abstract：:Transplantation of pancreatic progenitors or insulin-secreting cells derived from human embryonic stem cells (hESCs) has been proposed as a therapy for diabetes. We describe a seven-stage protocol that efficiently converts hESCs into insulin-producing cells. Stage (S) 7 cells expressed key markers of mature pancreatic...

journal_title：Nature biotechnology

authors： Rezania A,Bruin JE,Arora P,Rubin A,Batushansky I,Asadi A,O'Dwyer S,Quiskamp N,Mojibian M,Albrecht T,Yang YH,Johnson JD,Kieffer TJ

更新日期：2014-11-01 00:00:00

abstract：:Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogen...

journal_title：Nature biotechnology

authors： Li YH,Zhou G,Ma J,Jiang W,Jin LG,Zhang Z,Guo Y,Zhang J,Sui Y,Zheng L,Zhang SS,Zuo Q,Shi XH,Li YF,Zhang WK,Hu Y,Kong G,Hong HL,Tan B,Song J,Liu ZX,Wang Y,Ruan H,Yeung CK,Liu J,Wang H,Zhang LJ,Guan RX

更新日期：2014-10-01 00:00:00

abstract：:Despite developments in targeted gene sequencing and whole-genome analysis techniques, the robust detection of all genetic variation, including structural variants, in and around genes of interest and in an allele-specific manner remains a challenge. Here we present targeted locus amplification (TLA), a strategy to se...

journal_title：Nature biotechnology

authors： de Vree PJ,de Wit E,Yilmaz M,van de Heijning M,Klous P,Verstegen MJ,Wan Y,Teunissen H,Krijger PH,Geeven G,Eijk PP,Sie D,Ylstra B,Hulsman LO,van Dooren MF,van Zutven LJ,van den Ouweland A,Verbeek S,van Dijk KW,Cornel

更新日期：2014-10-01 00:00:00

abstract：:RNA-guided genome editing with the CRISPR-Cas9 system has great potential for basic and clinical research, but the determinants of targeting specificity and the extent of off-target cleavage remain insufficiently understood. Using chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq), we mapped genom...

journal_title：Nature biotechnology

authors： Kuscu C,Arslan S,Singh R,Thorpe J,Adli M

更新日期：2014-07-01 00:00:00

abstract：:The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthe...

journal_title：Nature biotechnology

authors： Galdzicki M,Clancy KP,Oberortner E,Pocock M,Quinn JY,Rodriguez CA,Roehner N,Wilson ML,Adam L,Anderson JC,Bartley BA,Beal J,Chandran D,Chen J,Densmore D,Endy D,Grünberg R,Hallinan J,Hillson NJ,Johnson JD,Kuchinsky

更新日期：2014-06-01 00:00:00

abstract：:Circular RNA transcripts were first identified in the early 1990s but knowledge of these species has remained limited, as their study through traditional methods of RNA analysis has been difficult. Now, novel bioinformatic approaches coupled with biochemical enrichment strategies and deep sequencing have allowed compr...

journal_title：Nature biotechnology

authors： Jeck WR,Sharpless NE

更新日期：2014-05-01 00:00:00

abstract：:We introduce Sailfish, a computational method for quantifying the abundance of previously annotated RNA isoforms from RNA-seq data. Because Sailfish entirely avoids mapping reads, a time-consuming step in all current methods, it provides quantification estimates much faster than do existing approaches (typically 20 ti...

journal_title：Nature biotechnology

authors： Patro R,Mount SM,Kingsford C

更新日期：2014-05-01 00:00:00

abstract：:Mice repopulated with human hematopoietic cells are a powerful tool for the study of human hematopoiesis and immune function in vivo. However, existing humanized mouse models cannot support development of human innate immune cells, including myeloid cells and natural killer (NK) cells. Here we describe two mouse strai...

journal_title：Nature biotechnology

authors： Rongvaux A,Willinger T,Martinek J,Strowig T,Gearty SV,Teichmann LL,Saito Y,Marches F,Halene S,Palucka AK,Manz MG,Flavell RA

更新日期：2014-04-01 00:00:00

abstract：:We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase ...

journal_title：Nature biotechnology

authors： Sherwood RI,Hashimoto T,O'Donnell CW,Lewis S,Barkal AA,van Hoff JP,Karun V,Jaakkola T,Gifford DK

