• Nature Genetics  ·  November 20, 2024

    Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations

    Marc J. Williams, Michael U. J. Oliphant, Vinci Au, Cathy Liu, Caroline Baril, Ciara O’Flanagan, Daniel Lai, Sean Beatty, Michael Van Vliet, Jacky CH Yiu, Lauren O’Connor, Walter L. Goh, Alicia Pollaci, Adam C. Weiner, Diljot Grewal, Andrew McPherson, Klarisa Norton, McKenna Moore, Vikas Prabhakar, Shailesh Agarwal, Judy E. Garber, Deborah A. Dillon, Sohrab P. Shah, Joan S. Brugge & Samuel Aparicio

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  • Nature Biotechnology  ·  November 21, 2024

    Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling.

    Rachel E. Yan, Alba Corman, Lyla Katgara, Xiao Wang, Xinhe Xue, Zoran Z. Gajic, Richard Sam, Michael Farid, Samuel M. Friedman, Jungwook Choo, Ivan Raimondi, Shridar Ganesan, Eugene Katsevich, Jeffrey P. Greenfield, Nadia Dahmane & Neville E. Sanjana

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  • bioRxiv  ·  November 14, 2024  ·  Preprint

    Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord.

    John F. Tuddenham, Masashi Fujita, Anthony Khairallah, Claire Harbison, Xena E. Flowers, Guillermo Coronas-Samano, Silas Maniatis, Aidan Daly, Julie A. Schneider, Andrew F. Teich, Jean Paul G. Vonsattel, Peter A. Sims, Wassim Elyaman, Elizabeth M. Bradshaw, Hemali Phatnani, Neil Shneider, David A. Bennett, Philip L. De Jager, Serge Przedborski, Vilas Menon and Marta Olah

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  • Genetics in Medicine  ·  November 12, 2024

    Upregulation vs. loss of function of NTRK2 in 44 affected individuals leads to two distinct neurodevelopmental disorders.

    Eva Berger, Robin-Tobias Jauss, Judith D Ranells, Emir Zonic, Lydia von Wintzingerode, Ashley Wilson, Johannes Wagner, Annabelle Tuttle, Amanda Thomas-Wilson, Björn Schulte, Rachel Rabin, John Pappas, Jacqueline A Odgis, Osama Muthaffar, Alejandra Mendez-Fadol, Matthew Lynch, Jonathan Levy, Daphné Lehalle, Nicole J Lake, Ilona Krey, Mariya Kozenko, Ellen Knierim, Guillaume Jouret, Vaidehi Jobanputra, Bertrand Isidor, David Hunt, Tzung-Chien Hsieh, Alexander M Holtz, Tobias B Haack, Nina B Gold, Désirée Dunstheimer, Mylène Donge, Wallid Deb, Katlin A De La Rosa Poueriet , Magdalena Danyel, John Christodoulou, Saurabh Chopra, Bert Callewaert, Andreas Busche, Lauren Brick, Bary G Bigay, Marie Arlt, Swathi S Anikar, Mohammad N Almohammal, Deanna Almanza, Amal Alhashem, Aida Bertoli-Avella, Heinrich Sticht, Rami Abou Jamra

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  • Alzheimer's & Dementia  ·  November 13, 2024

    Large-scale deep proteomic analysis in Alzheimer’s disease brain regions across race and ethnicity.

    Fatemeh Seifar, Edward J. Fox, Anantharaman Shantaraman, Yue Liu, Eric B. Dammer, Erica Modeste, Duc M. Duong, Luming Yin, Adam N. Trautwig, Qi Guo, Kaiming Xu, Lingyan Ping, Joseph S. Reddy, Mariet Allen, Zachary Quicksall, Laura Heath, Jo Scanlan, Erming Wang, Minghui Wang, Abby Vander Linden, William Poehlman, Xianfeng Chen, Saurabh Baheti, Charlotte Ho, Thuy Nguyen, Geovanna Yepez, Adriana O. Mitchell, Stephanie R. Oatman, Xue Wang, Minerva M. Carrasquillo, Alexi Runnels, Thomas Beach, Geidy E. Serrano, Dennis W. Dickson, Edward B. Lee, Todd E. Golde, Stefan Prokop, Lisa L. Barnes, Bin Zhang, Varham Haroutunian, Marla Gearing, James. J Lah, Philip De Jager, David A Bennett, Anna Greenwood, Nilüfer Ertekin-Taner, Allan I. Levey, Aliza Wingo, Thomas Wingo, Nicholas T. Seyfried

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  • Cell  ·  November 7, 2024

    Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells.

