• Briefing in Bioinformatics  ·  August 30, 2023

    SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data.

    Lindsay Lee, Miao Yu, Xiaoqi Li, Chenxu Zhu, Yanxiao Zhang, Hongyu Yu, Ziyin Chen, Shreya Mishra, Bing Ren, Yun Li, Ming Hu

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  • NPJ Digital Medicine  ·  August 21, 2023

    Deep learning based phenotyping of medical images improves power for gene discovery of complex disease.

    Brianna I. Flynn, Emily M. Javan, Eugenia Lin, Zoe Trutner, Karl Koenig, Kenoma O. Anighoro, Eucharist Kun, Alaukik Gupta, Tarjinder Singh, Prakash Jayakumar & Vagheesh M. Narasimhan

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  • Nature  ·  August 16, 2023

    Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers.

    Jeremy Setton, Kevin Hadi, Zi-Ning Choo, Katherine S. Kuchin, Huasong Tian, Arnaud Da Cruz Paula, Joel Rosiene, Pier Selenica, Julie Behr, Xiaotong Yao, Aditya Deshpande, Michael Sigouros, Jyothi Manohar, Jones T. Nauseef, Juan-Miguel Mosquera, Olivier Elemento, Britta Weigelt, Nadeem Riaz, Jorge S. Reis-Filho, Simon N. Powell & Marcin Imieliński

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  • Cell Stem Cell  ·  August 14, 2023

    Single-cell multi-omics defines the cell-type specific impact of splicing aberrations in human hematopoietic clonal outgrowths.

    Mariela Cortés-LópezPaulina Chamely, Allegra G. Hawkins, Robert F. Stanley, Ariel D. Swett, Saravanan Ganesan, Tarek H. Mouhieddine, Xiaoguang Dai, Lloyd Kluegel, Celine Chen, Kiran Batta, Nili Furer, Rahul S. Vedula, John Beaulaurier, Alexander W. Drong, Scott Hickey, Neville Dusaj, Gavriel Mullokandov, Adam M. Stasiw, Jiayu Su, Ronan Chaligné, Sissel Juul, Eoghan Harrington, David A. Knowles, Catherine J. Potenski, Daniel H. Wiseman, Amos Tanay, Liran Shlush, Robert C. Lindsley, Irene M. Ghobrial, Justin Taylor, Omar Abdel-Wahab, Federico Gaiti, Dan A. Landau

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  • Nature Communications  ·  August 12, 2023

    SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data.

    Lindsay Lee, Hongyu Yu, Bojing Blair Jia, Adam Jussila, Chenxu Zhu, Jiawen Chen, Liangqi Xie, Antonina Hafner, Shreya Mishra, Duan Dennis Wang, Caterina Strambio-De-Castillia, Alistair Boettiger, Bing Ren, Yun Li & Ming Hu

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  • Nature  ·  August 10, 2023

    Droplet-based single-cell joint profiling of histone modifications and transcriptomes.

    Yang Xie, Chenxu Zhu, Zhaoning Wang, Melodi Tastemel, Lei Chang, Yang Eric Li & Bing Ren

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  • Viruses  ·  August 5, 2023

    Molecular and Clinical Epidemiology of SARS-CoV-2 Infection among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey.

    Mediavilla JR, Lozy T, Lee A, Kim J, Kan VW, Titova E, Amin A, Zody MC, Corvelo A, Oschwald DM, Baldwin A, Fennessey S, Zuckerman JM, Kirn T, Chen L, Zhao Y, Chow KF, Maniatis T, Perlin DS, Kreiswirth BN

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  • Cell Reports  ·  August 2, 2023

    Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma.

    Miriam I Rosenberg, Erez Greenstein, Martin Buchkovich, Ayelet Peres, Eric Santoni-Rugiu, Lei Yang, Martin Mikl, Zalman Vaksman, David L Gibbs, Dan Reshef, Amy Salovin, Meredith S Irwin, Arlene Naranjo, Igor Ulitsky, Pedro A de Alarcon, Katherine K Matthay, Victor Weigman, Gur Yaari, Jessica A Panzer, Nir Friedman, John M Maris

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  • Genetics in Medicine  ·  July 30, 2023

    The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change.

    Heidi L Rehm, Joseph T Alaimo, Swaroop Aradhya, Pinar Bayrak-Toydemir, Hunter Best, Rhonda Brandon, Jillian G Buchan, Elizabeth C Chao, Elaine Chen, Jacob Clifford, Ana S A Cohen, Laura K Conlin, Soma Das, Kyle W Davis, Daniela Del Gaudio, Florencia Del Viso, Christina DiVincenzo, Marcia Eisenberg, Lucia Guidugli, Monia B Hammer, Steven M Harrison, Kathryn E Hatchell, Lindsay Havens Dyer, Lily U Hoang, James M Holt, Vaidehi Jobanputra, Izabela D Karbassi, Hutton M Kearney, Melissa A Kelly, Jacob M Kelly, Michelle L Kluge, Timothy Komala, Paul Kruszka, Lynette Lau, Matthew S Lebo, Christian R Marshall, Dianalee McKnight, Kirsty McWalter, Yan Meng, Narasimhan Nagan, Christian S Neckelmann, Nir Neerman, Zhiyv Niu, Vitoria K Paolillo, Sarah A Paolucci, Denise Perry, Tina Pesaran, Kelly Radtke, Kristen J Rasmussen, Kyle Retterer, Carol J Saunders, Elizabeth Spiteri, Christine Stanley, Anna Szuto, Ryan J Taft, Isabelle Thiffault, Brittany C Thomas, Amanda Thomas-Wilson, Erin Thorpe, Timothy J Tidwell, Meghan C Towne, Hana Zouk; Medical Genome Initiative

