• Cell Genomics  ·  April 28, 2022

    Benchmarking challenging small variants with linked and long reads.

    Justin Wagner, Nathan D Olson, Lindsay Harris, Ziad Khan, Jesse Farek, Medhat Mahmoud, Ana Stankovic, Vladimir Kovacevic, Aaron M Wenger, William J Rowell, Chunlin Xiao, Byunggil Yoo, Neil Miller, Jeffrey A Rosenfeld, Bohan Ni, Samantha Zarate, Melanie Kirsche, Sergey Aganezov, Michael Schatz, Giuseppe Narzisi, Marta Byrska-Bishop, Wayne Clarke, Uday S Evani, Charles Markello, Kishwar Shafin, Xin Zhou, Arend Sidow, Vikas Bansal, Alvaro Martinez Barrio, Ian T Fiddes, Arkarachai Fungtammasan, Chen-Shan Chin, Fritz J Sedlazeck, Andrew Carroll, Marc Salit, Justin M Zook, Genome in a Bottle Consortium
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  • bioRxiv  ·  April 19, 2022  ·  Preprint

    Predicting A/B compartments from histone modifications using deep learning.

    Suchen Zheng, Nitya Thakkar, Hannah L. Harris, Megan Zhang, Susanna Liu, Mark Gerstein, Erez Lieberman-Aiden, M. Jordan Rowley, William Stafford Noble, Gamze Gürsoy, Ritambhara Singh

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  • Nature Genetics  ·  April 11, 2022

    Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes.

    Jana Ebler, Peter Ebert, Wayne E. Clarke, Tobias Rausch, Peter A. Audano, Torsten Houwaart, Yafei Mao, Jan O. Korbel, Evan E. Eichler, Michael C. Zody, Alexander T. Dilthey & Tobias Marschall

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  • npj Genomic Medicine  ·  April 8, 2022

    Best practices for the interpretation and reporting of clinical whole genome sequencing.

    Christina A. Austin-Tse, Vaidehi Jobanputra, Denise L. Perry, David Bick, Ryan J. Taft, Eric Venner, Richard A. Gibbs, Ted Young, Sarah Barnett, John W. Belmont, Nicole Boczek, Shimul Chowdhury, Katarzyna A. Ellsworth, Saurav Guha, Shashikant Kulkarni, Cherisse Marcou, Linyan Meng, David R. Murdock, Atteeq U. Rehman, Elizabeth Spiteri, Amanda Thomas-Wilson, Hutton M. Kearney, Heidi L. Rehm & Medical Genome Initiative*

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  • Cell Stem Cell  ·  April 7, 2022

    Specification of fetal liver endothelial progenitors to functional zonated adult sinusoids requires c-Maf induction.

    Jesus Maria Gómez-Salinero, Franco Izzo, Yang Lin, Sean Houghton, Tomer Itkin, Fuqiang Geng, Yaron Bram, Robert P Adelson, Tyler M Lu, Giorgio Inghirami, Jenny Zhaoying Xiang, Raphael Lis, David Redmond, Ryan Schreiner, Sina Y Rabbany, Dan A Landau, Robert E Schwartz, Shahin Rafii

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  • Nature Neuroscience  ·  March 31, 2022

    Whole-genome sequencing reveals that variants in the Interleukin 18 Receptor Accessory Protein 3′UTR protect against ALS.

    Chen Eitan, Aviad Siany, Elad Barkan, Tsviya Olender, Kristel R. van Eijk, Matthieu Moisse, Sali M. K. Farhan, Yehuda M. Danino, Eran Yanowski, Hagai Marmor-Kollet, Natalia Rivkin, Nancy Sarah Yacovzada, Shu-Ting Hung, Johnathan Cooper-Knock, Chien-Hsiung Yu, Cynthia Louis, Seth L. Masters, Kevin P. Kenna, Rick A. A. van der Spek, William Sproviero, Ahmad Al Khleifat, Alfredo Iacoangeli, Aleksey Shatunov, Ashley R. Jones, Yael Elbaz-Alon, Yahel Cohen, Elik Chapnik, Daphna Rothschild, Omer Weissbrod, Gilad Beck, Elena Ainbinder, Shifra Ben-Dor, Sebastian Werneburg, Dorothy P. Schafer, Robert H. Brown Jr, Pamela J. Shaw, Philip Van Damme, Leonard H. van den Berg, Hemali Phatnani, Eran Segal, Justin K. Ichida, Ammar Al-Chalabi, Jan H. Veldink, Project MinE ALS Sequencing Consortium, NYGC ALS Consortium & Eran Hornstein

