9,505 results match your criteria Nature Biotechnology[Journal]


Engineered toxin-intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations.

Nat Biotechnol 2019 Apr 15. Epub 2019 Apr 15.

Unité de Plasticité du Génome Bactérie, Département Génomes et Génétique, Institut Pasteur, Paris, France.

Targeted killing of pathogenic bacteria without harming beneficial members of host microbiota holds promise as a strategy to cure disease and limit both antimicrobial-related dysbiosis and development of antimicrobial resistance. We engineer toxins that are split by inteins and deliver them by conjugation into a mixed population of bacteria. Our toxin-intein antimicrobial is only activated in bacteria that harbor specific transcription factors. Read More

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http://dx.doi.org/10.1038/s41587-019-0105-3DOI Listing

Increasing the specificity of CRISPR systems with engineered RNA secondary structures.

Nat Biotechnol 2019 Apr 15. Epub 2019 Apr 15.

Department of Biomedical Engineering, Duke University, Durham, NC, USA.

CRISPR (clustered regularly interspaced short palindromic repeat) systems have been broadly adopted for basic science, biotechnology, and gene and cell therapy. In some cases, these bacterial nucleases have demonstrated off-target activity. This creates a potential hazard for therapeutic applications and could confound results in biological research. Read More

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http://www.nature.com/articles/s41587-019-0095-1
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http://dx.doi.org/10.1038/s41587-019-0095-1DOI Listing
April 2019
5 Reads

Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts.

Nat Biotechnol 2019 Apr 8. Epub 2019 Apr 8.

Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

RNA aptamers and RNA aptamer-based devices can be genetically encoded and expressed in cells to probe and manipulate cellular function. However, their usefulness in the mammalian cell is limited by low expression and rapid degradation. Here we describe the Tornado (Twister-optimized RNA for durable overexpression) expression system for achieving rapid RNA circularization, resulting in RNA aptamers with high stability and expression levels. Read More

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http://dx.doi.org/10.1038/s41587-019-0090-6DOI Listing

Focus on wearable sensors.

Nat Biotechnol 2019 04;37(4):329

Nature Biotechnology.

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http://dx.doi.org/10.1038/s41587-019-0110-6DOI Listing

Duchenne muscular dystrophy awaits gene therapy.

Authors:
Dan Jones

Nat Biotechnol 2019 Apr;37(4):335-337

, Brighton, UK.

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http://dx.doi.org/10.1038/s41587-019-0103-5DOI Listing

Llama-inspired antibody fragment approved for rare blood disorder.

Authors:
Cormac Sheridan

Nat Biotechnol 2019 Apr;37(4):333-334

, Dublin, Ireland.

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http://dx.doi.org/10.1038/s41587-019-0101-7DOI Listing

Getting real with wearable data.

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Nat Biotechnol 2019 04;37(4):331

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http://dx.doi.org/10.1038/s41587-019-0109-zDOI Listing

FAIRsharing as a community approach to standards, repositories and policies.

Nat Biotechnol 2019 04;37(4):358-367

Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/s41587-019-0080-8DOI Listing
April 2019
3 Reads

Berkeley strikes back in CRISPR patent tussle.

Nat Biotechnol 2019 Apr;37(4):338-339

, Canterbury, UK.

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http://dx.doi.org/10.1038/s41587-019-0102-6DOI Listing

Around the world in a month.

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Nat Biotechnol 2019 Apr;37(4):337

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http://dx.doi.org/10.1038/s41587-019-0099-xDOI Listing

Oxford Nanopore bests PacBio.

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Nat Biotechnol 2019 Apr;37(4):336

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http://dx.doi.org/10.1038/s41587-019-0098-yDOI Listing

WHO to oversee genome editing.

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Nat Biotechnol 2019 Apr;37(4):338

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http://dx.doi.org/10.1038/s41587-019-0097-zDOI Listing

First Rounders: George Church.

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Nat Biotechnol 2019 Apr;37(4):339

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http://dx.doi.org/10.1038/s41587-019-0075-5DOI Listing

Toward a new generation of smart skins.

Nat Biotechnol 2019 04 2;37(4):382-388. Epub 2019 Apr 2.

Department of Dermatology, Keio University School of Medicine, Tokyo, Japan.

