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

abstract：:The biology of multicellular organisms is coordinated across multiple size scales, from the subnanoscale of molecules to the macroscale, tissue-wide interconnectivity of cell populations. Here we introduce a method for super-resolution imaging of the multiscale organization of intact tissues. The method, called magnif...

journal_title：Nature biotechnology

authors： Ku T,Swaney J,Park JY,Albanese A,Murray E,Cho JH,Park YG,Mangena V,Chen J,Chung K

更新日期：2016-09-01 00:00:00

abstract：:Delivery of short interfering RNAs (siRNAs) remains a key challenge in the development of RNA interference (RNAi) therapeutics. A better understanding of the mechanisms of siRNA cellular uptake, intracellular transport and endosomal release could critically contribute to the improvement of delivery methods. Here we mo...

journal_title：Nature biotechnology

authors： Gilleron J,Querbes W,Zeigerer A,Borodovsky A,Marsico G,Schubert U,Manygoats K,Seifert S,Andree C,Stöter M,Epstein-Barash H,Zhang L,Koteliansky V,Fitzgerald K,Fava E,Bickle M,Kalaidzidis Y,Akinc A,Maier M,Zerial M

更新日期：2013-07-01 00:00:00

abstract：:To select for bacterial strains with enhanced phenotypes, random fragments of a whole genome, or a defined region of the genome, are cloned in a nonreplicating vector. The resulting plasmids are integrated by recombination into the homologous DNA region of the original strain. Integration gives rise to a nontandem dir...

journal_title：Nature biotechnology

authors： Mavingui P,Flores M,Romero D,Martínez-Romero E,Palacios R

更新日期：1997-06-01 00:00:00

abstract：:We developed a modified flagellar type III secretion apparatus to secrete heterologous polypeptides into the growth medium of Escherichia coli. The secretion was facilitated by fusing the 173-bp untranslated DNA fragment upstream of the gene fliC (encoding flagellin) as well as a transcriptional terminator from fliC, ...

journal_title：Nature biotechnology

authors： Majander K,Anton L,Antikainen J,Lång H,Brummer M,Korhonen TK,Westerlund-Wikström B

更新日期：2005-04-01 00:00:00

abstract：:RNA interference (RNAi) is a powerful method for specifically silencing gene expression in diverse cell types. RNAi is mediated by approximately 21-nucleotide small interfering RNAs (siRNAs), which are produced from larger double-stranded RNAs (dsRNAs) in vivo through the action of Dicer, an RNase III-family enzyme. T...

journal_title：Nature biotechnology

authors： Myers JW,Jones JT,Meyer T,Ferrell JE Jr

更新日期：2003-03-01 00:00:00

abstract：:We have developed novel nucleic acid probes that recognize and report the presence of specific nucleic acids in homogeneous solutions. These probes undergo a spontaneous fluorogenic conformational change when they hybridize to their targets. Only perfectly complementary targets elicit this response, as hybridization d...

journal_title：Nature biotechnology

authors： Tyagi S,Kramer FR

更新日期：1996-03-01 00:00:00

abstract：:Genetic studies of human disease have traditionally focused on the detection of disease-causing mutations in afflicted individuals. Here we describe a complementary approach that seeks to identify healthy individuals resilient to highly penetrant forms of genetic childhood disorders. A comprehensive screen of 874 gene...

journal_title：Nature biotechnology

authors： Chen R,Shi L,Hakenberg J,Naughton B,Sklar P,Zhang J,Zhou H,Tian L,Prakash O,Lemire M,Sleiman P,Cheng WY,Chen W,Shah H,Shen Y,Fromer M,Omberg L,Deardorff MA,Zackai E,Bobe JR,Levin E,Hudson TJ,Groop L,Wang J,

更新日期：2016-05-01 00:00:00

abstract：:St. Louis wants to become a hub of agricultural biotechnology. All it needs is more start-ups and funds. ...

journal_title：Nature biotechnology

authors： Marris E

更新日期：2008-04-01 00:00:00

abstract：:We present two algorithms to predict the activity of AsCpf1 guide RNAs. Indel frequencies for 15,000 target sequences were used in a deep-learning framework based on a convolutional neural network to train Seq-deepCpf1. We then incorporated chromatin accessibility information to create the better-performing DeepCpf1 a...

journal_title：Nature biotechnology

authors： Kim HK,Min S,Song M,Jung S,Choi JW,Kim Y,Lee S,Yoon S,Kim HH

更新日期：2018-03-01 00:00:00

abstract：:Elastin-like polypeptides (ELPs) undergo a reversible, inverse phase transition. Below their transition temperature (Tt), ELPs are soluble in water, but when the temperature is raised above Tt, phase transition occurs, leading to aggregation of the polypeptide. We demonstrate a method for purification of soluble fusio...