更新日期：2014-02-01 00:00:00

abstract：:The sap-sucking insects (order Hemiptera), including aphids, planthoppers, whiteflies and stink bugs, present one of the greatest challenges for pest management in global agriculture. Insect neurotoxins offer an alternative to chemical insecticides for controlling these pests, but require delivery into the insect hemo...

journal_title：Nature biotechnology

authors： Bonning BC,Pal N,Liu S,Wang Z,Sivakumar S,Dixon PM,King GF,Miller WA

更新日期：2014-01-01 00:00:00

abstract：:Despite advances in DNA sequencing technology, assembly of complex genomes remains a major challenge, particularly for genomes sequenced using short reads, which yield highly fragmented assemblies. Here we show that genome-wide in vivo chromatin interaction frequency data, which are measurable with chromosome conforma...

journal_title：Nature biotechnology

authors： Kaplan N,Dekker J

更新日期：2013-12-01 00:00:00

abstract：:Heterologous pathways used in metabolic engineering may produce intermediates toxic to the cell. Dynamic control of pathway enzymes could prevent the accumulation of these metabolites, but such a strategy requires sensors, which are largely unknown, that can detect and respond to the metabolite. Here we applied whole-...

journal_title：Nature biotechnology

authors： Dahl RH,Zhang F,Alonso-Gutierrez J,Baidoo E,Batth TS,Redding-Johanson AM,Petzold CJ,Mukhopadhyay A,Lee TS,Adams PD,Keasling JD

更新日期：2013-11-01 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：: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：:New high-dimensional, single-cell technologies offer unprecedented resolution in the analysis of heterogeneous tissues. However, because these technologies can measure dozens of parameters simultaneously in individual cells, data interpretation can be challenging. Here we present viSNE, a tool that allows one to map h...

journal_title：Nature biotechnology

authors： Amir el-AD,Davis KL,Tadmor MD,Simonds EF,Levine JH,Bendall SC,Shenfeld DK,Krishnaswamy S,Nolan GP,Pe'er D

更新日期：2013-06-01 00:00:00

abstract：:Transplantation of oligodendrocyte precursor cells (OPCs) is a promising potential therapeutic strategy for diseases affecting myelin. However, the derivation of engraftable OPCs from human pluripotent stem cells has proven difficult and primary OPCs are not readily available. Here we report the generation of induced ...

journal_title：Nature biotechnology

authors： Yang N,Zuchero JB,Ahlenius H,Marro S,Ng YH,Vierbuchen T,Hawkins JS,Geissler R,Barres BA,Wernig M

更新日期：2013-05-01 00:00:00

abstract：:Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative ...

journal_title：Nature biotechnology

authors： Gat-Viks I,Chevrier N,Wilentzik R,Eisenhaure T,Raychowdhury R,Steuerman Y,Shalek AK,Hacohen N,Amit I,Regev A

更新日期：2013-04-01 00:00:00

abstract：:A Pennsylvania company hopes to turn synthetic DNA vaccines into rapid response agents against flu epidemics and cancer. ...

journal_title：Nature biotechnology

authors： Rohn J

更新日期：2013-02-01 00:00:00

abstract：:Epigenetic mechanisms integrate genetic and environmental causes of disease, but comprehensive genome-wide analyses of epigenetic modifications have not yet demonstrated robust association with common diseases. Using Illumina HumanMethylation450 arrays on 354 anti-citrullinated protein antibody-associated rheumatoid a...

journal_title：Nature biotechnology

authors： Liu Y,Aryee MJ,Padyukov L,Fallin MD,Hesselberg E,Runarsson A,Reinius L,Acevedo N,Taub M,Ronninger M,Shchetynsky K,Scheynius A,Kere J,Alfredsson L,Klareskog L,Ekström TJ,Feinberg AP

更新日期：2013-02-01 00:00:00

abstract：:Lysosomal storage diseases are treated with human lysosomal enzymes produced in mammalian cells. Such enzyme therapeutics contain relatively low levels of mannose-6-phosphate, which is required to target them to the lysosomes of patient cells. Here we describe a method for increasing mannose-6-phosphate modification o...

journal_title：Nature biotechnology

authors： Tiels P,Baranova E,Piens K,De Visscher C,Pynaert G,Nerinckx W,Stout J,Fudalej F,Hulpiau P,Tännler S,Geysens S,Van Hecke A,Valevska A,Vervecken W,Remaut H,Callewaert N

