Browse by Journal Title

Article

Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey, G. and Monlong, J. and Ebler, J. and Novak, A.M. and Eizenga, J.M. and Gao, Y. and Marschall, T. and Li, H. and Paten, B.
Nature Biotechnology 42 (4): 663-673. April 2024

Systematic benchmarking of single-cell ATAC-sequencing protocols.
De Rop, F.V. and Hulselmans, G. and Flerin, C. and Soler-Vila, P. and Rafels, A. and Christiaens, V. and González-Blas, C.B. and Marchese, D. and Caratù, G. and Poovathingal, S. and Rozenblatt-Rosen, O. and Slyper, M. and Luo, W. and Muus, C. and Duarte, F. and Shrestha, R. and Bagdatli, S.T. and Corces, M.R. and Mamanova, L. and Knights, A. and Meyer, K.B. and Mulqueen, R. and Taherinasab, A. and Maschmeyer, P. and Pezoldt, J. and Lambert, C.L.G. and Iglesias, M. and Najle, S.R. and Dossani, Z.Y. and Martelotto, L.G. and Burkett, Z. and Lebofsky, R. and Martin-Subero, J.I. and Pillai, S. and Sebé-Pedrós, A. and Deplancke, B. and Teichmann, S.A. and Ludwig, L.S. and Braun, T.P. and Adey, A.C. and Greenleaf, W.J. and Buenrostro, J.D. and Regev, A. and Aerts, S. and Heyn, H.
Nature Biotechnology 3 August 2023 (In Press)

Functional analysis of structural variants in single cells using Strand-seq.
Jeong, H. and Grimes, K. and Rauwolf, K.K. and Bruch, P.M. and Rausch, T. and Hasenfeld, P. and Benito, E. and Roider, T. and Sabarinathan, R. and Porubsky, D. and Herbst, S.A. and Erarslan-Uysal, B. and Jann, J.C. and Marschall, T. and Nowak, D. and Bourquin, J.P. and Kulozik, A.E. and Dietrich, S. and Bornhauser, B. and Sanders, A.D. and Korbel, J.O.
Nature Biotechnology 41 (6): 832-844. June 2023

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.
Malin-Mayor, C. and Hirsch, P. and Guignard, L. and McDole, K. and Wan, Y. and Lemon, W.C. and Kainmueller, D. and Keller, P.J. and Preibisch, S. and Funke, J.
Nature Biotechnology 44 (1): 44-49. January 2023

The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants.
Rothenberger, S. and Hurdiss, D.L. and Walser, M. and Malvezzi, F. and Mayor, J. and Ryter, S. and Moreno, H. and Liechti, N. and Bosshart, A. and Iss, C. and Calabro, V. and Cornelius, A. and Hospodarsch, T. and Neculcea, A. and Looser, T. and Schlegel, A. and Fontaine, S. and Villemagne, D. and Paladino, M. and Schiegg, D. and Mangold, S. and Reichen, C. and Radom, F. and Kaufmann, Y. and Schaible, D. and Schlegel, I. and Zitt, C. and Sigrist, G. and Straumann, M. and Wolter, J. and Comby, M. and Sacarcelik, F. and Drulyte, I. and Lyoo, H. and Wang, C. and Li, W. and Du, W. and Binz, H.K. and Herrup, R. and Lusvarghi, S. and Neerukonda, S.N. and Vassell, R. and Wang, W. and Adler, J.M. and Eschke, K. and Nascimento, M. and Abdelgawad, A. and Gruber, A.D. and Bushe, J. and Kershaw, O. and Knutson, C.G. and Balavenkatraman, K.K. and Ramanathan, K. and Wyler, E. and Teixeira Alves, L.G. and Lewis, S. and Watson, R. and Haeuptle, M.A. and Zürcher, A. and Dawson, K.M. and Steiner, D. and Weiss, C.D. and Amstutz, P. and van Kuppeveld, F.J.M. and Stumpp, M.T. and Bosch, B.J. and Engler, O. and Trimpert, J.
Nature Biotechnology 40 (12): 1845-1854. December 2022

