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Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX Nat. Protoc. (IF 14.8) Pub Date : 2024-03-15 Yupeng Wang, Haibao Tang, Xiyin Wang, Ying Sun, Paule V. Joseph, Andrew H. Paterson
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Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host–microbiota and other multi-omic interactions Nat. Protoc. (IF 14.8) Pub Date : 2024-03-12 Nolan K. Newman, Matthew S. Macovsky, Richard R. Rodrigues, Amanda M. Bruce, Jacob W. Pederson, Jyothi Padiadpu, Jigui Shan, Joshua Williams, Sankalp S. Patil, Amiran K. Dzutsev, Natalia Shulzhenko, Giorgio Trinchieri, Kevin Brown, Andrey Morgun
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Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales Nat. Protoc. (IF 14.8) Pub Date : 2024-03-11 Rafael Tapia-Rojo, Marc Mora, Sergi Garcia-Manyes
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Design and fabrication of wearable electronic textiles using twisted fiber-based threads Nat. Protoc. (IF 14.8) Pub Date : 2024-03-01 Kailin Zhang, Xiang Shi, Haibo Jiang, Kaiwen Zeng, Zihao Zhou, Peng Zhai, Lihua Zhang, Huisheng Peng
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Profiling native pulmonary basement membrane stiffness using atomic force microscopy Nat. Protoc. (IF 14.8) Pub Date : 2024-03-01 Bastian Hartmann, Lutz Fleischhauer, Monica Nicolau, Thomas Hartvig Lindkær Jensen, Florin-Andrei Taran, Hauke Clausen-Schaumann, Raphael Reuten
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Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets Nat. Protoc. (IF 14.8) Pub Date : 2024-02-29 Andreas Müller, Deborah Schmidt, Jan Philipp Albrecht, Lucas Rieckert, Maximilian Otto, Leticia Elizabeth Galicia Garcia, Gunar Fabig, Michele Solimena, Martin Weigert
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Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy Nat. Protoc. (IF 14.8) Pub Date : 2024-02-26 G. Heinrich, M. Kondratiuk, L. J. Gooßen, M. P. Wiesenfeldt
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High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination Nat. Protoc. (IF 14.8) Pub Date : 2024-02-27 Lei Tian, Kyle Jackson, Leon He, Shadman Khan, Mathura Thirugnanasampanthar, Mellissa Gomez, Fereshteh Bayat, Tohid F. Didar, Zeinab Hosseinidoust
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Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples Nat. Protoc. (IF 14.8) Pub Date : 2024-02-23 Tim H. H. Coorens, Michael Spencer Chapman, Nicholas Williams, Inigo Martincorena, Michael R. Stratton, Jyoti Nangalia, Peter J. Campbell
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rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data Nat. Protoc. (IF 14.8) Pub Date : 2024-02-23 Yuanyuan Wang, Zhijie Xie, Eric Kutschera, Jenea I. Adams, Kathryn E. Kadash-Edmondson, Yi Xing
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GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout Nat. Protoc. (IF 14.8) Pub Date : 2024-02-21 David Falck, Manfred Wuhrer
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Web-based multi-omics integration using the Analyst software suite Nat. Protoc. (IF 14.8) Pub Date : 2024-02-14 Jessica D. Ewald, Guangyan Zhou, Yao Lu, Jelena Kolic, Cara Ellis, James D. Johnson, Patrick E. Macdonald, Jianguo Xia
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Isoform-specific RNA structure determination using Nano-DMS-MaP Nat. Protoc. (IF 14.8) Pub Date : 2024-02-12 Anne-Sophie Gribling-Burrer, Patrick Bohn, Redmond P. Smyth
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Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models Nat. Protoc. (IF 14.8) Pub Date : 2024-02-08 John M. Ball, Wei Li