更新日期：2012-12-01 00:00:00

abstract：:Nucleotide variants, especially those related to epigenetic functions, provide critical regulatory information beyond simple genomic sequence, and they define cell status in higher organisms. 5-Methylcytosine, which is found in DNA, was until recently the only nucleotide variant studied in terms of epigenetics in euka...

journal_title：Nature biotechnology

authors： Song CX,Yi C,He C

更新日期：2012-11-01 00:00:00

abstract：:Complex interactions among genetic components often result in variable systemic performance in designed multigene systems. Using the bacterial clustered regularly interspaced short palindromic repeat (CRISPR) pathway we develop a synthetic RNA-processing platform, and show that efficient and specific cleavage of precu...

journal_title：Nature biotechnology

authors： Qi L,Haurwitz RE,Shao W,Doudna JA,Arkin AP

更新日期：2012-10-01 00:00:00

abstract：:The functional state of a cell is largely determined by the spatiotemporal organization of its proteome. Technologies exist for measuring particular aspects of protein turnover and localization, but comprehensive analysis of protein dynamics across different scales is possible only by combining several methods. Here w...

journal_title：Nature biotechnology

authors： Khmelinskii A,Keller PJ,Bartosik A,Meurer M,Barry JD,Mardin BR,Kaufmann A,Trautmann S,Wachsmuth M,Pereira G,Huber W,Schiebel E,Knop M

更新日期：2012-06-24 00:00:00

abstract：:Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chrom...

journal_title：Nature biotechnology

authors： Zhang G,Liu X,Quan Z,Cheng S,Xu X,Pan S,Xie M,Zeng P,Yue Z,Wang W,Tao Y,Bian C,Han C,Xia Q,Peng X,Cao R,Yang X,Zhan D,Hu J,Zhang Y,Li H,Li H,Li N,Wang J,Wang C,Wang R,Guo T,Cai Y,Liu C,Xiang H,

更新日期：2012-05-13 00:00:00

abstract：:Multiple intravenous injections of a cDNA library, derived from human melanoma cell lines and expressed using the highly immunogenic vector vesicular stomatitis virus (VSV), cured mice with established melanoma tumors. Successful tumor eradication was associated with the ability of mouse lymphoid cells to mount a tumo...

journal_title：Nature biotechnology

authors： Pulido J,Kottke T,Thompson J,Galivo F,Wongthida P,Diaz RM,Rommelfanger D,Ilett E,Pease L,Pandha H,Harrington K,Selby P,Melcher A,Vile R

更新日期：2012-03-18 00:00:00

abstract：:The reactive thiol in cysteine is used for coupling maleimide linkers in the generation of antibody conjugates. To assess the impact of the conjugation site, we engineered cysteines into a therapeutic HER2/neu antibody at three sites differing in solvent accessibility and local charge. The highly solvent-accessible si...

journal_title：Nature biotechnology

authors： Shen BQ,Xu K,Liu L,Raab H,Bhakta S,Kenrick M,Parsons-Reponte KL,Tien J,Yu SF,Mai E,Li D,Tibbitts J,Baudys J,Saad OM,Scales SJ,McDonald PJ,Hass PE,Eigenbrot C,Nguyen T,Solis WA,Fuji RN,Flagella KM,Patel D,Spe

更新日期：2012-01-22 00:00:00

abstract：:We describe tethered conformation capture (TCC), a method for genome-wide mapping of chromatin interactions. By performing ligations on solid substrates rather than in solution, TCC substantially enhances the signal-to-noise ratio, thereby facilitating a detailed analysis of interactions within and between chromosomes...

journal_title：Nature biotechnology

authors： Kalhor R,Tjong H,Jayathilaka N,Alber F,Chen L

更新日期：2011-12-25 00:00:00

abstract：:Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. W...

journal_title：Nature biotechnology

authors： Xu X,Liu X,Ge S,Jensen JD,Hu F,Li X,Dong Y,Gutenkunst RN,Fang L,Huang L,Li J,He W,Zhang G,Zheng X,Zhang F,Li Y,Yu C,Kristiansen K,Zhang X,Wang J,Wright M,McCouch S,Nielsen R,Wang J,Wang W

更新日期：2011-12-11 00:00:00

abstract：:We compared bona fide human induced pluripotent stem cells (iPSCs) derived from umbilical cord blood (CB) cells and neonatal keratinocytes (K). As a consequence of both incomplete erasure of tissue-specific methylation and aberrant de novo methylation, CB-iPSCs and K-iPSCs were distinct in genome-wide DNA methylation ...