Deep Visual Proteomics defines single-cell identity and heterogeneity.
Mund, A. and Coscia, F. and Kriston, A. and Hollandi, R. and Kovács, F. and Brunner, A.D. and Migh, E. and Schweizer, L. and Santos, A. and Bzorek, M. and Naimy, S. and Rahbek-Gjerdrum, L.M. and Dyring-Andersen, B. and Bulkescher, J. and Lukas, C. and Eckert, M.A. and Lengyel, E. and Gnann, C. and Lundberg, E. and Horvath, P. and Mann, M.
Nature Biotechnology 40 (8): 1231-1240. August 2022

A knowledge graph to interpret clinical proteomics data.
Santos, A. and Colaço, A.R. and Nielsen, A.B. and Niu, L. and Strauss, M. and Geyer, P.E. and Coscia, F. and Albrechtsen, N.J.W. and Mundt, F. and Jensen, L.J. and Mann, M.
Nature Biotechnology 40 (5): 692-702. 22 May 2022

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.
Fiskin, E. and Lareau, C.A. and Ludwig, L.S. and Eraslan, G. and Liu, F. and Ring, A.M. and Xavier, R.J. and Regev, A.
Nature Biotechnology 40 (3): 374-381. March 2022

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.
Miller, T.E. and Lareau, C.A. and Verga, J.A. and DePasquale, E.A.K. and Liu, V. and Ssozi, D. and Sandor, K. and Yin, Y. and Ludwig, L.S. and El Farran, C.A. and Morgan, D.M. and Satpathy, A.T. and Griffin, G.K. and Lane, A.A. and Love, J.C. and Bernstein, B.E. and Sankaran, V.G. and van Galen, P.
Nature Biotechnology 40 (7): 1030-1034. 24 February 2022

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
Mimitou, E.P. and Lareau, C.A. and Chen, K.Y. and Zorzetto-Fernandes, A.L. and Hao, Y. and Takeshima, Y. and Luo, W. and Huang, T.S. and Yeung, B.Z. and Papalexi, E. and Thakore, P.I. and Kibayashi, T. and Wing, J.B. and Hata, M. and Satija, R. and Nazor, K.L. and Sakaguchi, S. and Ludwig, L.S. and Sankaran, V.G. and Regev, A. and Smibert, P.
Nature Biotechnology 39 (10): 1246-1258. October 2021

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling.
Lareau, C.A. and Ludwig, L.S. and Muus, C. and Gohil, S.H. and Zhao, T. and Chiang, Z. and Pelka, K. and Verboon, J.M. and Luo, W. and Christian, E. and Rosebrock, D. and Getz, G. and Boland, G.M. and Chen, F. and Buenrostro, J.D. and Hacohen, N. and Wu, C.J. and Aryee, M.J. and Regev, A. and Sankaran, V.G.
Nature Biotechnology 39 (4): 451-461. April 2021

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.
Porubsky, D. and Ebert, P. and Audano, P.A. and Vollger, M.R. and Harvey, W.T. and Marijon, P. and Ebler, J. and Munson, K.M. and Sorensen, M. and Sulovari, A. and Haukness, M. and Ghareghani, M. and Lansdorp, P.M. and Paten, B. and Devine, S.E. and Sanders, A.D. and Lee, C. and Chaisson, M.J.P. and Korbel, J.O. and Eichler, E.E. and Marschall, T.
Nature Biotechnology 39 (3): 302-308. March 2021

GPSeq reveals the radial organization of chromatin in the cell nucleus.
Girelli, G. and Custodio, J. and Kallas, T. and Agostini, F. and Wernersson, E. and Spanjaard, B. and Mota, A. and Kolbeinsdottir, S. and Gelali, E. and Crosetto, N. and Bienko, M.
Nature Biotechnology 38 (10): 1184-1193. October 2020