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Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements) Nat. Protoc. (IF 14.8) Pub Date : 2024-02-07 Francisco M. Barriga, Scott W. Lowe
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Functionalized tetrahedral DNA frameworks for the capture of circulating tumor cells Nat. Protoc. (IF 14.8) Pub Date : 2024-02-05 Yirong Chen, Meihua Lin, Dekai Ye, Shaopeng Wang, Xiaolei Zuo, Min Li
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Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors Nat. Protoc. (IF 14.8) Pub Date : 2024-02-02 Aoxue Wang, Yejun Zou, Shuning Liu, Xiuze Zhang, Ting Li, Lijuan Zhang, Ruwen Wang, Yale Xia, Xie Li, Zhuo Zhang, Tiemin Liu, Zhenyu Ju, Ru Wang, Joseph Loscalzo, Yi Yang, Yuzheng Zhao
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Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids Nat. Protoc. (IF 14.8) Pub Date : 2024-02-01 João Pedro Alves-Lopes, Frederick C. K. Wong, M. Azim Surani
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Quantitative profiling of posttranslational modifications of pathological tau via sarkosyl fractionation and mass spectrometry Nat. Protoc. (IF 14.8) Pub Date : 2024-01-30 Kathrin Wenger, Arthur Viode, Mukesh Kumar, Hanno Steen, Judith A. Steen
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Mapping protein–RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2) Nat. Protoc. (IF 14.8) Pub Date : 2024-01-26 Martin Lewinski, Mirko Brüggemann, Tino Köster, Marlene Reichel, Thorsten Bergelt, Katja Meyer, Julian König, Kathi Zarnack, Dorothee Staiger
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Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments Nat. Protoc. (IF 14.8) Pub Date : 2024-01-24 Coral Barcenilla, José F. Cobo-Díaz, Francesca De Filippis, Vincenzo Valentino, Raul Cabrera Rubio, Dominic O’Neil, Lisa Mahler de Sanchez, Federica Armanini, Niccolò Carlino, Aitor Blanco-Míguez, Federica Pinto, Inés Calvete-Torre, Carlos Sabater, Susana Delgado, Patricia Ruas-Madiedo, Narciso M. Quijada, Monika Dzieciol, Sigurlaug Skírnisdóttir, Stephen Knobloch, Alba Puente, Mercedes López, Miguel
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An end-to-end workflow for nondestructive 3D pathology Nat. Protoc. (IF 14.8) Pub Date : 2024-01-23 Kevin W. Bishop, Lindsey A. Erion Barner, Qinghua Han, Elena Baraznenok, Lydia Lan, Chetan Poudel, Gan Gao, Robert B. Serafin, Sarah S. L. Chow, Adam K. Glaser, Andrew Janowczyk, David Brenes, Hongyi Huang, Dominie Miyasato, Lawrence D. True, Soyoung Kang, Joshua C. Vaughan, Jonathan T. C. Liu
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OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds Nat. Protoc. (IF 14.8) Pub Date : 2024-01-23 Jiacai Yi, Shaohua Shi, Li Fu, Ziyi Yang, Pengfei Nie, Aiping Lu, Chengkun Wu, Yafeng Deng, Changyu Hsieh, Xiangxiang Zeng, Tingjun Hou, Dongsheng Cao
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GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution Nat. Protoc. (IF 14.8) Pub Date : 2024-01-22 Weiguo Shen, Hanxiao Sun, Cong Liu, Yunpeng Yi, Yongkang Hou, Ye Xiao, Yufei Hu, Bo Lu, Jinying Peng, Jing Wang, Chengqi Yi
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Irreversible light-activated SpyLigation mediates split-protein assembly in 4D Nat. Protoc. (IF 14.8) Pub Date : 2024-01-22 Brizzia G. Munoz-Robles, Cole A. DeForest
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Production and use of antigen tetramers to study antigen-specific B cells Nat. Protoc. (IF 14.8) Pub Date : 2024-01-19 Allyssa Phelps, Diego Pazos-Castro, Francesca Urselli, Emily Grydziuszko, Olivia Mann-Delany, Allison Fang, Tina D. Walker, Rangana Talpe Guruge, Jaime Tome-Amat, Araceli Diaz-Perales, Susan Waserman, Jim Boonyaratanakornkit, Manel Jordana, Justin J. Taylor, Joshua F. E. Koenig
