• bioRxiv.  ·  January 29, 2024  ·  Pre-Print

    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  ·  Pre-Print

    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  ·  Pre-Print

    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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  • Cell Stem Cell  ·  December 7, 2023

    SON is an essential m6A target for hematopoietic stem cell fate.

    Hanzhi Luo, Mariela Cortés-López, Cyrus L. Tam, Michael Xiao, Isaac Wakiro, Karen L. Chu, Aspen Pierson, Mandy Chan, Kathryn Chang, Xuejing Yang, Daniel Fecko, Grace Han, Eun-Young Erin Ahn, Quaid D. Morris, Dan A. Landau, Michael G. Kharas

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  • Neuron  ·  December 6, 2023

    A reproducible signature of cytoskeletal and ALS-related genes in human motoneurons.

    Archana Yadav, Kaya J E Matson, Dylan Lee, Mor R Alkaslasi, R Brian Roome, Michael E Ward, Hemali Phatnani, Claire E Le Pichon, Vilas Menon, Ariel J Levine

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  • Cancer Discovery  ·  December 5, 2023

    Cancer Evolution: A Multifaceted Affair.

    Giovanni Ciriello, Luca Magnani, Sarah J Aitken, Leila Akkari, Sam Behjati, Douglas Hanahan, Dan A Landau, Nuria Lopez-Bigas, Darío G Lupiáñez, Jean-Christophe Marine, Ana Martin-Villalba, Gioacchino Natoli, Anna C Obenauf, Elisa Oricchio, Paola Scaffidi, Andrea Sottoriva, Alexander Swarbrick, Giovanni Tonon, Sakari Vanharanta, Johannes Zuber

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  • The American Journal of Surgical Pathology  ·  December 4, 2023

    NIPBL::NACC1 Fusion Hepatic Carcinoma.

    Erika Hissong, Majd Al Assaad, Munita Bal, Katelyn A Reed, Adele Fornelli, Max F Levine, Gunes Gundem, Alissa Semaan, Christine E Orr, Uma Sakhadeo, Jyothi Manohar, Michael Sigouros, David Wilkes, Andrea Sboner, Elizabeth A Montgomery, Rondell P Graham, Juan S Medina-Martínez, Nicolas Robine, Jiayun M Fang, Eun-Young K Choi, Maria Westerhoff, Jesús Delgado-de la Mora, Patricia Caudell, Rhonda K Yantiss, Elli Papaemmanuil, Olivier Elemento, Carlie Sigel, José Jessurun, Juan Miguel Mosquera

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  • Genetics in Medicine  ·  December 3, 2023

    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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  • Nature Biotechnology  ·  November 20, 2023

    Spatial host–microbiome sequencing reveals niches in the mouse gut.

    Britta Lötstedt, Martin Stražar, Ramnik Xavier, Aviv Regev & Sanja Vicković

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  • bioRxiv  ·  November 16, 2023  ·  Pre-Print

    DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data.

    Cameron Park, Shouvik Mani, Nicolas Beltran-Velez, Katie Maurer, Satyen Gohil, Shuqiang Li, Teddy Huang, David A. Knowles, Catherine J. Wu and Elham Azizi

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  • The Journal of Clinical Investigation  ·  November 14, 2023

    Spliceosome malfunction causes neurodevelopmental disorders with overlapping features.

    Dong Li, Qin Wang, Allan Bayat, Mark R. Battig, Yijing Zhou, Daniëlle G.M. Bosch, Gijs van Haaften, Leslie Granger, Andrea K. Petersen, Luis A. Pérez-Jurado, Gemma Aznar-Laín, Anushree Aneja, Miroslava Hancarova, Sarka Bendova, Martin Schwarz, Radka Kremlíková Pourová, Zdenek Sedlacek, Beth A. Keena, Michael E. March, Cuiping Hou, Nora O’Connor, Elizabeth J. Bhoj, Margaret H. Harr, Gabrielle Lemire, Kym M. Boycott, Meghan C. Towne, Megan Li, Mark Tarnopolsky, Lauren Brady, Michael J. Parker, Hanna Faghfoury, Lea Kristin Parsley, Emanuele Agolini, Maria Lisa Dentici, Antonio Novelli, Meredith S. Wright, Rachel Palmquist, Khanh Lai, Marcello Scala, Pasquale Striano, Michele Iacomino, Federico Zara, Annina Cooper, Timothy J. Maarup, Melissa Byler, Robert Roger Lebel, Tugce B. Balci, Raymond J. Louie, Michael J. Lyons, Jessica Douglas, Catherine B. Nowak, Alexandra Afenjar, Juliane Hoyer, Boris Keren, Saskia M. Maas, Mahdi M. Motazacker, Julian A. Martinez-Agosto, Ahna M. Rabani, Elizabeth M. McCormick, Marni Falk, Sarah M. Ruggiero, Ingo Helbig, Rikke S. Møller, Lino Tessarollo, Francesco Tomassoni-Ardori, Mary Ellen Palko, Tzung-Chien Hsieh, Peter M. Krawitz, Mythily Ganapathi, Bruce D. Gelb, Vaidehi Jobanputra, et al.

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