine to…

Sagan, L. On the origin of mitosing cells. J. Theor. Biol. 14, 225 (1967). Article  ADS  CAS  Google Scholar  McBride, H. M., Neuspiel, M. & Wasiak, S. Mitochondria: More than just a powerhouse. Curr. Biol. 16, R551–R560 (2006). Article  CAS  PubMed  Google Scholar  Dietrich, M. O., Liu, Z.-W. & Horvath,…

Jean Fan is an assistant professor at Johns Hopkins University in Baltimore, Maryland.Credit: Mayling Chen Art isn’t complete until it’s shared, the saying goes. If that’s true, is a computational method complete if others cannot use it? When I was a student, I was often eager to apply new computational…

Goldberg, A. D., Allis, C. D. & Bernstein, E. Epigenetics: A landscape takes shape. Cell 128, 635–638 (2007). Article  PubMed  Google Scholar  Mohn, F. & Schübeler, D. Genetics and epigenetics: Stability and plasticity during cellular differentiation. Trends Genet. 25, 129–136 (2009). Article  PubMed  Google Scholar  Takahashi, K. et al. Induction…

Abbott R, Albach D, Ansell S, Arntzen JW, Baird SJE, Bierne N, Zinner D (2013) Hybridization and speciation. J Evolut Biol 26:229–246. doi.org/10.1111/j.1420-9101.2012.02599.x Article  CAS  Google Scholar  Arntzen JW (2019) An amphibian species pushed out of Britain by a moving hybrid zone. Mol Ecol 28:5145–5154 Article  PubMed  PubMed Central  Google…

Groundbreaking clinical trials that could result in powerful new CRISPR treatments against HIV, genetic blindness, and other conditions are now underway, but some concerns around safety remain. One worry is that if CRISPR is put directly into patients’ bodies, they could have severe immune reactions to Cas9, the enzyme with…

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…

Bergqvist, C. et al. Neurofibromatosis 1 French national guidelines based on an extensive literature review since 1966. Orphanet J. Rare Dis. 15, 1–23 (2020). Article  Google Scholar  Martin, G. A. et al. The GAP-related domain of the neurofibromatosis type 1 gene product interacts with ras p21. Cell 63, 843–849 (1990)….

20 Apr 2023 Retroviruses lurking in the human genome aren’t the only potential troublemakers in neurodegenerative diseases (see Part 5 of this series). Herpes simplex virus type 1 (HSV-1) integrates into the genome of trigeminal ganglia nerves, can lie dormant for decades, and flare up as cold sores throughout a person’s…

Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Suttle, C. A. Marine viruses — major players in the global…

Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013;496:504–7. doi.org/10.1038/nature12060. Article  CAS  PubMed  PubMed Central  Google Scholar  WHO. WHO | Dengue Fever – Burkina Faso. World Health Organization 2017 www.who.int/emergencies/disease-outbreak-news/item/6-november-2017-dengue-burkina-faso-en; 2017. Tarnagda Z, Cissé A, Bicaba…

1 Introduction Abiotic stresses such as drought, heat, cold, salt, pesticides, metals and metalloids deteriorate agro-ecological conditions and hence, negatively impact upon agricultural production. The abiotic stress impairs with regular growth and development of plant plants, thus limiting their yield and quality of produce (Boyer, 1982; Pandey et al., 2017). Plants…

FAO. Faostat: FAO Statistical Databases. (Food & Agriculture Organization of the United Nations (FAO), 2000). The war in Ukraine is exposing gaps in the world’s food-systems research. Nature 604, 217–218 (2022). Chapman, M. A., He, Y. & Zhou, M. Beyond a reference genome: pangenomes and population genomics of underutilized and…

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…

Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006;4:102–12. Article  CAS  PubMed  Google Scholar  Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol. 2012;10:497–506….