journal_title：Nature biotechnology

authors： Meyer DE,Chilkoti A

更新日期：1999-11-01 00:00:00

abstract：:Analysis of abnormally methylated genes is increasingly important in basic research and in the development of cancer biomarkers. We have developed methyl-BEAMing technology to enable absolute quantification of the number of methylated molecules in a sample. Individual DNA fragments are amplified and analyzed either by...

journal_title：Nature biotechnology

authors： Li M,Chen WD,Papadopoulos N,Goodman SN,Bjerregaard NC,Laurberg S,Levin B,Juhl H,Arber N,Moinova H,Durkee K,Schmidt K,He Y,Diehl F,Velculescu VE,Zhou S,Diaz LA Jr,Kinzler KW,Markowitz SD,Vogelstein B

更新日期：2009-09-01 00:00:00

abstract：: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 pres...

journal_title：Nature biotechnology

authors： Krusche P,Trigg L,Boutros PC,Mason CE,De La Vega FM,Moore BL,Gonzalez-Porta M,Eberle MA,Tezak Z,Lababidi S,Truty R,Asimenos G,Funke B,Fleharty M,Chapman BA,Salit M,Zook JM,Global Alliance for Genomics and Health Benchma

更新日期：2019-05-01 00:00:00

abstract：:A T-cell receptor mimic peptide (TCRpep) consisting of an 8-amino-acid peptide, homologous to the transmembrane region of the T-cell receptor (TCR) alpha chain, blocks T-cell activation after systemic application. When dendritic cells (DCs) were transduced to secrete the TCRpep and injected into mice, evidence of immu...

journal_title：Nature biotechnology

authors： Mahnke K,Qian Y,Knop J,Enk AH

更新日期：2003-08-01 00:00:00

abstract：:Three national patent offices have consulted on patents that cover protein three-dimensional structural data and pharmacophores, with significant implications for the biotechnology industry. ...

journal_title：Nature biotechnology

authors： Shimbo I,Nakajima R,Yokoyama S,Sumikura K

更新日期：2004-01-01 00:00:00

abstract：:Methods to rapidly assess cell growth would be useful for many applications, including drug susceptibility testing, but current technologies have limited sensitivity or throughput. Here we present an approach to precisely and rapidly measure growth rates of many individual cells simultaneously. We flow cells in suspen...

journal_title：Nature biotechnology

authors： Cermak N,Olcum S,Delgado FF,Wasserman SC,Payer KR,A Murakami M,Knudsen SM,Kimmerling RJ,Stevens MM,Kikuchi Y,Sandikci A,Ogawa M,Agache V,Baléras F,Weinstock DM,Manalis SR

更新日期：2016-10-01 00:00:00

abstract：:The density and long-term stability of DNA make it an appealing storage medium, particularly for long-term data archiving. Existing DNA storage technologies involve the synthesis and sequencing of multiple nominally identical molecules in parallel, resulting in information redundancy. We report the development of enco...

journal_title：Nature biotechnology

authors： Anavy L,Vaknin I,Atar O,Amit R,Yakhini Z

更新日期：2019-10-01 00:00:00

abstract：:Programmable DNA cleavage using CRISPR-Cas9 enables efficient, site-specific genome engineering in single cells and whole organisms. In the research arena, versatile CRISPR-enabled genome editing has been used in various ways, such as controlling transcription, modifying epigenomes, conducting genome-wide screens and ...

journal_title：Nature biotechnology

authors： Barrangou R,Doudna JA

更新日期：2016-01-01 00:00:00

abstract：:Human embryonic stem cells (hESCs) have two properties of interest for the development of cell therapies: self-renewal and the potential to differentiate into all major lineages of somatic cells in the human body. Widespread clinical application of hESC-derived cells will require culture methods that are low-cost, rob...

journal_title：Nature biotechnology

authors： Melkoumian Z,Weber JL,Weber DM,Fadeev AG,Zhou Y,Dolley-Sonneville P,Yang J,Qiu L,Priest CA,Shogbon C,Martin AW,Nelson J,West P,Beltzer JP,Pal S,Brandenberger R

更新日期：2010-06-01 00:00:00

abstract：:Recent therapeutic successes have renewed interest in drug combinations, but experimental screening approaches are costly and often identify only small numbers of synergistic combinations. The DREAM consortium launched an open challenge to foster the development of in silico methods to computationally rank 91 compound...

