• Science Direct.  ·  March 11, 2024

    Recommendations for risk allele evidence curation, classification, and reporting from the ClinGen Low Penetrance/Risk Allele Working Group.

    Ryan J Schmidt, Marcie Steeves, Pinar Bayrak-Toydemir, Katherine A Benson, Bradley P Coe, Laura K Conlin, Mythily Ganapathi, John Garcia, Michael H Gollob, Vaidehi Jobanputra, Minjie Luo, Deqiong Ma, Glenn Maston, Kelly McGoldrick, T Blake Palculict, Tina Pesaran, Toni I Pollin, Emily Qian, Heidi L Rehm, Erin R Riggs, Samantha L P Schilit, Panagiotis I Sergouniotis, Tatiana Tvrdik, Nicholas Watkins, Lauren Zec, Wenying Zhang, Matthew S Lebo; ClinGen Low Penetrance/Risk Allele Working Group.

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  • bioRxiv  ·  March 7, 2024  ·  Preprint

    Nanopore sequencing of 1000 Genomes Project samples 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 Anderson, Sophie HR Storz, Sydney A. Ward, Maisha Sinha, Claudia Gonzaga-Jauregui, Wayne E. Clarke, Anna O. Basile, André Corvelo, Catherine Reeves, Adrienne Helland, Rajeeva Lochan Musunuri, Mahler Revsine, Karynne E. Patterson, Cate R. Paschal, Christina Zakarian, Sara Goodwin, Tanner D. Jensen, Esther Robb, The 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, Matt Loose, Miten Jain, Evan E. Eichler, Danny E. Miller

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  • Applied Clinical Informatics.  ·  March 6, 2024

    Examining the Generalizability of Pretrained De-identification Transformer Models on Narrative Nursing Notes.

    Fangyi Chen, Syed Mohtashim Abbas Bokhari, Kenrick Cato, Gamze Gürsoy, Sarah Collins Rossetti

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  • JAMA Surgery.  ·  March 6, 2024

    Tumor-Associated Lymphocytes and Breast Cancer Survival in Black and White Women.

    Newman LA, Chen Y, Martini R, Demaria S, Formenti S, Elemento O, Davis MB.

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  • Nature Aging.  ·  February 21, 2024

    Leveraging electronic health records and knowledge networks for Alzheimer’s disease prediction and sex-specific biological insights.

    Tang AS, Rankin KP, Cerono G, Miramontes S, Mills H, Roger J, Zeng B, Nelson C, Soman K, Woldemariam S, Li Y, Lee A, Bove R, Glymour M, Aghaeepour N, Oskotsky TT, Miller Z, Allen IE, Sanders SJ, Baranzini S, Sirota M.

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  • bioRxiv.  ·  February 11, 2024  ·  Preprint

    The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI.

    Liubomir Chorbadjiev, Murat Cokol, Zohar Weinstein, Kevin Shi, Chris Fleisch, Nikolay Dimitrov, Svetlin Mladenov, Simon Xu, Jake Hall, Steven Ford, Yoon-ha Lee, Boris Yamrom, Steven Marks, Adriana Munoz, Alex Lash, Natalia Volfovsky, Ivan Iossifov.

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  • Nature Biotechnology.  ·  February 9, 2024

    Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq.

    Dongsheng Bai, Xiaoting Zhang, Huifen Xiang, Zijian Guo, Chenxu Zhu & Chengqi Yi

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  • Annals of the American Thoracic Society.  ·  February 8, 2024

    Peripheral Blood Mononuclear Cell Gene Expression Associated with Pulmonary Microvascular Perfusion: The Multi-Ethnic Study of Atherosclerosis Chronic Obstructive Pulmonary Disease Study.

    Kristina L. Buschur, Tess D. Pottinger, Jens Vogel-Claussen, Charles A Powell, Francois Aguet, Norrina B Allen, Kristin Ardlie, David A. Bluemke, Peter Durda, Emilia A. Hermann, Eric A. Hoffman, João A.C. Lima, Yongmei Liu, Daniel Malinsky, Ani Manichaikul, Amin Motahari, Wendy S. Post, Martin R. Prince, Stephen S. Rich, Jerome I Rotter, Benjamin M. Smith, Russell P Tracy, Karol Watson, Hinrich B. Winther, Tuuli Lappalainen, R Graham Barr

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  • Muscle & Nerve.  ·  February 2, 2024

    Identification of gene fusions associated with amyotrophic lateral sclerosis.