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  • Science  ·  July 20, 2023

    The genetic architecture and evolution of the human skeletal form.

    Eucharist Kun, Emily M Javan, Olivia Smith, Faris Gulamali, Javier de la Fuente, Brianna I Flynn, Kushal Vajrala, Zoe Trutner, Prakash Jayakumar, Elliot M Tucker-Drob, Mashaal Sohail, Tarjinder Singh, Vagheesh M Narasimhan

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  • bioRxiv  ·  July 19, 2023  ·  Pre-Print

    Schizophrenia Risk Mapping and Functional Engineering of the 3D Genome in Three Neuronal Subtypes.

    Samuel K. Powell, Will Liao, Callan O’Shea, Sarah Kammourh, Sadaf Ghorbani, Raymond Rigat, Rahat Elahi, PJ Michael Deans, Derek J. Le, Poonam Agarwal, Wei Qiang Seow, Kevin C. Wang, Schahram Akbarian, Kristen J. Brennand

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  • Nature  ·  July 19, 2023

    An atlas of healthy and injured cell states and niches in the human kidney.

    Blue B. Lake, Rajasree Menon, Seth Winfree, Qiwen Hu, Ricardo Melo Ferreira, Kian Kalhor, Daria Barwinska, Edgar A. Otto, Michael Ferkowicz, Dinh Diep, Nongluk Plongthongkum, Amanda Knoten, Sarah Urata, Laura H. Mariani, Abhijit S. Naik, Sean Eddy, Bo Zhang, Yan Wu, Diane Salamon, James C. Williams, Xin Wang, Karol S. Balderrama, Paul J. Hoover, Evan Murray, Jamie L. Marshall, Teia Noel, Anitha Vijayan, Austin Hartman, Fei Chen, Sushrut S. Waikar, Sylvia E. Rosas, Francis P. Wilson, Paul M. Palevsky, Krzysztof Kiryluk, John R. Sedor, Robert D. Toto, Chirag R. Parikh, Eric H. Kim, Rahul Satija, Anna Greka, Evan Z. Macosko, Peter V. Kharchenko, Joseph P. Gaut, Jeffrey B. Hodgin, KPMP Consortium, Michael T. Eadon, Pierre C. Dagher, Tarek M. El-Achkar, Kun Zhang, Matthias Kretzler & Sanjay Jain

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  • bioRxiv  ·  July 18, 2023  ·  Pre-Print

    R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription.

    Elizabeth A. LaMarca, Atsushi Saito, Amara Plaza-Jennings, Allyse Hellmich, Michael B. Fernando, Behnam Javidfar, Sergio Espeso-Gil, Molly Estill, Will Liao, Kayla Townsley, Anna Florio, James E. Ethridge, Catherine Do, Benjamin Tycko, Li Shen, Atsushi Kamiya, Nadejda M. Tsankova, Kristen J. Brennand, Schahram Akbarian

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  • American Heart Association Journals  ·  July 7, 2023

    Implementation of Rapid Genome Sequencing for Critically Ill Infants With Complex Congenital Heart Disease.

    Thomas Hays, Rebecca Hernan, Michele Disco, Emily L. Griffin, Nimrod Goldshtrom, Diana Vargas, Ganga Krishnamurthy, Miles Bomback, Atteeq U. Rehman, Amanda T. Wilson, Saurav Guha, Shruti Phadke, Volkan Okur, Dino Robinson, Vanessa Felice, Avinash Abhyankar, Vaidehi Jobanputra and Wendy K. Chung

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  • Nature Aging  ·  July 3, 2023

    Spatial mapping of cellular senescence: emerging challenges and opportunities.