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  • Nature Communications  ·  March 28, 2022

    Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology.

    Satria P Sajuthi, Jamie L Everman, Nathan D Jackson, Benjamin Saef, Cydney L Rios, Camille M Moore, Angel C Y Mak, Celeste Eng, Ana Fairbanks-Mahnke, Sandra Salazar, Jennifer Elhawary, Scott Huntsman, Vivian Medina, Deborah A Nickerson, Soren Germer, Michael C Zody, Gonçalo Abecasis, Hyun Min Kang, Kenneth M Rice, Rajesh Kumar, Noah A Zaitlen, Sam Oh, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; José Rodríguez-Santana, Esteban G Burchard, Max A Seibold

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  • Nature Biotechnology  ·  March 24, 2022

    Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

    Bingjie Zhang, Avi Srivastava, Eleni Mimitou, Tim Stuart, Ivan Raimondi, Yuhan Hao, Peter Smibert & Rahul Satija

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  • bioRxiv  ·  March 18, 2022  ·  Preprint

    Integrated protein and transcriptome high-throughput spatial profiling.

    Nir Ben-Chetrit, Xiang Niu, Ariel D. Swett, Jesus Sotelo, Maria S. Jiao, Patrick Roelli, Marlon Stoeckius, Dan A. Landau

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  • Nature  ·  March 16, 2022

    A genome-scale screen for synthetic drivers of T cell proliferation.

    Mateusz Legut, Zoran Gajic, Maria Guarino, Zharko Daniloski, Jahan A. Rahman, Xinhe Xue, Congyi Lu, Lu Lu, Eleni P. Mimitou, Stephanie Hao, Teresa Davoli, Catherine Diefenbach, Peter Smibert & Neville E. Sanjana

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  • Cell Reports  ·  March 15, 2022

    The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes.

    Görkem Garipler, Congyi Lu, Alexis Morrissey, Lorena S. Lopez-Zepeda, Yingzhen Pei, Simon E. Vidal, Ana Paula Zen, Petisco Fiore, Begüm Aydin, Matthias Stadtfeld, Uwe Ohler, Shaun Mahony, Neville E. Sanjana, Esteban O. Mazzoni

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  • Cell Genomics  ·  March 9, 2022

    Single nucleus multi-omics identifies human cortical cell regulatory genome diversity.

    Chongyuan Luo, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, Wayne I. Doyle, Tim Stuart, Rebecca D. Hodge, Lijuan Hu, Bang-An Wang, Zhuzhu Zhang, Sebastian Preissl, Dong-Sung Lee, Jingtian Zhou, Sheng-Yong Niu, Rosa Castanon, Anna Bartlett, Angeline Rivkin, Xinxin Wang, Jacinta Lucero, Joseph R. Nery, David A. Davis, Deborah C. Mash, Rahul Satija, Jesse R. Dixon, Sten Linnarsson, Ed Lein, M. Margarita Behrens, Bing Ren, Eran A. Mukamel, Joseph R. Ecker

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  • bioRxiv  ·  March 8, 2022  ·  Preprint

    Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution.

    Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan A Landau, Silas Maniatis, Rahul Satija, and Ivan Raimondi

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  • bioRxiv  ·  February 24, 2022  ·  Preprint

    Dictionary learning for integrative, multimodal, and scalable single-cell analysis.