Credit : BlackJack3D / iStock / Getty Images Plus Decades ago, the oncology community took on the crucial challenge of detecting cancer at the earliest possible stage. Overall, survival rates improve dramatically for cancers detected before metastasis. For example, the U.S. Centers for Disease Control and Prevention (CDC) notes that…

Rojansky R, Cha M-Y, Chan DC (2016) Elimination of paternal mitochondria in mouse embryos occurs through autophagic degradation dependent on PARKIN and MUL1. eLife 5:e17896. doi.org/10.7554/eLife.17896 CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Wei W, Pagnamenta AT, Gleadall N et al (2020) Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA…

Jayaraman, V., Toledo-Patino, S., Noda-Garcia, L. & Laurino, P. Mechanisms of protein evolution. Protein Sci. 31, e4362 (2022). Article  CAS  PubMed  Google Scholar  Huang, R. et al. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates. Proc. Natl Acad. Sci. USA 109, 2966–2971 (2012). Article  CAS  PubMed  PubMed Central …

Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Milani, C. et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. 81, e00036-17…

When the topic of fungi arises, the majority of people would likely think about the mushrooms they gather in the autumn, or possibly the yeast they use in baking or wine-making. Some might even recollect the rotten bread or cucumbers they stumbled upon in their refrigerator last week. For ages,…

Maps showing the collection localities for the (A) Sanger sequences and (B) metabarcoding sequences that came with geo-coordinates (36,559 Sanger collection localities and 3,688 metabarcoding collection localities). Credit: MycoKeys (2023). DOI: 10.3897/mycokeys.96.102669 Mention fungi, and most people will probably think of the mushrooms they pick in fall, or maybe the…

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, Pavel, and was edited by…

Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article  CAS  PubMed  PubMed Central  Google Scholar  Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…

Schmitz, J. F. & Bornberg-Bauer, E. Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA. F1000Research 6, 57 (2017). Article  PubMed  PubMed Central  Google Scholar  Vakirlis, N. et al. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat. Commun. 11,…

Giovannoni, J. J. Genetic regulation of fruit development and ripening. Plant Cell 16, S170–S180 (2004). CAS  PubMed  PubMed Central  Google Scholar  Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). CAS  PubMed  Google Scholar  Peralta, I. E., Spooner, D. M. & Knapp, S….

Gorbalenya, A. E. et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 5(4), 536–544. doi.org/10.1038/s41564-020-0695-z (2020). Article  CAS  Google Scholar  Wang, Y., Grunewald, M. & Perlman, S. coronaviruses: an updated overview of their replication and pathogenesis. In Coronaviruses: Methods and Protocols (eds…

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…

David R. Liu, PhD, a professor at Harvard University, the Broad Institute of MIT and Harvard, and the Howard Hughes Medical Institute A research team led by gene editing pioneer David R. Liu, PhD, reports the application of base editing technology to develop a one-time treatment for spinal muscular atrophy…

Singer, M. et al. The third international consensus definitions for sepsis and septic shock (Sepsis-3). JAMA 315, 801–810 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Brecher, M. E. & Hay, S. N. Bacterial contamination of blood components. Clin. Microbiol. Rev. 18, 195–204 (2005). Article  PubMed  PubMed Central  Google Scholar …

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which is otherwise known as the coronavirus disease 2019 (COVID-19), continues to pose significant…

Uncover the mysteries of RNA dysregulation in cancer Our understanding of the complex biology of cancers is currently limited by the sequencing technology that we have available. For example, a study previously published in Science Advances showed that short-read based RNA-seq approaches only capture a faction of RNA isoforms that…

Bradley, B. A. et al. Cheatgrass (Bromus tectorum) distribution in the intermountain western United States and its relationship to fire frequency, seasonality, and ignitions. Biol. Invasions 20, 1493–1506 (2018). Article  Google Scholar  Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gomez-Dans, J. Introduced annual grass increases regional fire…

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Background Normative modeling is a statistical approach to quantify the degree to which a particular individual-level measure deviates from the pattern observed in a normative reference population. When applied to human brain morphometric measures it has the potential to inform about the significance of normative deviations for health and disease….