    Aditi U. Gurkar, Akos A. Gerencser, Ana L. Mora, Andrew C. Nelson, Anru R. Zhang, Anthony B. Lagnado, Archibald Enninful, Christopher Benz, David Furman, Delphine Beaulieu, Diana Jurk, Elizabeth L. Thompson, Fei Wu, Fernanda Rodriguez, Grant Barthel, Hao Chen, Hemali Phatnani, Indra Heckenbach, Jeffrey H. Chuang, Jeremy Horrell, Joana Petrescu, Jonathan K. Alder, Jun Hee Lee, Laura J. Niedernhofer, Manoj Kumar, Melanie Königshoff, Marta Bueno, Miiko Sokka, Morten Scheibye-Knudsen, Nicola Neretti, Oliver Eickelberg, Peter D. Adams, Qianjiang Hu, Quan Zhu, Rebecca A. Porritt, Runze Dong, Samuel Peters, Stella Victorelli, Thomas Pengo, Timur Khaliullin, Vidyani Suryadevara, Xiaonan Fu, Ziv Bar-Joseph, Zhicheng Ji & João F. Passos

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  • Nature Biotechnology  ·  July 3, 2023

    Prediction of on-target and off-target activity of CRISPR-Cas13d guide RNAs using deep learning.

    Hans-Hermann Wessels, Andrew Stirn, Alejandro Méndez-Mancilla, Eric J. Kim, Sydney K. Hart, David A. Knowles & Neville E. Sanjana

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  • medRxiv  ·  June 29, 2023  ·  Pre-Print

    Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed Whole Genome Sequencing Study.

    Yuxuan Wang, Margaret Sunitha Selvaraj, Xihao Li, Zilin Li, Jacob A Holdcraft, Donna K Arnett, Joshua C Bis, John Blangero, Eric Boerwinkle, Donald W Bowden, Brian E Cade, Jenna C Carlson, April P Carson, Yii-Der Ida Chen, Joanne E Curran, Paul S de Vries, Susan K Dutcher, Patrick T Ellinor, James S Floyd, Myriam Fornage, Barry I Freedman, Stacey Gabriel, Soren Germer, Richard A Gibbs, Xiuqing Guo, Jiang He, Nancy Heard-Costa, Bertha Hildalgo, Lifang Hou, Marguerite R Irvin, Roby Joehanes, Robert C Kaplan, Sharon LR Kardia, Tanika N Kelly, Ryan Kim, Charles Kooperberg, Brian G Kral, Daniel Levy, Changwei Li, Chunyu Liu, Don Lloyd-Jone, Ruth JF Loos, Michael C Mahaney, Lisa W Martin, Rasika A Mathias, Ryan L Minster, Braxton D Mitchell, May E Montasser, Alanna C Morrison, Joanne M Murabito, Take Naseri, Jeffrey R O’Connell, Nicholette D Palmer, Michael H Preuss, Bruce M Psaty, Laura M Raffield, Dabeeru C Rao, Susan Redline, Alexander P Reiner, Stephen S Rich, Muagututi’a Sefuiva Ruepena, Wayne H-H Sheu, Jennifer A Smith, Albert Smith, Hemant K Tiwari, Michael Y Tsai, Karine A Viaud-Martinez, Zhe Wang, Lisa R Yanek, Wei Zhao, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Jerome I Rotter, Xihong Lin, Pradeep Natarajan, Gina M Peloso

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  • bioRxiv  ·  June 26, 2023  ·  Pre-Print

    Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects.

    Silva Kasela, François Aguet, Sarah Kim-Hellmuth, Brielin C. Brown, Daniel C. Nachun, Russell P. Tracy, Peter Durda, Yongmei Liu, Kent D. Taylor, W. Craig Johnson, David Van Den Berg, Stacey Gabriel, Namrata Gupta, Joshua D. Smith, Thomas W. Blackwell, Jerome I. Rotter, Kristin G. Ardlie, Ani Manichaikul, Stephen E. Rich, R. Graham Barr and Tuuli Lappalainen

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  • PLoS Genetics  ·  June 23, 2023

    Genetic regulators of sputum mucin concentration and their associations with COPD phenotypes.

    Eric Van Buren, Giorgia Radicioni, Sarah Lester, Wanda K. O’Neal, Hong Dang, Silva Kasela, Suresh Garudadri, Jeffrey L. Curtis, MeiLan K. Han, Jerry A. Krishnan, Emily S. Wan, Edwin K. Silverman, Annette Hastie, Victor E. Ortega, Tuuli Lappalainen, Martijn C. Nawijn, Maarten van den Berge, Stephanie A. Christenson, Yun Li, Michael H. Cho, Mehmet Kesimer, Samir N. P. Kelada

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  • Genetics  ·  June 22, 2023

    Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants.

    Jonah Einson, Dafni Glinos, Eric Boerwinkle, Peter Castaldi, Dawood Darbar, Mariza de Andrade, Patrick Ellinor, Myriam Fornage, Stacey Gabriel, Soren Germer, Richard Gibbs, Craig Hersh, Jill Johnsen, Robert Kaplan, Barbara Konkle, Charles Kooperberg, Rami Nassir, Ruth J.F. Loos, Deborah A Meyers, Braxton D. Mitchell, Bruce Psaty, Ramachandran S. Vasan, Stephen S. Rich, Michael Rienstra, Jerome I. Rotter, Aabida Saferali, M. Benjamin Shoemaker, Edwin Silverman, Albert Vernon Smith, Pejman Mohammadi, Stephane E Castel, Ivan Iossifov, Tuuli Lappalainen

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