Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems by Alon, Shahar, Goodwin, Daniel Robert, Sinha, Anubhav, Wassie, Asmamaw T., Chen, Fei, Daugharthy, Evan R, Bando, Yosuke, Kajita, Atsushi, Xue, Andrew G., Marrett, Karl, Prior, Robert, Cui, Yi, Payne, Andrew C, Yao, Chun-Chen, Suk, Ho-Jun., Wang, Ru, Yu, Chih-Chieh, Tillberg, Paul W., Reginato, Paul Louis, Pak, Nikita, Liu, Songlei, Punthambaker, Sukanya, Iyer, Eswar P. R., Kohman, Richie E, Miller, Jeremy A, Lein, Ed S, Lako, Ana, Cullen, Nicole, Rodig, Scott, Helvie, Karla, Abravanel, Daniel L, Wagle, Nikhil, Johnson, Bruce E, Klughammer, Johanna, Slyper, Michal, Waldman, Julia, Jané-Valbuena, Judit, Rozenblatt-Rosen, Orit, Regev, Aviv, IMAXT Consortium, Church, George M, Marblestone, Adam Henry, Boyden, Edward

“…We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. …”
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Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate by Mertins, Philipp, Regev, Aviv

Subjects: “…Cell Biology…”
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The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution by Regev, Aviv

Subjects: “…Developmental Biology…”
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The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease by Regev, Aviv

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Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming by Cleary, Brian Lowman, Lin, Stacie, Jaenisch, Rudolf, Regev, Aviv, Lander, Eric Steven

Subjects: “…General Biochemistry, Genetics and Molecular Biology…”
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Combinatorial prediction of marker panels from single‐cell transcriptomic data by Regev, Aviv, Kuchroo, Vijay K, Singer, Meromit

Subjects: “…General Biochemistry, Genetics and Molecular Biology…”
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Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation by Regev, Aviv

Subjects: “…General Biochemistry, Genetics and Molecular Biology…”
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Nuclei multiplexing with barcoded antibodies for single-nucleus genomics by Regev, Aviv

Subjects: “…General Biochemistry, Genetics and Molecular Biology…”
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Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces by Ding, Jiarui, Regev, Aviv

“…<jats:title>Abstract</jats:title><jats:p>Single-cell RNA-Seq (scRNA-seq) is invaluable for studying biological systems. Dimensionality reduction is a crucial step in interpreting the relation between cells in scRNA-seq data. …”
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Evolution, Evolvability, Expression and Engineering by Vaishnav, Eeshit Dhaval

“…In the first part of this thesis, I present a framework for understanding and engineering biological sequences, and solving sequence→function problems by building ‘Complete Fitness Landscapes’ in sequence space. …”
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Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation by Ji, Zhe, He, Lizhi, Rotem, Asaf, Janzer, Andreas, Cheng, Christine S., Regev, Aviv, Struhl, Kevin

“…The combined experimental and computational pipeline represents a general approach to comprehensively identify transcriptional regulators important for a biological process.…”
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DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction by Weinstein, Joshua A., Regev, Aviv, Zhang, Feng

“…Analyzing the spatial organization of molecules in cells and tissues is a cornerstone of biological research and clinical practice. However, despite enormous progress in molecular profiling of cellular constituents, spatially mapping them remains a disjointed and specialized machinery-intensive process, relying on either light microscopy or direct physical registration. …”
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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets by Macosko, Evan Z., Satija, Rahul, Nemesh, James, Shekhar, Karthik, Goldman, Melissa, Tirosh, Itay, Bialas, Allison R., Kamitaki, Nolan, Martersteck, Emily M., Trombetta, John J., Weitz, David A., Sanes, Joshua R., McCarroll, Steven A., Shalek, Alexander K, Regev, Aviv, Basu, Anindita, 1978-

“…Cells, the basic units of biological structure and function, vary broadly in type and state. …”
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Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs by Shishkin, Alexander A., Zhu, Xiaopeng, Kadri, Sabah, Maza, Itay, Guttman, Mitchell, Hanna, Jacob H., Garber, Manuel, Chen, Jenny, Regev, Aviv

“…Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. …”
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Strategies to discover regulatory circuits of the mammalian immune system by Amit, Ido, Regev, Aviv, Hacohen, Nir

“…One application with great potential to enhance our understanding of biological systems is the unbiased reconstruction of genetic and molecular networks. …”
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Transcriptome-scale RNase-footprinting of RNA-protein complexes by Ji, Zhe, Song, Ruisheng, Huang, Hailiang, Regev, Aviv, Struhl, Kevin

“…Although only a subset of lncRNAs show RNase footprints, many of these have multiple footprints, and the protected regions are evolutionarily conserved, suggestive of biological functions.…”
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DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction by Weinstein, Joshua A, Regev, Aviv, Zhang, Feng

“…Analyzing the spatial organization of molecules in cells and tissues is a cornerstone of biological research and clinical practice. However, despite enormous progress in molecular profiling of cellular constituents, spatially mapping them remains a disjointed and specialized machinery-intensive process, relying on either light microscopy or direct physical registration. …”
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A quantitative framework for characterizing the evolutionary history of mammalian gene expression by Chen, Jenny (Jennifer), Regev, Aviv

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Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity by Kinker, Gabriela S, Greenwald, Alissa C, Tal, Rotem, Orlova, Zhanna, Cuoco, Michael S, McFarland, James M, Warren, Allison, Rodman, Christopher, Roth, Jennifer A, Bender, Samantha A, Kumar, Bhavna, Rocco, James W, Fernandes, Pedro ACM, Mader, Christopher C, Keren-Shaul, Hadas, Plotnikov, Alexander, Barr, Haim, Tsherniak, Aviad, Rozenblatt-Rosen, Orit, Krizhanovsky, Valery, Puram, Sidharth V, Regev, Aviv, Tirosh, Itay

“…These programs are associated with diverse biological processes, including cell cycle, senescence, stress and interferon responses, epithelial–mesenchymal transition and protein metabolism. …”
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A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex by Regev, Aviv

“…With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. …”
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