    Wen-Wei Liang, Simon Müller, Sydney K. Hart, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Akash Sookdeo, Olivia Choi, Christina Caragine, Alba Corman, Lu Lu, Olena Kolumba, Breanna Williams, Neville E. Sanjana

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  • Nature  ·  October 30, 2024

    RAS-mutant leukaemia stem cells drive clinical resistance to venetoclax.

    Junya Sango, Saul Carcamo, Maria Sirenko, Abhishek Maiti, Hager Mansour, Gulay Ulukaya, Lewis E. Tomalin, Nataly Cruz-Rodriguez, Tiansu Wang, Malgorzata Olszewska, Emmanuel Olivier, Manon Jaud, Bettina Nadorp, Benjamin Kroger, Feng Hu, Lewis Silverman, Stephen S. Chung, Elvin Wagenblast, Ronan Chaligne, Ann-Kathrin Eisfeld, Deniz Demircioglu, Dan A. Landau, Piro Lito, Elli Papaemmanuil, Courtney D. DiNardo, Dan Hasson, Marina Konopleva & Eirini P. Papapetrou

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  • European Journal of Radiology  ·  October 15, 2024

    [18F]-Fluoroestradiol (FES) brain PET in the evaluation of patients with estrogen receptor positive breast cancer and known or suspected brain metastases.

    Jana Ivanidze, Arman Sharbatdaran, Aliah McCalla, Andrew Brandmaier, Eleni Andreopoulou, Massimo Cristofanilli, Tessa Cigler, Onyinye D Balogun, Rajiv S Magge, Benjamin Liechty, Nicolas A Karakatsanis, Sadek A Nehmeh ,Matthew A Agee, Jolie Jean, Joseph R Osborne, Kathryn Beal, Theodore H Schwartz, Susan C Pannullo, Jonathan P S Knisely, Rohan Ramakrishna

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  • bioRxiv  ·  October 17, 2024  ·  Preprint

    An analysis of RNA quality metrics in human brain tissue.

    Jiahe Tian, Tiffany Lam, Sophie Ross, Benjamin Ciener, Sandra Leskinen, Sharanya Sivakumar, David A Bennett, Vilas Menon, Guy M McKhann, Alexi Runnels, Andrew Teich

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  • bioRxiv  ·  October 16, 2024  ·  Preprint

    A Reproducibility Focused Meta-Analysis Method for Single-Cell Transcriptomic Case-Control Studies Uncovers Robust Differentially Expressed Genes.

    Nathan Joel Nakatsuka, Drew Adler, Longda Jiang, Austin Hartman, Evan Cheng, Eric Klann, Rahul Satija

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  • bioRxiv  ·  October 15, 2024  ·  Preprint

    Efficient indexing and querying of annotations in a pangenome graph.

    Adam M. Novak, Dickson Chung, Glenn Hickey, Sarah Djebali, Toshiyuki T. Yokoyama, Erik Garrison, Giuseppe Narzisi, Benedict Paten, Jean Monlong

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  • bioRxiv  ·  October 11, 2024  ·  Preprint

    Targetable treatment resistance in thyroid cancer with clonal hematopoiesis.

    Vera Tiedje, Pablo Sánchez Vela, Julie L. Yang, Brian R. Untch, Laura Boucai, Aaron J. Stonestrom, Alberto Bueno Costa, Sebastià Franch Expósito, Avi Srivastava, Marina Kerpelev, Jillian Greenberg, Mathew Wereski, Amanda Kulick, Kevin Chen, Tianyue Qin, Soo-Yeon Im, Aishwarya Krishnan, Anthony R. Martinez Benitez, Raquel Pluvinet, Merve Sahin, Kamal Menghrajani, Gnana P. Krishnamoorthy, Elisa de Stanchina, Ahmet Zehir, Rahul Satija, Jeffrey Knauf, Robert L Bowman, Manel Esteller, Sean Devlin, Michael F. Berger, Richard P. Koche, James A. Fagin, Ross L Levine

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  • Nature  ·  October 9, 2024

    The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution.