Rapid advances in soft electronics, microfabrication technologies, miniaturization and electronic skins are facilitating the development of wearable sensor devices that are highly conformable and intimately associated with human skin. These devices-referred to as 'smart skins'-offer new opportunities in the research study of human biology, in physiological tracking for fitness and wellness applications, and in the examination and treatment of medical conditions. Over the past 12 months, electronic skins have been developed that are self-healing, intrinsically stretchable, designed into an artificial afferent nerve, and even self-powered. Read More

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http://www.nature.com/articles/s41587-019-0079-1
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http://dx.doi.org/10.1038/s41587-019-0079-1DOI Listing
April 2019
9 Reads

To the stomach and beyond.

Authors:
Irene Jarchum

Nat Biotechnol 2019 Apr;37(4):381

Nature Biotechnology, .

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http://dx.doi.org/10.1038/s41587-019-0089-zDOI Listing

Evolution of CAR T-cell immunotherapy in terms of patenting activity.

Nat Biotechnol 2019 04;37(4):370-375

European Patent Office, Vienna, Austria.

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http://dx.doi.org/10.1038/s41587-019-0083-5DOI Listing

As the life science industry evolves, so do its talent needs.

Nat Biotechnol 2019 Apr;37(4):481-483

Life sciences strategy and operations consultant, Redwood City, CA, USA.

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http://www.nature.com/articles/s41587-019-0091-5
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http://dx.doi.org/10.1038/s41587-019-0091-5DOI Listing
April 2019
4 Reads

Wearable technology in healthcare.

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Nat Biotechnol 2019 04;37(4):376

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http://dx.doi.org/10.1038/s41587-019-0093-3DOI Listing

What compassionate use means for gene therapies.

Nat Biotechnol 2019 04;37(4):352-355

Division of Medical Ethics, Department of Population Health, NYU School of Medicine, New York, NY, USA.

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http://dx.doi.org/10.1038/s41587-019-0081-7DOI Listing

Sweet sensation.

Authors:
Emily Waltz

Nat Biotechnol 2019 Apr;37(4):340-344

, Nashville, Tennessee, USA.

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http://www.nature.com/articles/s41587-019-0086-2
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http://dx.doi.org/10.1038/s41587-019-0086-2DOI Listing
April 2019
5 Reads

Mapping the European startup landscape.

Nat Biotechnol 2019 Apr;37(4):345-349

Forbion Capital Partners, Naarden, the Netherlands.

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http://www.nature.com/articles/s41587-019-0076-4
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http://dx.doi.org/10.1038/s41587-019-0076-4DOI Listing
April 2019
1 Read

Inferring population dynamics from single-cell RNA-sequencing time series data.

Nat Biotechnol 2019 04 1;37(4):461-468. Epub 2019 Apr 1.

Institute of Computational Biology, Helmholz Zentrum München, Neuherberg, Germany.

Recent single-cell RNA-sequencing studies have suggested that cells follow continuous transcriptomic trajectories in an asynchronous fashion during development. However, observations of cell flux along trajectories are confounded with population size effects in snapshot experiments and are therefore hard to interpret. In particular, changes in proliferation and death rates can be mistaken for cell flux. Read More

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http://www.nature.com/articles/s41587-019-0088-0
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http://dx.doi.org/10.1038/s41587-019-0088-0DOI Listing
April 2019
5 Reads

Specification of positional identity in forebrain organoids.

Nat Biotechnol 2019 04 1;37(4):436-444. Epub 2019 Apr 1.

The Center for Stem Cell Biology, Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA.

Human brain organoids generated with current technologies recapitulate histological features of the human brain, but they lack a reproducible topographic organization. During development, spatial topography is determined by gradients of signaling molecules released from discrete signaling centers. We hypothesized that introduction of a signaling center into forebrain organoids would specify the positional identity of neural tissue in a distance-dependent manner. Read More

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http://dx.doi.org/10.1038/s41587-019-0085-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447454PMC
April 2019
1 Read

Polarizing brain organoids.

Nat Biotechnol 2019 Apr;37(4):377-378

Department of Psychiatry and Behavioral Sciences & Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1038/s41587-019-0084-4DOI Listing
April 2019
1 Read

An open resource for accurately benchmarking small variant and reference calls.

Nat Biotechnol 2019 Apr 1. Epub 2019 Apr 1.

Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.

Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) Consortium, we apply a reproducible, cloud-based pipeline to integrate multiple short- and linked-read sequencing datasets and provide benchmark calls for human genomes. We generate benchmark calls for one previously analyzed GIAB sample, as well as six genomes from the Personal Genome Project. Read More

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http://dx.doi.org/10.1038/s41587-019-0074-6DOI Listing
April 2019
2 Reads

Engineering a HER2-specific antibody-drug conjugate to increase lysosomal delivery and therapeutic efficacy.

Nat Biotechnol 2019 Apr 1. Epub 2019 Apr 1.

Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA.

We improve the potency of antibody-drug conjugates (ADCs) containing the human epidermal growth factor receptor 2 (HER2)-specific antibody pertuzumab by substantially reducing their affinity for HER2 at acidic endosomal pH relative to near neutral pH. These engineered pertuzumab variants show increased lysosomal delivery and cytotoxicity towards tumor cells expressing intermediate HER2 levels. In HER2 xenograft tumor models in mice, the variants show higher therapeutic efficacy than the parent ADC and a clinically approved HER2-specific ADC. Read More

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http://dx.doi.org/10.1038/s41587-019-0073-7DOI Listing

Assembly of long, error-prone reads using repeat graphs.

Nat Biotechnol 2019 Apr 1. Epub 2019 Apr 1.

Department of Computer Science and Engineering, University of California, San Diego, CA, USA.

Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. Read More

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http://dx.doi.org/10.1038/s41587-019-0072-8DOI Listing

Yeast-secreted, dried and food-admixed monomeric IgA prevents gastrointestinal infection in a piglet model.

Nat Biotechnol 2019 Apr 1. Epub 2019 Apr 1.

Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium.

Oral antibodies that interfere with gastrointestinal targets and can be manufactured at scale are needed. Here we show that a single-gene-encoded monomeric immunoglobulin A (IgA)-like antibody, composed of camelid variable single domain antibodies (VHH) fused to IgA Fc (mVHH-IgA), prevents infection by enterotoxigenic Escherichia coli (F4-ETEC) in piglets. The mVHH-IgA can be produced in soybean seeds or secreted from the yeast Pichia pastoris, freeze- or spray-dried and orally delivered within food. Read More

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http://dx.doi.org/10.1038/s41587-019-0070-xDOI Listing

TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets.

Nat Biotechnol 2019 04 1;37(4):469-479. Epub 2019 Apr 1.

Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA.

Although mass spectrometry is well suited to identifying thousands of potential protein post-translational modifications (PTMs), it has historically been biased towards just a few. To measure the entire set of PTMs across diverse proteomes, software must overcome the dual challenges of covering enormous search spaces and distinguishing correct from incorrect spectrum interpretations. Here, we describe TagGraph, a computational tool that overcomes both challenges with an unrestricted string-based search method that is as much as 350-fold faster than existing approaches, and a probabilistic validation model that we optimized for PTM assignments. Read More

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http://dx.doi.org/10.1038/s41587-019-0067-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447449PMC

A comparison of single-cell trajectory inference methods.

Nat Biotechnol 2019 Apr 1. Epub 2019 Apr 1.

Data mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.

Trajectory inference approaches analyze genome-wide omics data from thousands of single cells and computationally infer the order of these cells along developmental trajectories. Although more than 70 trajectory inference tools have already been developed, it is challenging to compare their performance because the input they require and output models they produce vary substantially. Here, we benchmark 45 of these methods on 110 real and 229 synthetic datasets for cellular ordering, topology, scalability and usability. Read More

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http://dx.doi.org/10.1038/s41587-019-0071-9DOI Listing

Author Correction: Best practices for benchmarking germline small-variant calls in human genomes.

Nat Biotechnol 2019 Mar 21. Epub 2019 Mar 21.

Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.

In the version of this article initially published online, two pairs of headings were switched with each other in Table 4: "Recall (PCR free)" was switched with "Recall (with PCR)," and "Precision (PCR free)" was switched with "Precision (with PCR)." The error has been corrected in the print, PDF and HTML versions of this article. Read More

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http://www.nature.com/articles/s41587-019-0108-0
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http://dx.doi.org/10.1038/s41587-019-0108-0DOI Listing
March 2019
8 Reads

Characterization of cell fate probabilities in single-cell data with Palantir.