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Hyperspectral confocal imaging for high-throughput readout and analysis of bio-integrated microlasers Nat. Protoc. (IF 14.8) Pub Date : 2024-01-18 Vera M. Titze, Soraya Caixeiro, Vinh San Dinh, Matthias König, Matthias Rübsam, Nachiket Pathak, Anna-Lena Schumacher, Maximilian Germer, Christian Kukat, Carien M. Niessen, Marcel Schubert, Malte C. Gather
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Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0 Nat. Protoc. (IF 14.8) Pub Date : 2024-01-18 Yu Chen, Johan Gustafsson, Albert Tafur Rangel, Mihail Anton, Iván Domenzain, Cheewin Kittikunapong, Feiran Li, Le Yuan, Jens Nielsen, Eduard J. Kerkhoven
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Bacterial genome engineering using CRISPR-associated transposases Nat. Protoc. (IF 14.8) Pub Date : 2024-01-12 Diego Rivera Gelsinger, Phuc Leo H. Vo, Sanne E. Klompe, Carlotta Ronda, Harris H. Wang, Samuel H. Sternberg
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Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy Nat. Protoc. (IF 14.8) Pub Date : 2024-01-11 Duo Zhang, Abigail H. Cleveland, Elisavet Krimitza, Katherine Han, Chenlong Yi, Andrea L. Stout, Wei Zou, Jay F. Dorsey, Yanqing Gong, Yi Fan
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Streamlining spatial omics data analysis with Pysodb Nat. Protoc. (IF 14.8) Pub Date : 2023-12-22 Senlin Lin, Fangyuan Zhao, Zihan Wu, Jianhua Yao, Yi Zhao, Zhiyuan Yuan
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Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution Nat. Protoc. (IF 14.8) Pub Date : 2023-12-21 José Ramón Bárcenas-Walls, Federico Ansaloni, Bastien Hervé, Emilia Strandback, Tomas Nyman, Gonçalo Castelo-Branco, Marek Bartošovič
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Collections from Nature Protocols Nat. Protoc. (IF 14.8) Pub Date : 2023-12-19
In 2023, Nature Protocols launched four new collections (on organoids, neural probes, cognitive neuroscience frameworks and neurostimulation) to help readers navigate our content and highlight areas of particular current interest.
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Profiling human brain vascular cells using single-cell transcriptomics and organoids Nat. Protoc. (IF 14.8) Pub Date : 2023-12-15 Elizabeth E. Crouch, Loukas N. Diafos, Edward J. Valenzuela, Kaylee Wedderburn-Pugh, Janeth Ochoa Birrueta, Jaela Caston, Tara Joseph, Madeline G. Andrews, Aparna Bhaduri, Eric J. Huang
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Design and build of small-scale magnetic soft-bodied robots with multimodal locomotion Nat. Protoc. (IF 14.8) Pub Date : 2023-12-14 Ziyu Ren, Metin Sitti
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High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities Nat. Protoc. (IF 14.8) Pub Date : 2023-12-13 Patrick Müller, Jacobo de la Cuesta-Zuluaga, Michael Kuhn, Maral Baghai Arassi, Tim Treis, Sonja Blasche, Michael Zimmermann, Peer Bork, Kiran Raosaheb Patil, Athanasios Typas, Sarela Garcia-Santamarina, Lisa Maier
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Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice Nat. Protoc. (IF 14.8) Pub Date : 2023-12-13 Kris G. Samsom, Linda J. W. Bosch, Luuk J. Schipper, Daoin Schout, Paul Roepman, Mirjam C. Boelens, Ferry Lalezari, Elisabeth G. Klompenhouwer, Adrianus J. de Langen, Tineke E. Buffart, Berit M. H. van Linder, Kelly van Deventer, Kay van den Burg, Unga Unmehopa, Efraim H. Rosenberg, Roelof Koster, Frans B. L. Hogervorst, José G. van den Berg, Immy Riethorst, Lieke Schoenmaker, Daphne van Beek, Ewart