journal_title：Nature biotechnology

authors： Kim K,Zhao R,Doi A,Ng K,Unternaehrer J,Cahan P,Huo H,Loh YH,Aryee MJ,Lensch MW,Li H,Collins JJ,Feinberg AP,Daley GQ

更新日期：2011-11-27 00:00:00

abstract：:Transcriptomic analyses have revealed an unexpected complexity to the human transcriptome, whose breadth and depth exceeds current RNA sequencing capability. Using tiling arrays to target and sequence select portions of the transcriptome, we identify and characterize unannotated transcripts whose rare or transient exp...

journal_title：Nature biotechnology

authors： Mercer TR,Gerhardt DJ,Dinger ME,Crawford J,Trapnell C,Jeddeloh JA,Mattick JS,Rinn JL

更新日期：2011-11-13 00:00:00

abstract：:Excessive and prolonged activity of inflammatory monocytes is a hallmark of many diseases with an inflammatory component. In such conditions, precise targeting of these cells could be therapeutically beneficial while sparing many essential functions of the innate immune system, thus limiting unwanted effects. Inflamma...

journal_title：Nature biotechnology

authors： Leuschner F,Dutta P,Gorbatov R,Novobrantseva TI,Donahoe JS,Courties G,Lee KM,Kim JI,Markmann JF,Marinelli B,Panizzi P,Lee WW,Iwamoto Y,Milstein S,Epstein-Barash H,Cantley W,Wong J,Cortez-Retamozo V,Newton A,Love K,

更新日期：2011-10-09 00:00:00

abstract：:Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer-associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencin...

journal_title：Nature biotechnology

authors： Prensner JR,Iyer MK,Balbin OA,Dhanasekaran SM,Cao Q,Brenner JC,Laxman B,Asangani IA,Grasso CS,Kominsky HD,Cao X,Jing X,Wang X,Siddiqui J,Wei JT,Robinson D,Iyer HK,Palanisamy N,Maher CA,Chinnaiyan AM

更新日期：2011-07-31 00:00:00

abstract：:Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity...

journal_title：Nature biotechnology

authors： Grabherr MG,Haas BJ,Yassour M,Levin JZ,Thompson DA,Amit I,Adiconis X,Fan L,Raychowdhury R,Zeng Q,Chen Z,Mauceli E,Hacohen N,Gnirke A,Rhind N,di Palma F,Birren BW,Nusbaum C,Lindblad-Toh K,Friedman N,Regev A

更新日期：2011-05-15 00:00:00

abstract：:One-size-fits-all intravenous delivery of biologics may be giving way to alternate delivery routes that enable safer and more efficient drug administration. Michael Eisenstein reports. ...

journal_title：Nature biotechnology

authors： Eisenstein M

更新日期：2011-02-01 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：:Genetic testing for rare heart conditions might someday expand to more common cardiac ailments. Already there are signs testing is dramatically changing how some conditions are treated and doctors' definition of who a patient is. Stephen Strauss reports. ...

journal_title：Nature biotechnology

authors： Strauss S

更新日期：2010-10-01 00:00:00

abstract：:Epigenetic modifications constitute a complex regulatory layer on top of the genome sequence. Pluripotent and differentiated cells provide a powerful system for investigating how the epigenetic code influences cellular fate. High-throughput sequencing of these cell types has yielded DNA methylation maps at single-nucl...

journal_title：Nature biotechnology

authors： Meissner A

更新日期：2010-10-01 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：:The ability to detect single protein molecules in blood could accelerate the discovery and use of more sensitive diagnostic biomarkers. To detect low-abundance proteins in blood, we captured them on microscopic beads decorated with specific antibodies and then labeled the immunocomplexes (one or zero labeled target pr...

journal_title：Nature biotechnology

authors： Rissin DM,Kan CW,Campbell TG,Howes SC,Fournier DR,Song L,Piech T,Patel PP,Chang L,Rivnak AJ,Ferrell EP,Randall JD,Provuncher GK,Walt DR,Duffy DC

更新日期：2010-06-01 00:00:00

abstract：:The study of induced pluripotency often relies on experimental approaches that average measurements across a large population of cells, the majority of which do not become pluripotent. Here we used high-resolution, time-lapse imaging to trace the reprogramming process over 2 weeks from single mouse embryonic fibroblas...

journal_title：Nature biotechnology

authors： Smith ZD,Nachman I,Regev A,Meissner A

更新日期：2010-05-01 00:00:00