Nat Biotechnol 2019 04 21;37(4):451-460. Epub 2019 Mar 21.

Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Single-cell RNA sequencing studies of differentiating systems have raised fundamental questions regarding the discrete versus continuous nature of both differentiation and cell fate. Here we present Palantir, an algorithm that models trajectories of differentiating cells by treating cell fate as a probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Palantir generates a high-resolution pseudo-time ordering of cells and, for each cell state, assigns a probability of differentiating into each terminal state. Read More

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http://dx.doi.org/10.1038/s41587-019-0068-4DOI Listing

Publisher Correction: CRISPR target prediction remains blunt tool for clinical applications.

Authors:
John Hodgson

Nat Biotechnol 2019 04;37(4):480

, Cambridge, UK.

In the version of this article initially published, we reported that Sangamo's SB-318 had failed to change baseline leukocyte α-L-iduronidase in a phase 1/2 trial. The drug failed to change baseline plasma α-L-iduronidase but did increase leukocyte α-L-iduronidase to within the normal range. The error has been corrected in the HTML and PDF versions of the article. Read More

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http://dx.doi.org/10.1038/s41587-019-0107-1DOI Listing

Publisher Correction: Federated discovery and sharing of genomic data using Beacons.

Nat Biotechnol 2019 04;37(4):480

ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK.

In the version of this article initially published, Lena Dolman's second affiliation was given as Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. The correct second affiliation is Ontario Institute for Cancer Research, Toronto, Ontario, Canada. The error has been corrected in the HTML and PDF versions of the article. Read More

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http://dx.doi.org/10.1038/s41587-019-0094-2DOI Listing

Engineered immune cells as highly sensitive cancer diagnostics.

Nat Biotechnol 2019 Mar 18. Epub 2019 Mar 18.

Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA.

Endogenous biomarkers remain at the forefront of early disease detection efforts, but many lack the sensitivities and specificities necessary to influence disease management. Here, we describe a cell-based in vivo sensor for highly sensitive early cancer detection. We engineer macrophages to produce a synthetic reporter on adopting an M2 tumor-associated metabolic profile by coupling luciferase expression to activation of the arginase-1 promoter. Read More

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http://dx.doi.org/10.1038/s41587-019-0064-8DOI Listing
March 2019
1 Read
41.514 Impact Factor

Precise gene replacement in rice by RNA transcript-templated homologous recombination.

Nat Biotechnol 2019 04 18;37(4):445-450. Epub 2019 Mar 18.

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

One of the main obstacles to gene replacement in plants is efficient delivery of a donor repair template (DRT) into the nucleus for homology-directed DNA repair (HDR) of double-stranded DNA breaks. Production of RNA templates in vivo for transcript-templated HDR (TT-HDR) could overcome this problem, but primary transcripts are often processed and transported to the cytosol, rendering them unavailable for HDR. We show that coupling CRISPR-Cpf1 (CRISPR from Prevotella and Francisella 1) to a CRISPR RNA (crRNA) array flanked with ribozymes, along with a DRT flanked with either ribozymes or crRNA targets, produces primary transcripts that self-process to release the crRNAs and DRT inside the nucleus. Read More

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http://dx.doi.org/10.1038/s41587-019-0065-7DOI Listing

The International Cancer Genome Consortium Data Portal.

Nat Biotechnol 2019 04;37(4):367-369

Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41587-019-0055-9DOI Listing
April 2019
3 Reads
41.514 Impact Factor

Did a permissive scientific culture encourage the 'CRISPR babies' experiment?

Nat Biotechnol 2019 04;37(4):355-357

Center for Genetics and Society, Berkeley, CA, USA.

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http://dx.doi.org/10.1038/s41587-019-0077-3DOI Listing

International regulatory changes poised to reshape access to marine genes.

Authors:
Robert Blasiak

Nat Biotechnol 2019 04;37(4):357-358

Stockholms Universitet, Stockholm Resilience Centre, Stockholm, Sweden.

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http://dx.doi.org/10.1038/s41587-019-0087-1DOI Listing

Brain maps at the nanoscale.

Nat Biotechnol 2019 Apr;37(4):378-380

Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY, USA.

