VISTA : visualizing global DNA sequence alignments of arbitrary length by Mayor, Chris, Brudno, Michael, Schwartz, Jody R., Poliakov, Alexander, Rubin, Edward M., Frazer, Kelly A., Pachter, Lior S., Dubchak, Inna

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A multimodal cell census and atlas of the mammalian primary motor cortex by Callaway, Edward M., Dong, Hong-Wei, Ecker, Joseph R., Hawrylycz, Michael J., Huang, Z. Josh, Lein, Ed S., Ngai, John, Osten, Pavel, Ren, Bing, Tolias, Andreas Savas, White, Owen, Zeng, Hongkui, Zhuang, Xiaowei, Ascoli, Giorgio A., Behrens, M. Margarita, Chun, Jerold, Feng, Guoping, Gee, James C., Ghosh, Satrajit S., Halchenko, Yaroslav O., Hertzano, Ronna, Lim, Byung Kook, Martone, Maryann E., Ng, Lydia, Pachter, Lior, Ropelewski, Alexander J., Tickle, Timothy L., Yang, X. William, Zhang, Kun, Bakken, Trygve E., Berens, Philipp, Daigle, Tanya L., Harris, Julie A., Jorstad, Nikolas L., Kalmbach, Brian E., Kobak, Dmitry, Li, Yang Eric, Liu, Hanqing, Matho, Katherine S., Mukamel, Eran A., Naeemi, Maitham, Scala, Federico, Tan, Pengcheng, Ting, Jonathan T., Xie, Fangming, Zhang, Meng, Zhang, Zhuzhu, Zhou, Jingtian, Zingg, Brian, Armand, Ethan, Yao, Zizhen, Bertagnolli, Darren, Casper, Tamara, Crichton, Kirsten, Dee, Nick, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Dougherty, Elizabeth L., Fong, Olivia, Goldman, Melissa, Goldy, Jeff, Hodge, Rebecca D., Hu, Lijuan, Keene, C. Dirk, Krienen, Fenna M., Kroll, Matthew, Lake, Blue B., Lathia, Kanan, Linnarsson, Sten, Liu, Christine S., Macosko, Evan Z., McCarroll, Steven A., McMillen, Delissa, Nadaf, Naeem M., Nguyen, Thuc Nghi, Palmer, Carter R., Pham, Thanh, Plongthongkum, Nongluk, Reed, Nora M., Regev, Aviv, Rimorin, Christine, Romanow, William J., Savoia, Steven, Siletti, Kimberly, Smith, Kimberly, Sulc, Josef, Tasic, Bosiljka, Tieu, Michael, Torkelson, Amy, Tung, Herman, van Velthoven, Cindy T. J., Vanderburg, Charles R., Yanny, Anna Marie, Fang, Rongxin, Hou, Xiaomeng, Lucero, Jacinta D., Osteen, Julia K., Pinto-Duarte, Antonio, Poirion, Olivier

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Deciphering the impact of genomic variation on function by Engreitz, Jesse M., Lawson, Heather A., Singh, Harinder, Starita, Lea M., Hon, Gary C., Carter, Hannah, Sahni, Nidhi, Reddy, Timothy E., Lin, Xihong, Li, Yun, Munshi, Nikhil V., Chahrour, Maria H., Boyle, Alan P., Hitz, Benjamin C., Mortazavi, Ali, Craven, Mark, Mohlke, Karen L., Pinello, Luca, Wang, Ting, Kundaje, Anshul, Yue, Feng, Cody, Sarah, Farrell, Nina P., Love, Michael I., Muffley, Lara A., Pazin, Michael J., Reese, Fairlie, Van Buren, Eric, Dey, Kushal K., Kircher, Martin, Ma, Jian, Radivojac, Predrag, Balliu, Brunilda, Williams, Brian A., Huangfu, Danwei, Park, Chong Y., Quertermous, Thomas, Das, Jishnu, Calderwood, Michael A., Fowler, Douglas M., Vidal, Marc, Ferreira, Lucas, Mooney, Sean D., Pejaver, Vikas, Zhao, Jingjing, Gazal, Steven, Koch, Evan, Reilly, Steven K., Sunyaev, Shamil, Carpenter, Anne E., Buenrostro, Jason D., Leslie, Christina S., Savage, Rachel E., Giric, Stefanija, Luo, Chongyuan, Plath, Kathrin, Barrera, Alejandro, Schubach, Max, Gschwind, Andreas R., Moore, Jill E., Ahituv, Nadav, Yi, S. Stephen, Hallgrimsdottir, Ingileif, Gaulton, Kyle J., Sakaue, Saori, Booeshaghi, Sina, Mattei, Eugenio, Nair, Surag, Pachter, Lior, Wang, Austin T., Shendure, Jay, Agarwal, Vikram, Blair, Andrew, Chalkiadakis, Theofilos, Chardon, Florence M., Dash, Pyaree M., Deng, Chengyu, Hamazaki, Nobuhiko, Keukeleire, Pia, Kubo, Connor, Lalanne, Jean-Benoît, Maass, Thorben, Martin, Beth, McDiarmid, Troy A., Nobuhara, Mai, Page, Nicholas F., Regalado, Sam, Sims, Jasmine, Ushiki, Aki, Best, Sabrina M., Boyle, Gabe, Camp, Nathan, Casadei, Silvia, Da, Estelle Y., Dawood, Moez, Dawson, Samantha C., Fayer, Shawn, Hamm, Audrey, James, Richard G., Jarvik, Gail P.

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Optimization of Air Vehicle Operations Using Mixed-Integer Linear Programming by Schumacher, Corey, Chandler, Phillip R, Pachter, Meir, Pachter, Lior S

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The specious art of single-cell genomics by Chari, Tara, Pachter, Lior

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Modeling bursty transcription and splicing with the chemical master equation by Gorin, Gennady, Pachter, Lior

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Efficient querying of genomic reference databases with gget by Luebbert, Laura, Pachter, Lior

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RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq by Svensson, Valentine, Pachter, Lior

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Interpretable factor models of single-cell RNA-seq via variational autoencoders by Svensson, Valentine, Gayoso, Adam, Yosef, Nir, Pachter, Lior

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New and notable: Revisiting the “two cultures” through extrinsic noise by Gorin, Gennady, Pachter, Lior

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Identification of novel transcripts in annotated genomes using RNA-Seq by ROBERTS, Adam, PIMENTEL, Harold, TRAPNELL, Cole, PACHTER, Lior

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RNA velocity unraveled by Gorin, Gennady, Fang, Meichen, Chari, Tara, Pachter, Lior

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SWALO: scaffolding with assembly likelihood optimization by Rahman, Atif, Pachter, Lior

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Protein velocity and acceleration from single-cell multiomics experiments by Gorin, Gennady, Svensson, Valentine, Pachter, Lior

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Association mapping from sequencing reads using k -mers by Rahman, Atif, Hallgrímsdóttir, Ingileif, Eisen, Michael, Pachter, Lior

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Analysis of Length Biases in Single-Cell RNA Sequencing of Unspliced mRNA by Markov Modeling by Gorin, Gennady, Pachter, Lior

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A curated database reveals trends in single-cell transcriptomics by Svensson, Valentine, da Veiga Beltrame, Eduardo, Pachter, Lior

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Near-optimal probabilistic RNA-seq quantification by Bray, Nicolas L, Pimentel, Harold, Melsted, Páll, Pachter, Lior

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Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing by Gorin, Gennady, Yoshida, Shawn, Pachter, Lior

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Barcode identification for single cell genomics by Tambe, Akshay, Pachter, Lior

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