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Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz Nat. Protoc. (IF 14.8) Pub Date : 2023-12-12 Marco Schiavina, Lorenzo Bracaglia, Maria Anna Rodella, Rainer Kümmerle, Robert Konrat, Isabella C. Felli, Roberta Pierattelli
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Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy Nat. Protoc. (IF 14.8) Pub Date : 2023-12-12 Benjamin W. Gregor, Mackenzie E. Coston, Ellen M. Adams, Joy Arakaki, Antoine Borensztejn, Thao P. Do, Margaret A. Fuqua, Amanda Haupt, Melissa C. Hendershott, Winnie Leung, Irina A. Mueller, Aditya Nath, Angelique M. Nelson, Susanne M. Rafelski, Emmanuel E. Sanchez, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Winfried Wiegraebe, Brian P. Whitney, Calysta Yan, Ruwanthi N. Gunawardane
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In vivo identification of astrocyte and neuron subproteomes by proximity-dependent biotinylation Nat. Protoc. (IF 14.8) Pub Date : 2023-12-07 Joselyn S. Soto, Yasaman Jami-Alahmadi, James A. Wohlschlegel, Baljit S. Khakh
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Head-mounted central venous access during optical recordings and manipulations of neural activity in mice Nat. Protoc. (IF 14.8) Pub Date : 2023-12-06 Christine Liu, Daniel J. Freeman, Stephan Lammel
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Small RNA structural biochemistry in a post-sequencing era Nat. Protoc. (IF 14.8) Pub Date : 2023-12-06 Juan Pablo Tosar, Mauricio Castellano, Bruno Costa, Alfonso Cayota
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Synthesis and functionalization of scalable and versatile 2D protein films via amyloid-like aggregation Nat. Protoc. (IF 14.8) Pub Date : 2023-12-04 Yongchun Liu, Shuting Miao, Hao Ren, Lihua Tian, Jian Zhao, Peng Yang
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Biomimetic tail-to-head terpene cyclizations using the resorcin[4]arene capsule catalyst Nat. Protoc. (IF 14.8) Pub Date : 2023-12-01 Ivan Cornu, Leonidas-Dimitrios Syntrivanis, Konrad Tiefenbacher
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Reproducible strategy for excisional skin-wound-healing studies in mice Nat. Protoc. (IF 14.8) Pub Date : 2023-11-29 Matan Yampolsky, Ido Bachelet, Yaron Fuchs
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CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction Nat. Protoc. (IF 14.8) Pub Date : 2023-11-28 Kristiana Grigoriadis, Ariana Huebner, Abigail Bunkum, Emma Colliver, Alexander M. Frankell, Mark S. Hill, Kerstin Thol, Nicolai J. Birkbak, Charles Swanton, Simone Zaccaria, Nicholas McGranahan
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A platform for whole-genome speed introgression from Aegilops tauschii to wheat for breeding future crops Nat. Protoc. (IF 14.8) Pub Date : 2023-11-28 Hao Li, Lele Zhu, Ruixiao Fan, Zheng Li, Yifan Liu, Aaqib Shaheen, Fang Nie, Can Li, Xuqin Liu, Yuanyuan Li, Wenjuan Liu, Yingying Yang, Tutu Guo, Yu Zhu, Mengchen Bu, Chenglin Li, Huihui Liang, Shenglong Bai, Feifei Ma, Guanghui Guo, Zhen Zhang, Jinling Huang, Yun Zhou, Chun-Peng Song
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Spatiotemporal control of RNA metabolism and CRISPR–Cas functions using engineered photoswitchable RNA-binding proteins Nat. Protoc. (IF 14.8) Pub Date : 2023-11-30 Renmei Liu, Jing Yao, Siyu Zhou, Jing Yang, Yaqiang Zhang, Xiaoyan Yang, Leshi Li, Yunbin Zhang, Yingping Zhuang, Yi Yang, Xianjun Chen
