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Article

Systematic benchmarking of single-cell ATAC-sequencing protocols.
De Rop, F.V., Hulselmans, G., Flerin, C., Soler-Vila, P., Rafels, A., Christiaens, V., González-Blas, C.B., Marchese, D., Caratù, G., Poovathingal, S., Rozenblatt-Rosen, O., Slyper, M., Luo, W., Muus, C., Duarte, F., Shrestha, R., Bagdatli, S.T., Corces, M.R., Mamanova, L., Knights, A., Meyer, K.B., Mulqueen, R., Taherinasab, A., Maschmeyer, P., Pezoldt, J., Lambert, C.L.G., Iglesias, M., Najle, S.R., Dossani, Z.Y., Martelotto, L.G., Burkett, Z., Lebofsky, R., Martin-Subero, J.I., Pillai, S., Sebé-Pedrós, A., Deplancke, B., Teichmann, S.A., Ludwig, L.S., Braun, T.P., Adey, A.C., Greenleaf, W.J., Buenrostro, J.D., Regev, A., Aerts, S. and Heyn, H.
Nature Biotechnology 42 (6): 916-926. June 2024

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

Functional analysis of structural variants in single cells using Strand-seq.
Jeong, H., Grimes, K., Rauwolf, K.K., Bruch, P.M., Rausch, T., Hasenfeld, P., Benito, E., Roider, T., Sabarinathan, R., Porubsky, D., Herbst, S.A., Erarslan-Uysal, B., Jann, J.C., Marschall, T., Nowak, D., Bourquin, J.P., Kulozik, A.E., Dietrich, S., Bornhauser, B., 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., Hirsch, P., Guignard, L., McDole, K., Wan, Y., Lemon, W.C., Kainmueller, D., Keller, P.J., 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., Hurdiss, D.L., Walser, M., Malvezzi, F., Mayor, J., Ryter, S., Moreno, H., Liechti, N., Bosshart, A., Iss, C., Calabro, V., Cornelius, A., Hospodarsch, T., Neculcea, A., Looser, T., Schlegel, A., Fontaine, S., Villemagne, D., Paladino, M., Schiegg, D., Mangold, S., Reichen, C., Radom, F., Kaufmann, Y., Schaible, D., Schlegel, I., Zitt, C., Sigrist, G., Straumann, M., Wolter, J., Comby, M., Sacarcelik, F., Drulyte, I., Lyoo, H., Wang, C., Li, W., Du, W., Binz, H.K., Herrup, R., Lusvarghi, S., Neerukonda, S.N., Vassell, R., Wang, W., Adler, J.M., Eschke, K., Nascimento, M., Abdelgawad, A., Gruber, A.D., Bushe, J., Kershaw, O., Knutson, C.G., Balavenkatraman, K.K., Ramanathan, K., Wyler, E., Teixeira Alves, L.G., Lewis, S., Watson, R., Haeuptle, M.A., Zürcher, A., Dawson, K.M., Steiner, D., Weiss, C.D., Amstutz, P., van Kuppeveld, F.J.M., Stumpp, M.T., Bosch, B.J., Engler, O. and Trimpert, J.
Nature Biotechnology 40 (12): 1845-1854. December 2022