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
Mereu, E. and Lafzi, A. and Moutinho, C. and Ziegenhain, C. and McCarthy, D.J. and Álvarez-Varela, A. and Batlle, E. and Sagar, and Grün, D. and Lau, J.K. and Boutet, S.C. and Sanada, C. and Ooi, A. and Jones, R.C. and Kaihara, K. and Brampton, C. and Talaga, Y. and Sasagawa, Y. and Tanaka, K. and Hayashi, T. and Braeuning, C. and Fischer, C. and Sauer, S. and Trefzer, T. and Conrad, C. and Adiconis, X. and Nguyen, L.T. and Regev, A. and Levin, J.Z. and Parekh, S. and Janjic, A. and Wange, L.E. and Bagnoli, J.W. and Enard, W. and Gut, M. and Sandberg, R. and Nikaido, I. and Gut, I. and Stegle, O. and Heyn, H.
Nature Biotechnology 38 (6): 747-755. June 2020

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.
Sanders, A.D. and Meiers, S. and Ghareghani, M. and Porubsky, D. and Jeong, H. and van Vliet, M.A.C.C. and Rausch, T. and Richter-Pechańska, P. and Kunz, J.B. and Jenni, S. and Bolognini, D. and Longo, G.M.C. and Raeder, B. and Kinanen, V. and Zimmermann, J. and Benes, V. and Schrappe, M. and Mardin, B.R. and Kulozik, A.E. and Bornhauser, B. and Bourquin, J.P. and Marschall, T. and Korbel, J.O.
Nature Biotechnology 38 (3): 343-354. March 2020

Self-organizing neuruloids model developmental aspects of Huntington's disease in the ectodermal compartment.
Haremaki, T. and Metzger, J.J. and Rito, T. and Ozair, M.Z. and Etoc, F. and Brivanlou, A.H.
Nature Biotechnology 37 (10): 1198-1208. October 2019

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Haghverdi, L. and Lun, A.T.L. and Morgan, M.D. and Marioni, J.C.
Nature Biotechnology 36 (5): 421-427. May 2018

Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars.
Spanjaard, B. and Hu, B. and Mitic, N. and Olivares-Chauvet, P. and Janjuha, S. and Ninov, N. and Junker, J.P.
Nature Biotechnology 36 (5): 469-473. May 2018

Towards standards for human fecal sample processing in metagenomic studies.
Costea, P.I. and Zeller, G. and Sunagawa, S. and Pelletier, E. and Alberti, A. and Levenez, F. and Tramontano, M. and Driessen, M. and Hercog, R. and Jung, F.E. and Kultima, J.R. and Hayward, M.R. and Coelho, L.P. and Allen-Vercoe, E. and Bertrand, L. and Blaut, M. and Brown, J.R.M. and Carton, T. and Cools-Portier, S. and Daigneault, M. and Derrien, M. and Druesne, A. and de Vos, W.M. and Finlay, B.B. and Flint, H.J. and Guarner, F. and Hattori, M. and Heilig, H. and Luna, R.A. and van Hylckama Vlieg, J. and Junick, J. and Klymiuk, I. and Langella, P. and Le Chatelier, Z. and Mai, V. and Manichanh, C. and Martin, J.C. and Mery, C. and Morita, H. and O'Toole, P.W. and Orvain, C. and Patil, K.R. and Penders, J. and Persson, S. and Pons, N. and Popova, M. and Salonen, A. and Saulnier, D. and Scott, K.P. and Singh, B. and Slezak, K. and Veiga, P. and Versalovic, J. and Zhao, L. and Zoetendal, E.G. and Ehrlich, S.D. and Dore, J. and Bork, P.
Nature Biotechnology 35 (11): 1069-1076. November 2017

Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells.
Chu, V.T. and Weber, T. and Wefers, B. and Wurst, W. and Sander, S. and Rajewsky, K. and Kühn, R.
Nature Biotechnology 33 (5): 543-548. May 2015