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Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input Nat. Protoc. (IF 14.8) Pub Date : 2023-11-29 Tetsuya Handa, Akihito Harada, Kazumitsu Maehara, Shoko Sato, Masaru Nakao, Naoki Goto, Hitoshi Kurumizaka, Yasuyuki Ohkawa, Hiroshi Kimura
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High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ Nat. Protoc. (IF 14.8) Pub Date : 2023-11-27 Jianshi Jin, Reiko Yamamoto, Katsuyuki Shiroguchi
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Fabrication of angstrom-scale two-dimensional channels for mass transport Nat. Protoc. (IF 14.8) Pub Date : 2023-11-27 Ankit Bhardwaj, Marcos Vinicius Surmani Martins, Yi You, Ravalika Sajja, Max Rimmer, Solleti Goutham, Rongrong Qi, Sidra Abbas Dar, Boya Radha, Ashok Keerthi
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Ultra-fast supercritically solvothermal polymerization for large single-crystalline covalent organic frameworks Nat. Protoc. (IF 14.8) Pub Date : 2023-11-24 Jiang Sun, Xuejun Wang, Qiankun Wang, Lan Peng, Yunqi Liu, Dacheng Wei
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Robust scoring of selective drug responses for patient-tailored therapy selection Nat. Protoc. (IF 14.8) Pub Date : 2023-11-23 Yingjia Chen, Liye He, Aleksandr Ianevski, Pilar Ayuda-Durán, Swapnil Potdar, Jani Saarela, Juho J. Miettinen, Sari Kytölä, Susanna Miettinen, Mikko Manninen, Caroline A. Heckman, Jorrit M. Enserink, Krister Wennerberg, Tero Aittokallio
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Analyzing somatic mutations by single-cell whole-genome sequencing Nat. Protoc. (IF 14.8) Pub Date : 2023-11-23 Lei Zhang, Moonsook Lee, Alexander Y. Maslov, Cristina Montagna, Jan Vijg, Xiao Dong
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Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS Nat. Protoc. (IF 14.8) Pub Date : 2023-11-21 Jeanette A. I. Johnson, Ashley P. Tsang, Jacob T. Mitchell, David L. Zhou, Julia Bowden, Emily Davis-Marcisak, Thomas Sherman, Ted Liefeld, Melanie Loth, Loyal A. Goff, Jacquelyn W. Zimmerman, Ben Kinny-Köster, Elizabeth M. Jaffee, Pablo Tamayo, Jill P. Mesirov, Michael Reich, Elana J. Fertig, Genevieve L. Stein-O’Brien
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Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain Nat. Protoc. (IF 14.8) Pub Date : 2023-11-20 Mara Zilocchi, Matineh Rahmatbakhsh, Mohamed Taha Moutaoufik, Kirsten Broderick, Alla Gagarinova, Matthew Jessulat, Sadhna Phanse, Hiroyuki Aoki, Khaled A. Aly, Mohan Babu
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A nanobody-based strategy for rapid and scalable purification of human protein complexes Nat. Protoc. (IF 14.8) Pub Date : 2023-11-16 Taylor Anthony Stevens, Giovani Pinton Tomaleri, Masami Hazu, Sophia Wei, Vy N. Nguyen, Charlene DeKalb, Rebecca M. Voorhees, Tino Pleiner
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Genetic manipulation of giant viruses and their host, Acanthamoeba castellanii Nat. Protoc. (IF 14.8) Pub Date : 2023-11-14 Nadege Philippe, Avi Shukla, Chantal Abergel, Hugo Bisio
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BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution Nat. Protoc. (IF 14.8) Pub Date : 2023-11-15 Li-Sheng Zhang, Chang Ye, Cheng-Wei Ju, Boyang Gao, Xinran Feng, Hui-Lung Sun, Jiangbo Wei, Fan Yang, Qing Dai, Chuan He
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In situ label-free X-ray imaging for visualizing the localization of nanomedicines and subcellular architecture in intact single cells Nat. Protoc. (IF 14.8) Pub Date : 2023-11-13 Mingjing Cao, Yaling Wang, Liming Wang, Kai Zhang, Yong Guan, Yuecong Guo, Chunying Chen