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

A knowledge graph to interpret clinical proteomics data.
Santos, A., Colaço, A.R., Nielsen, A.B., Niu, L., Strauss, M., Geyer, P.E., Coscia, F., Albrechtsen, N.J.W., Mundt, F., 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., Lareau, C.A., Ludwig, L.S., Eraslan, G., Liu, F., Ring, A.M., 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., Lareau, C.A., Verga, J.A., DePasquale, E.A.K., Liu, V., Ssozi, D., Sandor, K., Yin, Y., Ludwig, L.S., El Farran, C.A., Morgan, D.M., Satpathy, A.T., Griffin, G.K., Lane, A.A., Love, J.C., Bernstein, B.E., 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., Lareau, C.A., Chen, K.Y., Zorzetto-Fernandes, A.L., Hao, Y., Takeshima, Y., Luo, W., Huang, T.S., Yeung, B.Z., Papalexi, E., Thakore, P.I., Kibayashi, T., Wing, J.B., Hata, M., Satija, R., Nazor, K.L., Sakaguchi, S., Ludwig, L.S., Sankaran, V.G., 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., Ludwig, L.S., Muus, C., Gohil, S.H., Zhao, T., Chiang, Z., Pelka, K., Verboon, J.M., Luo, W., Christian, E., Rosebrock, D., Getz, G., Boland, G.M., Chen, F., Buenrostro, J.D., Hacohen, N., Wu, C.J., Aryee, M.J., 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., Ebert, P., Audano, P.A., Vollger, M.R., Harvey, W.T., Marijon, P., Ebler, J., Munson, K.M., Sorensen, M., Sulovari, A., Haukness, M., Ghareghani, M., Lansdorp, P.M., Paten, B., Devine, S.E., Sanders, A.D., Lee, C., Chaisson, M.J.P., Korbel, J.O., 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., Custodio, J., Kallas, T., Agostini, F., Wernersson, E., Spanjaard, B., Mota, A., Kolbeinsdottir, S., Gelali, E., 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., Lafzi, A., Moutinho, C., Ziegenhain, C., McCarthy, D.J., Álvarez-Varela, A., Batlle, E., Sagar, Grün, D., Lau, J.K., Boutet, S.C., Sanada, C., Ooi, A., Jones, R.C., Kaihara, K., Brampton, C., Talaga, Y., Sasagawa, Y., Tanaka, K., Hayashi, T., Braeuning, C., Fischer, C., Sauer, S., Trefzer, T., Conrad, C., Adiconis, X., Nguyen, L.T., Regev, A., Levin, J.Z., Parekh, S., Janjic, A., Wange, L.E., Bagnoli, J.W., Enard, W., Gut, M., Sandberg, R., Nikaido, I., Gut, I., 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., Meiers, S., Ghareghani, M., Porubsky, D., Jeong, H., van Vliet, M.A.C.C., Rausch, T., Richter-Pechańska, P., Kunz, J.B., Jenni, S., Bolognini, D., Longo, G.M.C., Raeder, B., Kinanen, V., Zimmermann, J., Benes, V., Schrappe, M., Mardin, B.R., Kulozik, A.E., Bornhauser, B., Bourquin, J.P., 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., Metzger, J.J., Rito, T., Ozair, M.Z., 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., Lun, A.T.L., 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., Hu, B., Mitic, N., Olivares-Chauvet, P., Janjuha, S., 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., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., Tramontano, M., Driessen, M., Hercog, R., Jung, F.E., Kultima, J.R., Hayward, M.R., Coelho, L.P., Allen-Vercoe, E., Bertrand, L., Blaut, M., Brown, J.R.M., Carton, T., Cools-Portier, S., Daigneault, M., Derrien, M., Druesne, A., de Vos, W.M., Finlay, B.B., Flint, H.J., Guarner, F., Hattori, M., Heilig, H., Luna, R.A., van Hylckama Vlieg, J., Junick, J., Klymiuk, I., Langella, P., Le Chatelier, Z., Mai, V., Manichanh, C., Martin, J.C., Mery, C., Morita, H., O'Toole, P.W., Orvain, C., Patil, K.R., Penders, J., Persson, S., Pons, N., Popova, M., Salonen, A., Saulnier, D., Scott, K.P., Singh, B., Slezak, K., Veiga, P., Versalovic, J., Zhao, L., Zoetendal, E.G., Ehrlich, S.D., 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., Weber, T., Wefers, B., Wurst, W., Sander, S., 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., Leitão, C., Leisegang, M., Chen, X., Gavvovidis, I., van der Bruggen, P., Uckert, W., 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., Woodhouse, S., Haghverdi, L., Lilly, A.J., Tanaka, Y., Wilkinson, A.C., Buettner, F., Macaulay, I.C., Jawaid, W., Diamanti, E., Nishikawa, S.I., Piterman, N., Kouskoff, V., Theis, F.J., 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., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J.R., Prifti, E., Nielsen, T., Juncker, A.S., Manichanh, C., Chen, B., Zhang, W., Levenez, F., Wang, J., Xu, X., Xiao, L., Liang, S., Zhang, D., Zhang, Z., Chen, W., Zhao, H., Al-Aama, J.Y., Edris, S., Yang, H., Wang, J., Hansen, T., Nielsen, H.B., Brunak, S., Kristiansen, K., Guarner, F., Pedersen, O., Dore, J., Ehrlich, S.D., 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., Almeida, M., Juncker, A.S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D.R., Gautier, L., Pedersen, A.G., Le Chatelier, E., Pelletier, E., Bonde, I., Nielsen, T., Manichanh, C., Arumugam, M., Batto, J.M., Quintanilha Dos Santos, M.B., Blom, N., Borruel, N., Burgdorf, K.S., Boumezbeur, F., Casellas, F., Dore, J., Dworzynski, P., Guarner, F., Hansen, T., Hildebrand, F., Kaas, R.S., Kennedy, S., Kristiansen, K., Kultima, J.R., Leonard, P., Levenez, F., Lund, O., Moumen, B., Le Paslier, D., Pons, N., Pedersen, O., Prifti, E., Qin, J., Raes, J., Sorensen, S., Tap, J., Tims, S., Ussery, D.W., Yamada, T., Renault, P., Sicheritz-Ponten, T., Bork, P., Wang, J., 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., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., 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., Jensen, L.J., 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., Montecchi-Palazzi, L., Bader, G., Wojcik, R., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y.X., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S.G.N., Sander, C., Bork, P., Zhu, W.M., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, L., Eisenberg, D., Steipe, B., Hogue, C. and Apweiler, R.
Nature Biotechnology 22 (2): 177-183. 1 January 2004

Systematic discovery of analogous enzymes in thiamin biosynthesis.
Morett, E., Korbel, J., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Steffen, S., 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., Rode, A., Jentsch, I., Samuel, C., Hennek, T., Tintrup, H., Zevnik, B., Erwin, J., Loring, J., Jackson-Grusby, L., Speicher, M.R., 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., 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., Sabat, R., Misselwitz, R., Welfle, H., 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., Gotthardt, M., Willnow, T.E., 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., Fung, S., Aydin, A., Bähring, S., 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., Ruiz-Orera, J., Prensner, J.R., Brunet, M.A., Calvet, F., Jungreis, I., Gonzalez, Jo.M., Magrane, M., Martinez, T.F., Schulz, J.F., Yang, Y.T., Albà, M.M., Aspden, J.L., Baranov, P.V., Bazzini, A.A., Bruford, E., Martin, M.J., Calviello, L., Carvunis, A.R., Chen, J., Couso, J.P., Deutsch, E.W., Flicek, P., Frankish, A., Gerstein, M., Hubner, N., Ingolia, N.T., Kellis, M., Menschaert, G., Moritz, R.L., Ohler, U., Roucou, X., Saghatelian, A., 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., 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., Eckstein, F., Christoffersen, R.E., Mehta, V., Cotter, F.E., Bennett, C.F., Agrawal, S., Haller, H., Dorr, F.A. and Grinstead, E.A.
Nature Biotechnology 16 (13): 1319-1321. December 1998