Identification of human T-cell receptors with optimal affinity to cancer antigens using antigen-negative humanized mice.
Obenaus, M. and Leitão, C. and Leisegang, M. and Chen, X. and Gavvovidis, I. and van der Bruggen, P. and Uckert, W. and Schendel, D.J. and Blankenstein, T.
Nature Biotechnology 33 (4): 402-407. April 2015

Decoding the regulatory network of early blood development from single-cell gene expression measurements.
Moignard, V. and Woodhouse, S. and Haghverdi, L. and Lilly, A.J. and Tanaka, Y. and Wilkinson, A.C. and Buettner, F. and Macaulay, I.C. and Jawaid, W. and Diamanti, E. and Nishikawa, S.I. and Piterman, N. and Kouskoff, V. and Theis, F.J. and Fisher, J. and Göttgens, B.
Nature Biotechnology 33 (3): 269-276. March 2015

An integrated catalog of reference genes in the human gut microbiome.
Li, J. and Jia, H. and Cai, X. and Zhong, H. and Feng, Q. and Sunagawa, S. and Arumugam, M. and Kultima, J.R. and Prifti, E. and Nielsen, T. and Juncker, A.S. and Manichanh, C. and Chen, B. and Zhang, W. and Levenez, F. and Wang, J. and Xu, X. and Xiao, L. and Liang, S. and Zhang, D. and Zhang, Z. and Chen, W. and Zhao, H. and Al-Aama, J.Y. and Edris, S. and Yang, H. and Wang, J. and Hansen, T. and Nielsen, H.B. and Brunak, S. and Kristiansen, K. and Guarner, F. and Pedersen, O. and Dore, J. and Ehrlich, S.D. and Bork, P. and Wang, J.
Nature Biotechnology 32 (8): 834-841. August 2014

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen, H.B. and Almeida, M. and Juncker, A.S. and Rasmussen, S. and Li, J. and Sunagawa, S. and Plichta, D.R. and Gautier, L. and Pedersen, A.G. and Le Chatelier, E. and Pelletier, E. and Bonde, I. and Nielsen, T. and Manichanh, C. and Arumugam, M. and Batto, J.M. and Quintanilha Dos Santos, M.B. and Blom, N. and Borruel, N. and Burgdorf, K.S. and Boumezbeur, F. and Casellas, F. and Dore, J. and Dworzynski, P. and Guarner, F. and Hansen, T. and Hildebrand, F. and Kaas, R.S. and Kennedy, S. and Kristiansen, K. and Kultima, J.R. and Leonard, P. and Levenez, F. and Lund, O. and Moumen, B. and Le Paslier, D. and Pons, N. and Pedersen, O. and Prifti, E. and Qin, J. and Raes, J. and Sorensen, S. and Tap, J. and Tims, S. and Ussery, D.W. and Yamada, T. and Renault, P. and Sicheritz-Ponten, T. and Bork, P. and Wang, J. and Brunak, S. and Ehrlich, S.D.
Nature Biotechnology 32 (8): 822-828. August 2014

Discovering microRNAs from deep sequencing data using miRDeep.
Friedlaender, M.R. and Chen, W. and Adamidi, C. and Maaskola, J. and Einspanier, R. and Knespel, S. and Rajewsky, N.
Nature Biotechnology 26 (4): 407-415. April 2008

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.
Korbel, J.O. and Jensen, L.J. and von Mering, C. and Bork, P.
Nature Biotechnology 22 (7): 911-917. 1 July 2004