    Yogindra Raghav BS, Allison A. Dilliott PhD, Tiziana Petrozziello PhD, Spencer E. Kim BA, James D. Berry MD, Merit E. Cudkowicz MD, Khashayar Vakili MD, NYGC ALS Consortium, Ernest Fraenkel PhD, Sali M. K. Farhan PhD, Ghazaleh Sadri-Vakili PhD

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  • bioRxiv.  ·  January 29, 2024  ·  Preprint

    Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens.

    Longda JiangCarol DalgarnoEfthymia PapalexiIsabella MascioHans-Hermann WesselsHuiyoung Yun, Nika Iremadze, Gila Lithwick-Yanai, Doron Lipson, Rahul Satija

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  • EMBO Reports  ·  January 16, 2024

    Osteocalcin of maternal and embryonic origins synergize to establish homeostasis in offspring.

    Danilo Correa Pinto Junior, Isabella Canal Delgado, Haiyang Yang, Alisson Clemenceau, André Corvelo, Giuseppe Narzisi, Rajeeva Musunuri, Julian Meyer Berger, Lauren E Hendricks, Kazuya Tokumura, Na Luo, Hongchao Li, Franck Oury, Patricia Ducy, Vijay K Yadav, Xiang Li, Gerard Karsenty

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  • Cancer Discovery  ·  January 12, 2024

    Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms.

    Andrew J Dunbar, Robert L Bowman, Young C Park, Kavi O’Connor, Franco Izzo, Robert M Myers, Abdul Karzai, Zach Zaroogian, Won Jun Kim, Ines Fernandez-Maestre, Michael R Waarts, Abbas Nazir, Wenbin Xiao, Tamara Codilupi, Max Brodsky, Mirko Farina, Louise Cai, Sheng F Cai, Benjamin Wang, Wenbin An, Julie L Yang, Shoron Mowla, Shira E Eisman, Amritha Varshini Hanasoge Somasundara, Jacob L Glass, Tanmay Mishra, Remie Houston, Emily Guzzardi, Anthony R Martinez Benitez, Aaron D Viny, Richard P Koche, Sara C Meyer, Dan A Landau, Ross L Levine

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  • American Journal of Human Genetics  ·  January 4, 2023

    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 S. Rich, R. Graham Barr, Tuuli Lappalainen

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  • CA Cancer J Clin  ·  January 4, 2024

    Interpreting and integrating genomic tests results in clinical cancer care: Overview and practical guidance.

    Raffaella Casolino MD, PhD, Philip A. Beer MD, PhD, Debyani Chakravarty PhD, Melissa B. Davis PhD, Umberto Malapelle PhD, Luca Mazzarella MD, PhD, Nicola Normanno MD, Chantal Pauli MD, Vivek Subbiah MD, Clare Turnbull MD PhD, C. Benedikt Westphalen MD, Andrew V. Biankin FRCS, PhD

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  • bioRxiv  ·  December 31, 2023  ·  Preprint

    Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs.

    Mariia Minaeva, Julia Domingo, Philipp Rentzsch, Tuuli Lappalainen

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  • bioRxiv  ·  December 26, 2023  ·  Preprint

    CRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue.

    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, Steve Niu, Jacqueline Chou, Dan A. Landau, Elham Azizi, Edmond M. Chan, Alberto Ciccia, Jellert T. Gaublomme

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  • BMC Genomics  ·  December 19, 2023

    Evaluation of noninvasive biospecimens for transcriptome studies.

    Molly Martorella, Silva Kasela, Renee Garcia-Flores, Alper Gokden, Stephane E. Castel & Tuuli Lappalainen

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  • Genome Biology  ·  December 18, 2023

    Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data.

    Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Supo Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David A. Knowles & Raul Rabadan

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  • Nature Communications  ·  December 15, 2023

    Essential transcription factors for induced neuron differentiation.

    Congyi Lu, Görkem Garipler, Chao Dai, Timothy Roush, Jose Salome-Correa, Alex Martin, Noa Liscovitch-Brauer, Esteban O. Mazzoni & Neville E. Sanjana

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  • Genome Research  ·  December 14, 2023

    Assessing and mitigating privacy risk of sparse, noisy genotypes by local alignment to haplotype databases.

    Prashant Emani, Maya Geradi, Gamze Gürsoy, Monica Grasty, Andrew Miranker, and Mark Gerstein

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