• Genome Biology  ·  December 18, 2024

    SQUiD: ultra-secure storage and analysis of genetic data for the advancement of precision medicine.

    Jacob Blindenbach, Jiayi Kang, Seungwan Hong, Caline Karam, Thomas Lehner & Gamze Gürsoy

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  • medRxiv  ·  December 8, 2024  ·  Preprint

    Epigenome-wide Association Analysis of Mitochondrial Heteroplasmy Provides Insight into Molecular Mechanisms of Disease.

    Meng Lai, Kyeezu Kim, Yinan Zheng, Christina A. Castellani, Scott M. Ratliff, Mengyao Wang, Xue Liu, Jeffrey Haessler, Tianxiao Huan, Lawrence F. Bielak, Wei Zhao, Roby Joehanes, Jiantao Ma, Xiuqing Guo, JoAnn E. Manson, Megan L. Grove, Jan Bressler, Kent D. Taylor, Tuuli Lappalainen, Silva Kasela, Thomas W. Blackwell, Nicole J. Lake, Jessica D. Faul, Kendra R. Ferrier, Lifang Hou, Charles Kooperberg, Alexander P. Reiner, Kai Zhang, Patricia A. Peyser, Myriam Fornage, Eric Boerwinkle, Laura M. Raffield, April P. Carson, Stephen S. Rich, Yongmei Liu, Daniel Levy, Jerome I. Rotter, Jennifer A. Smith, Dan E. Arking, Chunyu Liu, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium.

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  • medRxiv  ·  December 13, 2024  ·  Preprint

    Deriving Mendelian Randomization-based Causal Networks of Brain Imaging Phenotypes and Bipolar Disorder.

    Shane O’Connell, Brielin C. Brown, Dara M. Cannon, Pilib Ó Broin, David A. Knowles, Nadine Parker, Dag Alnæs, Lars T. Westlye, Saikat Banerjee, Leila Nabulsi, Emma Corley, Ole A. Andreassen, Niamh Mullins

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  • medRxiv  ·  December 8, 2024  ·  Preprint

    Leveraging functional annotations to map rare variants associated with Alzheimer’s disease with gruyere.

    Anjali Das, Chirag Lakhani, Chloé Terwagne, Jui-Shan Lin, Tatsuhiko Naito, Towfique Raj, David A Knowles

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  • American Journal of Human Genetics  ·  December 5, 2024

    Employing effective recruitment and retention strategies to engage a diverse pediatric population in genomics research.

    Michelle A Ramos, Katherine E Bonini, Laura Scarimbolo, Nicole R Kelly, Beverly Insel, Sabrina A Suckiel, Kaitlyn Brown, Miranda Di Biase, Katie M Gallagher, Jessenia Lopez, Karla López Aguiñiga, Priya N Marathe, Estefany Maria, Jacqueline A Odgis, Jessica E Rodriguez, Michelle A Rodriguez, Nairovylex Ruiz, Monisha Sebastin, Nicole M Yelton, Charlotte Cunningham-Rundles, Melvin Gertner, Irma Laguerre, Thomas V McDonald, Patricia E McGoldrick, Mimsie Robinson, Arye Rubinstein, Lisa H Shulman, Trinisha Williams, Steven M Wolf, Elissa G Yozawitz, Randi E Zinberg, Noura S Abul-Husn, Laurie J Bauman, George A Diaz, Bart S Ferket, John M Greally, Vaidehi Jobanputra, Bruce D Gelb, Eimear E Kenny, Melissa P Wasserstein, Carol R Horowitz

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  • Genome Research  ·  December 5, 2024

    An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.

    Chong Li, Marc Jan Bonder, Sabriya Syed, Matthew Jensen; Human Genome Structural Variation Consortium (HGSVC); HGSVC Functional Analysis Working Group; Mark B Gerstein , Michael C Zody, Mark J P Chaisson, Michael E Talkowski, Tobias Marschall, Jan O Korbel, Evan E Eichler, Charles Lee, Xinghua Shi

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  • BMC Cancer  ·  December 2, 2024

    Patterns of breast cancer locoregional relapse, metastasis, and subtypes in Ghana.

    Gloria Agyekum Boaitey, Rachel Martini, Brian Stonaker, Ernest Osei Bonsu, Ernest Adjei, Ishmael Kyei, Mavis Bobie Ansah, Lisa Newman, Christian Obirikorang, Melissa B. Davis & Linda Ahenkorah Fondjo

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  • Science  ·  November 28, 2024

    A panoramic view of cell population dynamics in mammalian aging.

    Zehao Zhang, Chloe Schaefer, Weirong Jiang, Ziyu Lu, Jasper Lee, Andras Sziraki, Abdulraouf Abdulraouf, Brittney Wick, Maximilian Haeussler, Zhuoyan Li, Gesmira Molla, Rahul Satija, Wei Zhou, Junyue Cao

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  • bioRxiv  ·  November 27, 2024  ·  Preprint

    Paired CRISPR screens to map gene regulation in cis and trans.

    Xinhe Xue, Zoran Z. Gajic, Christina M. Caragine, Mateusz Legut, Conor Walker, James Y.S. Kim, Xiao Wang, Rachel E. Yan, Hans-Hermann Wessels,Congyi Lu, Neil Bapodra,Gamze Gürsoy, Neville E. Sanjana

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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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  • 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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  • 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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  • Computational Biology and Chemistry  ·  November 16, 2024

    Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries.

    Daniel H Um, David A Knowles, Gail E Kaiser

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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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  • 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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  • 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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  • 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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