The HUPO PSI's Molecular Interaction format - a community standard for the representation of protein interaction data.
Hermjakob, H. and Montecchi-Palazzi, L. and Bader, G. and Wojcik, R. and Salwinski, L. and Ceol, A. and Moore, S. and Orchard, S. and Sarkans, U. and von Mering, C. and Roechert, B. and Poux, S. and Jung, E. and Mersch, H. and Kersey, P. and Lappe, M. and Li, Y.X. and Zeng, R. and Rana, D. and Nikolski, M. and Husi, H. and Brun, C. and Shanker, K. and Grant, S.G.N. and Sander, C. and Bork, P. and Zhu, W.M. and Pandey, A. and Brazma, A. and Jacq, B. and Vidal, M. and Sherman, D. and Legrain, P. and Cesareni, G. and Xenarios, L. and Eisenberg, D. and Steipe, B. and Hogue, C. and Apweiler, R.
Nature Biotechnology 22 (2): 177-183. 1 January 2004

Systematic discovery of analogous enzymes in thiamin biosynthesis.
Morett, E. and Korbel, J. and Rajan, E. and Saab-Rincon, G. and Olvera, L. and Olvera, M. and Steffen, S. and Snel, B. and Bork, P.
Nature Biotechnology 21 (7): 790-795. July 2003

Male and female mice derived from the same embryonic stem cell clone by tetraploid embryo complementation.
Eggan, K. and Rode, A. and Jentsch, I. and Samuel, C. and Hennek, T. and Tintrup, H. and Zevnik, B. and Erwin, J. and Loring, J. and Jackson-Grusby, L. and Speicher, M.R. and Kuehn, R. and Jaenisch, R.
Nature Biotechnology 20 (5): 455-459. May 2002

A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks.
Schuster, S. and Fell, D.A. and Dandekar, T.
Nature Biotechnology 18 (3): 326-332. 1 March 2000

A synthetic mimic of a discontinuous binding site on interleukin-10.
Reineke, U. and Sabat, R. and Misselwitz, R. and Welfle, H. and Volk, H.D. and Schneider-Mergener, J.
Nature Biotechnology 17 : 271-275. 1 March 1999

Sustained somatic gene inactivation by viral transfer of Cre recombinase.
Rohlmann, A. and Gotthardt, M. and Willnow, T.E. and Hammer, R.E. and Herz, J.
Nature Biotechnology 14 (11): 1562-1565. 1 November 1996

Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemia.
Baron, H. and Fung, S. and Aydin, A. and Bähring, S. and Luft, F.C. and Schuster, H.
Nature Biotechnology 14 (10): 1279-1282. 1 October 1996

Letter

Standardized annotation of translated open reading frames.
Mudge, J.M. and Ruiz-Orera, J. and Prensner, J.R. and Brunet, M.A. and Calvet, F. and Jungreis, I. and Gonzalez, Jo.M. and Magrane, M. and Martinez, T.F. and Schulz, J.F. and Yang, Y.T. and Albà, M.M. and Aspden, J.L. and Baranov, P.V. and Bazzini, A.A. and Bruford, E. and Martin, M.J. and Calviello, L. and Carvunis, A.R. and Chen, J. and Couso, J.P. and Deutsch, E.W. and Flicek, P. and Frankish, A. and Gerstein, M. and Hubner, N. and Ingolia, N.T. and Kellis, M. and Menschaert, G. and Moritz, R.L. and Ohler, U. and Roucou, X. and Saghatelian, A. and Weissman, J.S. and van Heesch, S.
Nature Biotechnology 40 (7): 994–999. July 2022

Editorial

Single-cell multi-omics allows functional characterization of structural variants.
Korbel, J.O. and Sanders, A.D.
Nature Biotechnology 24 November 2022

Sizing up beta cells made from stem cells.
Nguyen-Ngoc, K.V. and Wortham, M. and Sander, M.
Nature Biotechnology 40 (7): 1006-1008. July 2022

Receptor combinations hone T-cell therapy.
Blankenstein, T.
Nature Biotechnology 34 (4): 389-391. 7 April 2016

Antisense 98: Work in progress.
Crooke, S.T. and Eckstein, F. and Christoffersen, R.E. and Mehta, V. and Cotter, F.E. and Bennett, C.F. and Agrawal, S. and Haller, H. and Dorr, F.A. and Grinstead, E.A.
Nature Biotechnology 16 (13): 1319-1321. December 1998