    Yuhan Hao, Tim Stuart, Madeline Kowalski, Saket Choudhary, Paul Hoffman, Austin Hartman, Avi Srivastava, Gesmira Molla, Shaista Madad, Carlos Fernandez-Granda, Rahul Satija

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  • Blood  ·  February 24, 2022

    A BAX door to venetoclax resistance.

    Franco Izzo, Dan A. Landau

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  • Nature  ·  February 23, 2022

    TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A.

    Anna-Leigh Brown, Oscar G. Wilkins, Matthew J. Keuss, Sarah E. Hill, Matteo Zanovello, Weaverly Colleen Lee, Alexander Bampton, Flora C. Y. Lee, Laura Masino, Yue A. Qi, Sam Bryce-Smith, Ariana Gatt, Martina Hallegger, Delphine Fagegaltier, Hemali Phatnani, NYGC ALS Consortium, Jia Newcombe, Emil K. Gustavsson, Sahba Seddighi, Joel F. Reyes, Steven L. Coon, Daniel Ramos, Giampietro Schiavo, Elizabeth M. C. Fisher, Towfique Raj, Maria Secrier, Tammaryn Lashley, Jernej Ule, Emanuele Buratti, Jack Humphrey, Michael E. Ward & Pietro Fratta

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  • Cell Reports Medicine  ·  February 15, 2022

    System-wide transcriptome damage and tissue identity loss in COVID-19 patients.

    Jiwoon Park, Jonathan Foox, Tyler Hether, David C. Danko, Sarah Warren, Youngmi Kim, Jason Reeves, Daniel J. Butler, Christopher Mozsary, Joel Rosiene, Alon Shaiber, Evan E. Afshin, Matthew MacKay, Andre´ F. Rendeiro, Yaron Bram, Vasuretha Chandar, Heather Geiger, Arryn Craney, Priya Velu, Ari M. Melnick, Iman Hajirasouliha, Afshin Beheshti, Deanne Taylor, Amanda Saravia-Butler, Urminder Singh, Eve Syrkin Wurtele, Jonathan Schisler, Samantha Fennessey, Andre´ Corvelo, Michael C. Zody, Soren Germer, Steven Salvatore, Shawn Levy, Shixiu Wu, Nicholas P. Tatonetti, Sagi Shapira,22 Mirella Salvatore,8,23 Lars F. Westblade,7,8 Melissa Cushing,7 Hanna Rennert,7 Alison J. Kriegel,24 Olivier Elemento, Marcin Imielinski, Charles M. Rice, Alain C. Borczuk, Cem Meydan, Robert E. Schwartz, and Christopher E. Mason

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  • Nature Communications  ·  February 11, 2022

    Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.

    Sanja Vicković, Denis Schapiro, Konstantin Carlberg, Britta Lötstedt, Ludvig Larsson, Franziska Hildebrandt, Marina Korotkova, Aase H. Hensvold, Anca I. Catrina, Peter K. Sorger, Vivianne Malmström, Aviv Regev & Patrik L. Ståhl

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  • Nature Biotechnology  ·  February 7, 2022

    Curated variation benchmarks for challenging medically relevant autosomal genes.

    Justin Wagner, Nathan D Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Arkarachai Fungtammasan, Yih-Chii Hwang, Richa Gupta, Aaron M Wenger, William J Rowell, Ziad M Khan, Jesse Farek, Yiming Zhu, Aishwarya Pisupati, Medhat Mahmoud, Chunlin Xiao, Byunggil Yoo, Sayed Mohammad Ebrahim Sahraeian, Danny E Miller, David Jaspez, Jose M Lorenzo-Salazar, Adrian Munoz-Barrera, Luis A Rubio-Rodriguez, Carlos Flores, Giuseppe Narzisi, Uday Shanker Evani, Wayne E Clarke, Joyce Lee, Christopher E Mason, Stephen E Lincoln, Karen H. Miga, Mark TW Ebbert, Alaina Shumate, Heng Li, Chen-Shan Chin, Justin M Zook, Fritz J Sedlazeck

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