    Duy D. Nguyen, William F. Hooper, Weisi Liu, Timothy R. Chu, Heather Geiger, Jennifer M. Shelton, Minita Shah, Zoe R. Goldstein, Lara Winterkorn, Adrienne Helland, Michael Sigouros, Jyothi Manohar, Jenna Moyer, Majd Al Assaad, Alissa Semaan, Sandra Cohen, Florencia Madorsky Rowdo, David Wilkes, Mohamed Osman, Rahul R. Singh, Andrea Sboner, Henkel L. Valentine, Phillip Abbosh, Scott T. Tagawa, David M. Nanus, Jones T. Nauseef, Cora N. Sternberg, Ana M. Molina, Douglas Scherr, Giorgio Inghirami, Juan Miguel Mosquera, Olivier Elemento, Nicolas Robine & Bishoy M. Faltas

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  • Nature Biotechnology  ·  October 7, 2024

    Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap.

    Jiacheng Gu, Abhishek Iyer, Ben Wesley, Angelo Taglialatela, Giuseppe Leuzzi, Sho Hangai, Aubrianna Decker, Ruoyu Gu, Naomi Klickstein, Yuanlong Shuai, Kristina Jankovic, Lucy Parker-Burns, Yinuo Jin, Jia Yi Zhang, Justin Hong, Xiang Niu, Jonathon A. Costa, Mikael G. Pezet, Jacqueline Chou, Hans-Willem Snoeck, Dan A. Landau, Elham Azizi, Edmond M. Chan, Alberto Ciccia & Jellert T. Gaublomme

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  • American Journal of Human Genetics  ·  October 3, 2024

    Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies.

    Derek Shyr, Rounak Dey, Xihao Li, Hufeng Zhou, Eric Boerwinkle, Steve Buyske, Mark Daly, Richard A Gibbs, Ira Hall, Tara Matise, Catherine Reeves, Nathan O Stitziel, Michael Zody, Benjamin M Neale, Xihong Lin

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  • Genome Research  ·  October 2, 2024

    High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.

    Jonas A Gustafson, Sophia B Gibson, Nikhita Damaraju, Miranda PG Zalusky, Kendra Hoekzema, David Twesigomwe, Lei Yang, Anthony A Snead, Phillip A Richmond, Wouter De Coster, Nathan D Olson, Andrea Guarracino, Qiuhui Li, Angela L Miller, Joy Goffena, Zachery B Anderson, Sophie HR Storz, Sydney A Ward, Maisha Sinha, Claudia Gonzaga-Jauregui, Wayne E Clarke, Anna O Basile, Andre Corvelo, Catherine E Reeves, Adrienne Helland, Rajeeva Lochan Musunuri, Mahler Revsine, Karynne E Patterson, Cate Paschal, Christina Zakarian, Sara Goodwin, Tanner D Jensen, Esther Robb, 1000 Genomes ONT Sequencing Consortium, University of Washington Center for Rare Disease Research (UW-CRDR), Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium, W. Richard McCombie, Fritz J Sedlazeck, Justin M Zook, Stephen B Montgomery, Erik Garrison, Mikhail Kolmogorov, Michael C Schatz, Richard N McLaughlin Jr., Harriet Dashnow, Michael C Zody, Matthew Loose, Miten Jain, Evan E Eichler and Danny E. Miller

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  • Cell  ·  October 2, 2024

    Private information leakage from single-cell count matrices.

    Conor R. Walker, Xiaoting Li, Manav Chakravarthy, William Lounsbery-Scaife, Yoolim A. Choi, Ritambhara Singh, Gamze Gürsoy

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  • bioRxiv  ·  September 25, 2024  ·  Preprint

    Complex genetic variation in nearly complete human genomes.