Development of QSAR Models to Identify Mycobacterium tuberculosis enoyl-ACP-reductase Enzyme Inhibitors bioRxiv – Bioinformatics Pub Date : 2023-03-19 , DOI: 10.1101/2023.03.13.532463 Aureo Andre Karolczak, Luis Fernando Saraiva Macedo Timmers,…

doi: 10.26502/jbb.2642-91280067. Epub 2023 Jan 20. Affiliations Expand Affiliations 1 Department of Computer Science and Engineering, University of Michigan Ann Arbor, MI 48109, USA. 2 NVIDIA Corporation, Santa Clara, CA 95051, USA. Free PMC article Item in Clipboard Harisankar Sadasivan et al. J Biotechnol Biomed. 2023. Free PMC article Show details…

Brown JS O’Carrigan B Jackson SP Yap TA Targeting DNA Repair in Cancer: Beyond PARP Inhibitors. Cancer Discov. 2017; 7: 20-37 Farmer H McCabe N Lord CJ Tutt AN Johnson DA Richardson TB Santarosa M Dillon KJ Hickson I Knights C Martin NM Jackson SP Smith GC Ashworth A Targeting…

Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014). Article  PubMed  PubMed Central  Google Scholar  Weyrich, L. S. et al. Laboratory contamination over time during low-biomass sample analysis. Mol. Ecol. Resour. 19, 982–996 (2019). Article  CAS  PubMed  PubMed Central …

NEW YORK – Lipid nanoparticles that inhibit cellular uptake of cell-free DNA (cfDNA) and engineered antibodies that protect cfDNA from degradation are showing early success in boosting liquid biopsy cfDNA yields, which could eventually lead to improved cancer diagnostic and prognostic assays. Investigators from the Broad Institute and the Koch…

In molecular biology, Circular RNAs (circRNAs) refer to a class of circular RNA molecules found across all kingdoms of life.[1][2][3] Studies in 2013 have suggested that circRNAs play important regulatory roles in miRNA activity. Researchers found that CDR1as circRNA acts as a miR-7 super-sponge that contains about 70 target sites…

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…

doi: 10.15252/msb.202311587. Online ahead of print. Affiliations Expand Affiliations 1 Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany. 2 Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany. 3 Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany. 4 Institute of Chemical Biology, National…

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Omar Abudayyeh, PhD, McGovern fellow at MIT’s McGovern Institute for Brain Research A recently patented genome editing tool called PASTE holds genuine promise for expanding the universe of treatable genetic diseases. The approach combines elements of CRISPR and prime editing with a pair of enzymes designed to enable the integration…

Introduction In recent years, CIN has gained great importance due to its implications for both, the diagnosis and prognosis of cancer. Recent studies have suggested that both CIN and clonal heterogeneity, influence cancer progression, aggressiveness, prognosis, and response to therapy.1–4 The above because both, CIN and clonal heterogeneity, lead to…

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Traditional sequencing is often likened to making a smoothie: researchers blend a bunch of cells, obtain an average sequence, and draw conclusions on the ingredients that comprise the slush. More recently, scientists have gained the ability to perform single-cell sequencing, which can reveal rare variations between cells and the evolution…

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03 Mar 2023 Of the dozens of loci genome-wide association studies have linked to Alzheimer’s, most are mysterious to scientists. How do they contribute to disease? Much work focuses on changes in expression of individual genes, but as reported in a preprint posted to medRxiv on February 8, scientists led…

Long-read sequencing technologies such as PacBio HiFi sequencing are quickly becoming the new gold standard in genomics research. This article provides an introductory look at what long-read sequencing is, and explores topics including advantages, applications, and more. Background Deciphering the essence of what makes living things work has been a…

BridgePRS 1 Hi there, I am reading the new method of PRS – BridgePRS (www.biorxiv.org/content/10.1101/2023.02.17.528938v1), this is a very interesting paper regarding the transferability of PRS. I am trying to study about the methods (my statistics and mathematics background is quite weak), but one thing I don’t understand is that…

Researchers at the University of Alabama at Birmingham have demonstrated a novel way of fixing cells and preserving their biomolecules prior to single cell dissociation without the need for harsh enzymatic/mechanical approaches. Single-cell RNA sequencing has the opportunity to deconstruct cellular networks but was previously limited by the loss of…

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