journal_title：Nature biotechnology

authors： Bansal M,Yang J,Karan C,Menden MP,Costello JC,Tang H,Xiao G,Li Y,Allen J,Zhong R,Chen B,Kim M,Wang T,Heiser LM,Realubit R,Mattioli M,Alvarez MJ,Shen Y,NCI-DREAM Community.,Gallahan D,Singer D,Saez-Rodriguez J,

更新日期：2014-12-01 00:00:00

abstract：:A central hurdle in developing small interfering RNAs (siRNAs) as therapeutics is the inefficiency of their delivery across the plasma and endosomal membranes to the cytosol, where they interact with the RNA interference machinery. With the aim of improving endosomal release, a poorly understood and inefficient proces...

journal_title：Nature biotechnology

authors： Wittrup A,Ai A,Liu X,Hamar P,Trifonova R,Charisse K,Manoharan M,Kirchhausen T,Lieberman J

更新日期：2015-08-01 00:00:00

abstract：:The interaction between the HSP90 chaperone and its client kinases is sensitive to the conformational status of the kinase, and stabilization of the kinase fold by small molecules strongly decreases chaperone interaction. Here we exploit this observation and assay small-molecule binding to kinases in living cells, usi...

journal_title：Nature biotechnology

authors： Taipale M,Krykbaeva I,Whitesell L,Santagata S,Zhang J,Liu Q,Gray NS,Lindquist S

更新日期：2013-07-01 00:00:00

abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

journal_title：Nature biotechnology

authors： Röst HL,Rosenberger G,Navarro P,Gillet L,Miladinović SM,Schubert OT,Wolski W,Collins BC,Malmström J,Malmström L,Aebersold R

更新日期：2020-03-01 00:00:00

abstract：:Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlatio...

journal_title：Nature biotechnology

authors： Cox J,Mann M

更新日期：2008-12-01 00:00:00

abstract：:Efficiently generating evidence of clinical utility is a major challenge for ensuring clinical adoption of valuable diagnostics. A new approach to reimbursement in the United States offers a balance between evidence and incentives for molecular diagnostic tests. ...

journal_title：Nature biotechnology

authors： Schulman KA,Tunis SR

更新日期：2010-11-01 00:00:00

abstract：:Through sequential generations of random mutagenesis and screening, we have directed the evolution of an esterase for deprotection of an antibiotic p-nitrobenzyl ester in aqueous-organic solvents. Because rapid screening directly on the desired antibiotic (loracarbef) nucleus p-nitrobenzyl ester was not feasible, the ...

journal_title：Nature biotechnology

authors： Moore JC,Arnold FH

更新日期：1996-04-01 00:00:00

abstract：:Purging of tumor cells and selection of stem cells are key technologies for enabling stem cell transplantation and stem cell gene therapy. Here we report a strategy for cell selection based on physical properties of the cells. Exposing cells to an external pulsed electric field (PEF) increases the natural potential di...

journal_title：Nature biotechnology

authors： Eppich HM,Foxall R,Gaynor K,Dombkowski D,Miura N,Cheng T,Silva-Arrieta S,Evans RH,Mangano JA,Preffer FI,Scadden DT

更新日期：2000-08-01 00:00:00

abstract：:The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy. Metagenomic sequencing could identify LRI pathogens much faster than culture, but methods are needed to remove the large amoun...

journal_title：Nature biotechnology

authors： Charalampous T,Kay GL,Richardson H,Aydin A,Baldan R,Jeanes C,Rae D,Grundy S,Turner DJ,Wain J,Leggett RM,Livermore DM,O'Grady J

更新日期：2019-07-01 00:00:00

abstract：:The human genome encodes approximately 100,000 different genes, and at least partial sequence information for nearly all will be available soon. Sequence information alone, however, is insufficient for a full understanding of gene function, expression, regulation, and splice-site variation. Because cellular processes ...

journal_title：Nature biotechnology

authors： Lockhart DJ,Dong H,Byrne MC,Follettie MT,Gallo MV,Chee MS,Mittmann M,Wang C,Kobayashi M,Horton H,Brown EL

更新日期：1996-12-01 00:00:00

abstract：:Transgenic crops are approved for release in some countries, while many more countries are wrestling with the issue of how to conduct risk assessments. Controls on field trials often include monitoring of horizontal gene transfer (HGT) from crops to surrounding soil microorganisms. Our analysis of antibiotic-resistant...

journal_title：Nature biotechnology

authors： Heinemann JA,Traavik T

更新日期：2004-09-01 00:00:00

abstract：:Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downst...

journal_title：Nature biotechnology

authors： Tafer H,Ameres SL,Obernosterer G,Gebeshuber CA,Schroeder R,Martinez J,Hofacker IL

更新日期：2008-05-01 00:00:00