    Glennis A. Logsdon, Peter Ebert, Peter A. Audano, Mark Loftus, David Porubsky, Jana Ebler, Feyza Yilmaz, Pille Hallast, Timofey Prodanov, DongAhn Yoo, Carolyn A. Paisie, William T. Harvey, Xuefang Zhao, Gianni V. Martino, Mir Henglin, Katherine M. Munson, Keon Rabbani, Chen-Shan Chin, Bida Gu, Hufsah Ashraf, Olanrewaju Austine-Orimoloye, Parithi Balachandran, Marc Jan Bonder, Haoyu Cheng, Zechen Chong, Jonathan Crabtree, Mark Gerstein, Lisbeth A Guethlein, Patrick Hasenfeld, Glenn Hickey, Kendra Hoekzema, Sarah E Hunt, Matthew Jensen, Yunzhe Jiang, Sergey Koren, Youngjun Kwon, Chong Li, Heng Li, Jiaqi Li, Paul J Norman, Keisuke K. Oshima, Benedict Paten, Adam M. Phillippy, Nicholas R Pollock, Tobias Rausch, Mikko Rautiainen, Stephan Scholz, Yuwei Song, Arda Soylev, Arvis Sulovari, Likhitha Surapaneni, Vasiliki Tsapalou, Weichen Zhou, Ying Zhou, Qihui Zhu, Michael C. Zody, Ryan E. Mills, Scott E. Devine, Xinghua Shi, Mike E Talkowski, Mark J.P. Chaisson, Alexander T Dilthey, Miriam K. Konkel, Jan O. Korbel, Charles Lee, Christine R. Beck, Evan E. Eichler and Tobias Marschall

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  • Proceedings of the National Academy of Sciences  ·  September 23, 2024

    Nr2f1 enhancers have distinct functions in controlling Nr2f1 expression during cortical development.

    Zhidong Liu, Athéna R Ypsilanti, Eirene Markenscoff-Papadimitriou, Diane E Dickel, Stephan J Sanders, Shan Dong, Len A Pennacchio, Axel Visel, John L Rubenstein

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  • Nature Genetics  ·  September 24, 2024

    Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution.

    Joshua S. Schiffman, Andrew R. D’Avino, Tamara Prieto, Yakun Pang, Yilin Fan, Srinivas Rajagopalan, Catherine Potenski, Toshiro Hara, Mario L. Suvà, Charles Gawad & Dan A. Landau

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  • bioRxiv  ·  September 22, 2024  ·  Preprint

    Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks.

    Jennifer H. McDaniel, Vaidehi Patel, Nathan D. Olson, Hua-Jun He, Zhiyong He, Anthony Schmitt, Kristin Sikkink, Fritz Sedlazeck, Harsha Doddapaneni, Shalini N. Jhangiani, Donna M. Muzny, Marie-Claude Gingras, Heer Mehta, Luis F. Paulin, Alex R. Hastie, Hung-Chun Yu, Victor Weigman, Alison Rojas, Katie Kennedy, Jamie Remington, Isai Gonzalez, Mitch Sudkamp, Kelly Wiseman, Bryan Lajoie, Shawn Levy, Miten Jain, Stuart Akeson, Giuseppe Narzisi, Zoe Steinsnyder, Catherine Reeves, Jennifer Shelton, Sarah B. Kingan, Christine Lambert, Primo Bayabyan, Aaron M. Wenger, Ian J. McLaughlin, Aaron Adamson, Christopher Kingsley, Melanie Wescott, Young Kim, Benedict Paten, Jimin Park, Ivo Violich, Karen H. Miga, Joshua Gardner, Brandy McNulty, Gail Rosen, Rajiv McCoy, Lesley Chapman Hannah, Doron Lipson, Hila Benjamin, Nika Iremadze, Ilya Soifer, Stephen Eacker, Mary Wood, Erin Cross, Greg Husar, Stephen Gross, Michael Vernich, Mikhail Komogorov, Tanveer Ahmad, Ayse Keskus, Asher Bryant, Francoise Thibaud-Nissen, Jonathan Trow, Justin Wagner, Chunlin Xiao, Andrew S Liss, Justin M. Zook

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