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http://www.nature.com/articles/s41587-019-0078-2
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http://dx.doi.org/10.1038/s41587-019-0078-2DOI Listing
April 2019
4 Reads

Best practices for benchmarking germline small-variant calls in human genomes.

Nat Biotechnol 2019 Mar 11. Epub 2019 Mar 11.

Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.

Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant-calling tools and the metrics used to assess their performance continue to improve, important challenges remain. Here, as part of the Global Alliance for Genomics and Health (GA4GH), we present a benchmarking framework for variant calling. Read More

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http://dx.doi.org/10.1038/s41587-019-0054-xDOI Listing

Publisher Correction: Death by inflammation: drug makers chase the master controller.

Authors:
Cormac Sheridan

Nat Biotechnol 2019 04;37(4):480

, Dublin, Ireland.

In the version of this article initially published, a GlaxoSmithKline compound referred to as GSK298559 was listed in Table 1 as a RIPK1 inhibitor in phase 1 trials for inflammatory bowel disease. The correct designation is GSK2983559; however, this compound is a RIPK2 inhibitor and thus should not have been included in the table in question. The table row has been deleted. Read More

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http://www.nature.com/articles/s41587-019-0082-6
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http://dx.doi.org/10.1038/s41587-019-0082-6DOI Listing
April 2019
6 Reads

One-step genome editing of elite crop germplasm during haploid induction.

Nat Biotechnol 2019 03 4;37(3):287-292. Epub 2019 Mar 4.

Seeds Research, Syngenta Crop Protection, Research Triangle Park, North Carolina, United States.

Genome editing using CRISPR-Cas9 works efficiently in plant cells, but delivery of genome-editing machinery into the vast majority of crop varieties is not possible using established methods. We co-opted the aberrant reproductive process of haploid induction (HI) to induce edits in nascent seeds of diverse monocot and dicot species. Our method, named HI-Edit, enables direct genomic modification of commercial crop varieties. Read More

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http://dx.doi.org/10.1038/s41587-019-0038-xDOI Listing
March 2019
7 Reads

Tubuloids derived from human adult kidney and urine for personalized disease modeling.

Nat Biotechnol 2019 03 4;37(3):303-313. Epub 2019 Mar 4.

Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, Utrecht, the Netherlands.

Adult stem cell-derived organoids are three-dimensional epithelial structures that recapitulate fundamental aspects of their organ of origin. We describe conditions for the long-term growth of primary kidney tubular epithelial organoids, or 'tubuloids'. The cultures are established from human and mouse kidney tissue and can be expanded for at least 20 passages (>6 months) while retaining a normal number of chromosomes. Read More

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http://www.nature.com/articles/s41587-019-0048-8
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http://dx.doi.org/10.1038/s41587-019-0048-8DOI Listing
March 2019
15 Reads

Challenges in the quest for 'clean meat'.

Nat Biotechnol 2019 03;37(3):215-216

Brown University, Providence, RI, USA.

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http://dx.doi.org/10.1038/s41587-019-0043-0DOI Listing
March 2019
1 Read

Drug developers switch gears to inhibit STING.

Authors:
Cormac Sheridan

Nat Biotechnol 2019 03;37(3):199-201

, Dublin, Ireland.

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http://dx.doi.org/10.1038/s41587-019-0060-zDOI Listing
March 2019
1 Read

First CD123-targeted drug approved after wowing in rare cancer.

Authors:
Elie Dolgin

Nat Biotechnol 2019 03;37(3):202-203

, Somerville, Massachusetts, USA.

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http://dx.doi.org/10.1038/s41587-019-0056-8DOI Listing

CRISPR target prediction remains blunt tool for clinical applications.

Authors:
John Hodgson

Nat Biotechnol 2019 03;37(3):204-205

, Cambridge, UK.

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http://dx.doi.org/10.1038/s41587-019-0057-7DOI Listing

Banking on health.

Authors:

Nat Biotechnol 2019 03;37(3):197

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http://dx.doi.org/10.1038/s41587-019-0069-3DOI Listing
March 2019
1 Read

Drug pipeline: 4Q18.

Nat Biotechnol 2019 03;37(3):206-208

Senior Editor at Nature Biotechnology, .

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http://dx.doi.org/10.1038/s41587-019-0052-zDOI Listing
March 2019
1 Read