Advance online publication


The latest research papers, published online ahead of print. These online versions are definitive and may be cited using the digital object identifier (DOI).

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Research

Articles

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

George Rosenberger, Yansheng Liu, Hannes L Röst, Christina Ludwig, Alfonso Buil, Ariel Bensimon, Martin Soste, Tim D Spector, Emmanouil T Dermitzakis, Ben C Collins, Lars Malmström & Ruedi Aebersold

Published online: 12 June 2017 | doi:10.1038/nbt.3908

Detection of post-translational modifications by mass spectrometry is enhanced with an analytic method for data-independent acquisition proteomics.


Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding

Freeman Lan, Benjamin Demaree, Noorsher Ahmed & Adam R Abate

Published online: 29 May 2017 | doi:10.1038/nbt.3880

More than 50,000 single-cell genomes are sequenced in a single run using droplet barcoding.


HLA-E-expressing pluripotent stem cells escape allogeneic responses and lysis by NK cells

Germán G Gornalusse, Roli K Hirata, Sarah E Funk, Laura Riolobos, Vanda S Lopes, Gabriel Manske, Donna Prunkard, Aric G Colunga, Laïla-Aïcha Hanafi, Dennis O Clegg, Cameron Turtle & David W Russell

Published online: 15 May 2017 | doi:10.1038/nbt.3860

Expression of the minimally polymorphic HLA-E molecule prevents NK-cell-mediated rejection of cells lacking expression of HLA-A, B and C.


Targeting genomic rearrangements in tumor cells through Cas9-mediated insertion of a suicide gene

Zhang-Hui Chen, Yan P Yu, Ze-Hua Zuo, Joel B Nelson, George K Michalopoulos, Satdatshan Monga, Silvia Liu, George Tseng & Jian-Hua Luo

Published online: 01 May 2017 | doi:10.1038/nbt.3843

Insertion of the sequence encoding herpes simplex virus 1 thymidine kinase at the breakpoints of fusion genes in cancer cells causes cell death and regression of mouse xenograft tumors.


Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development

Abbas H Rizvi, Pablo G Camara, Elena K Kandror, Thomas J Roberts, Ira Schieren, Tom Maniatis & Raul Rabadan

Published online: 01 May 2017 | doi:10.1038/nbt.3854

Analysis of RNA-seq data from individual developing mouse motor neuron cells with topological data analysis sheds light on crucial cell-fate decisions during neurogenesis.


CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

Tyler S Klann, Joshua B Black, Malathi Chellappan, Alexias Safi, Lingyun Song, Isaac B Hilton, Gregory E Crawford, Timothy E Reddy & Charles A Gersbach

Published online: 03 April 2017 | doi:10.1038/nbt.3853

Regulatory elements for specific human genes are rapidly identified with CRISPR epigenome editing.


Letters

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site

Eva-Maria Strauch, Steffen M Bernard, David La, Alan J Bohn, Peter S Lee, Caitlin E Anderson, Travis Nieusma, Carly A Holstein, Natalie K Garcia, Kathryn A Hooper, Rashmi Ravichandran, Jorgen W Nelson, William Sheffler, Jesse D Bloom, Kelly K Lee, Andrew B Ward, Paul Yager, Deborah H Fuller, Ian A Wilson & David Baker

Published online: 12 June 2017 | doi:10.1038/nbt.3907

A method to target trimeric membrane proteins by designing geometrically matched trimeric protein binders is demonstrated for the influenza-virus glycoprotein hemagglutinin.


Engineered Cpf1 variants with altered PAM specificities

Linyi Gao, David B T Cox, Winston X Yan, John C Manteiga, Martin W Schneider, Takashi Yamano, Hiroshi Nishimasu, Osamu Nureki, Nicola Crosetto & Feng Zhang

Published online: 05 June 2017 | doi:10.1038/nbt.3900

The targeting range of the CRISPR endonuclease Cpf1 is increased three-fold by molecular engineering.


Guided self-organization and cortical plate formation in human brain organoids

Madeline A Lancaster, Nina S Corsini, Simone Wolfinger, E Hilary Gustafson, Alex W Phillips, Thomas R Burkard, Tomoki Otani, Frederick J Livesey & Juergen A Knoblich

Published online: 31 May 2017 | doi:10.1038/nbt.3906

Engineering human brain organoids with floating scaffolds enhances the maturity and reproducibility of cortical tissue structure.


Digital-to-biological converter for on-demand production of biologics

Kent S Boles, Krishna Kannan, John Gill, Martina Felderman, Heather Gouvis, Bolyn Hubby, Kurt I Kamrud, J Craig Venter & Daniel G Gibson

Published online: 29 May 2017 | doi:10.1038/nbt.3859

Sequence information is converted into nucleic acids, proteins and phage particles without human intervention to enable on-demand bio-manufacturing.


Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation

David T Riglar, Tobias W Giessen, Michael Baym, S Jordan Kerns, Matthew J Niederhuber, Roderick T Bronson, Jonathan W Kotula, Georg K Gerber, Jeffrey C Way & Pamela A Silver

Published online: 29 May 2017 | doi:10.1038/nbt.3879

An engineered commensal E. coli strain can function as a living diagnostic for a marker of inflammation in the murine gut for 200 days.


Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

Anupriya Kaur Thind, Thomas Wicker, Hana Šimková, Dario Fossati, Odile Moullet, Cécile Brabant, Jan Vrána, Jaroslav Doležel & Simon G Krattinger

Published online: 15 May 2017 | doi:10.1038/nbt.3877

Rapid cloning of genes from any crop plant species (or cultivar) whose chromosomes can be flow sorted is enabled by a combination of short-read sequencing and proximity ligation.


Generation of inner ear organoids containing functional hair cells from human pluripotent stem cells

Karl R Koehler, Jing Nie, Emma Longworth-Mills, Xiao-Ping Liu, Jiyoon Lee, Jeffrey R Holt & Eri Hashino

Published online: 01 May 2017 | doi:10.1038/nbt.3840

Human pluripotent stem cells are differentiated into inner ear organoids containing cells similar to hair cells and sensory neurons.


Transplantation of engineered organoids enables rapid generation of metastatic mouse models of colorectal cancer

Kevin P O'Rourke, Evangelia Loizou, Geulah Livshits, Emma M Schatoff, Timour Baslan, Eusebio Manchado, Janelle Simon, Paul B Romesser, Benjamin Leach, Teng Han, Chantal Pauli, Himisha Beltran, Mark A Rubin, Lukas E Dow & Scott W Lowe

Published online: 01 May 2017 | doi:10.1038/nbt.3837

Genetically engineered colon organoids form tumors that undergo a stepwise progression toward metastatic disease after orthotopic transplantation.


In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis

Jatin Roper, Tuomas Tammela, Naniye Malli Cetinbas, Adam Akkad, Ali Roghanian, Steffen Rickelt, Mohammad Almeqdadi, Katherine Wu, Matthias A Oberli, Francisco Sánchez-Rivera, Yoona K Park, Xu Liang, George Eng, Martin S Taylor, Roxana Azimi, Dmitriy Kedrin, Rachit Neupane, Semir Beyaz, Ewa T Sicinska, Yvelisse Suarez, James Yoo, Lillian Chen, Lawrence Zukerberg, Pekka Katajisto, Vikram Deshpande, Adam J Bass, Philip N Tsichlis, Jacqueline Lees, Robert Langer, Richard O Hynes, Jianzhu Chen, Arjun Bhutkar, Tyler Jacks & Ömer H Yilmaz

Published online: 01 May 2017 | doi:10.1038/nbt.3836

Metastatic progression of colorectal cancer is modeled in mice using in vivo genome editing and transplantation of engineered organoids.


Resources

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Supratim Mukherjee, Rekha Seshadri, Neha J Varghese, Emiley A Eloe-Fadrosh, Jan P Meier-Kolthoff, Markus Göker, R Cameron Coates, Michalis Hadjithomas, Georgios A Pavlopoulos, David Paez-Espino, Yasuo Yoshikuni, Axel Visel, William B Whitman, George M Garrity, Jonathan A Eisen, Philip Hugenholtz, Amrita Pati, Natalia N Ivanova, Tanja Woyke, Hans-Peter Klenk & Nikos C Kyrpides

Published online: 12 June 2017 | doi:10.1038/nbt.3886

Metagenomic and microbial sequence data are made easier to interpret with the addition of 1,003 genomes to the Genomic Encyclopedia of Bacteria and Archaea.


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Opinion and Comment

Commentary

Making individualized drugs a reality

Huub Schellekens, Mohammed Aldosari, Herre Talsma & Enrico Mastrobattista

Published online: 05 June 2017 | doi:10.1038/nbt.3888

Magistral drug preparation offers a model to circumvent many of the technological, regulatory and financial challenges that prevent provision of the right drug at the right time to the right patient.


Until print versions of AOP papers are published, they should be cited in the style "Author(s) Nature Biotechnology advance online publication, day month year (doi:10.1038/nbtXXXXX)". Once the print version (identical to the AOP) is published, it should be cited as follows: "Author(s) Nature Biotechnology volume, page (year); advance online publication, (doi:10.1038/nbtXXXXX)".

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