Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies von Fusi, Nicoló, Stegle, Oliver, Lawrence, Neil D

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Unravelling the enigma of selective vulnerability in neurodegeneration: motor neurons resistant to degeneration in ALS show distinct gene expression characteristics and decreased s... von Brockington, Alice, Ning, Ke, Heath, Paul R., Wood, Elizabeth, Kirby, Janine, Fusi, Nicolò, Lawrence, Neil, Wharton, Stephen B., Ince, Paul G., Shaw, Pamela J.

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Transcriptomic indices of fast and slow disease progression in two mouse models of amyotrophic lateral sclerosis von NARDO, Giovanni, IENNACO, Raffaele, FUSI, Nicolò, HEATH, Paul R, MARINO, Marianna, TROLESE, Maria C, FERRAIUOLO, Laura, LAWRENCE, Neil, SHAW, Pamela J, BENDOTTI, Caterina

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Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs von Listgarten, Jennifer, Weinstein, Michael, Kleinstiver, Benjamin P., Sousa, Alexander A., Joung, J. Keith, Crawford, Jake, Gao, Kevin, Hoang, Luong, Elibol, Melih, Doench, John G., Fusi, Nicolo

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Warped linear mixed models for the genetic analysis of transformed phenotypes von Fusi, Nicolo, Lippert, Christoph, Lawrence, Neil D., Stegle, Oliver

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Detecting regulatory gene-environment interactions with unmeasured environmental factors von Fusi, Nicoló, Lippert, Christoph, Borgwardt, Karsten, Lawrence, Neil D, Stegle, Oliver

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A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control von Bartha, István, Carlson, Jonathan M, Brumme, Chanson J, McLaren, Paul J, Brumme, Zabrina L, John, Mina, Haas, David W, Martinez-Picado, Javier, Dalmau, Judith, López-Galíndez, Cecilio, Casado, Concepción, Rauch, Andri, Günthard, Huldrych F, Bernasconi, Enos, Vernazza, Pietro, Klimkait, Thomas, Yerly, Sabine, O'Brien, Stephen J, Listgarten, Jennifer, Pfeifer, Nico, Lippert, Christoph, Fusi, Nicolo, Kutalik, Zoltán, Allen, Todd M, Müller, Viktor, Harrigan, P Richard, Heckerman, David, Telenti, Amalio, Fellay, Jacques

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Flexible Modeling of Genetic Effects on Function-Valued Traits von Fusi, Nicolo, Listgarten, Jennifer

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Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 von Doench, John G, Fusi, Nicolo, Sullender, Meagan, Hegde, Mudra, Vaimberg, Emma W, Donovan, Katherine F, Smith, Ian, Tothova, Zuzana, Wilen, Craig, Orchard, Robert, Virgin, Herbert W, Listgarten, Jennifer, Root, David E

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Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens von Najm, Fadi J, Strand, Christine, Donovan, Katherine F, Hegde, Mudra, Sanson, Kendall R, Vaimberg, Emma W, Sullender, Meagan E, Hartenian, Ella, Kalani, Zohra, Fusi, Nicolo, Listgarten, Jennifer, Younger, Scott T, Bernstein, Bradley E, Root, David E, Doench, John G

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Further Improvements to Linear Mixed Models for Genome-Wide Association Studies von Widmer, Christian, Lippert, Christoph, Weissbrod, Omer, Fusi, Nicolo, Kadie, Carl, Davidson, Robert, Listgarten, Jennifer, Heckerman, David

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Flexible Modelling of Genetic Effects on Function-Valued Traits von Fusi, Nicolo, Listgarten, Jennifer

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Convolutions are competitive with transformers for protein sequence pretraining von Yang, Kevin K., Fusi, Nicolo, Lu, Alex X.

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A foundation model for clinical-grade computational pathology and rare cancers detection von Vorontsov, Eugene, Bozkurt, Alican, Casson, Adam, Shaikovski, George, Zelechowski, Michal, Severson, Kristen, Zimmermann, Eric, Hall, James, Tenenholtz, Neil, Fusi, Nicolo, Yang, Ellen, Mathieu, Philippe, van Eck, Alexander, Lee, Donghun, Viret, Julian, Robert, Eric, Wang, Yi Kan, Kunz, Jeremy D., Lee, Matthew C. H., Bernhard, Jan H., Godrich, Ran A., Oakley, Gerard, Millar, Ewan, Hanna, Matthew, Wen, Hannah, Retamero, Juan A., Moye, William A., Yousfi, Razik, Kanan, Christopher, Klimstra, David S., Rothrock, Brandon, Liu, Siqi, Fuchs, Thomas J.

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Impact of pre-adapted HIV transmission von Carlson, Jonathan M, Du, Victor Y, Pfeifer, Nico, Bansal, Anju, Tan, Vincent Y F, Power, Karen, Brumme, Chanson J, Kreimer, Anat, DeZiel, Charles E, Fusi, Nicolo, Schaefer, Malinda, Brockman, Mark A, Gilmour, Jill, Price, Matt A, Kilembe, William, Haubrich, Richard, John, Mina, Mallal, Simon, Shapiro, Roger, Frater, John, Harrigan, P Richard, Ndung'u, Thumbi, Allen, Susan, Heckerman, David, Sidney, John, Allen, Todd M, Goulder, Philip J R, Brumme, Zabrina L, Hunter, Eric, Goepfert, Paul A

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LANA: Latency Aware Network Acceleration von Molchanov, Pavlo, Hall, Jimmy, Yin, Hongxu, Kautz, Jan, Fusi, Nicolo, Vahdat, Arash

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Impact of Pre-adapted HIV Transmission von Carlson, Jonathan M, Du, Victor Y, Pfeifer, Nico, Bansal, Anju, Tan, Vincent Y.F, Power, Karen, Brumme, Chanson J, Kreimer, Anat, DeZiel, Charles E, Fusi, Nicolo, Schaefer, Malinda, Brockman, Mark A, Gilmour, Jill, Price, Matt A, Kilembe, William, Haubrich, Richard, John, Mina, Mallal, Simon, Shapiro, Roger, Frater, John, Harrigan, P. Richard, Ndung’u, Thumbi, Allen, Susan, Heckerman, David, Sidney, John, Allen, Todd M, Goulder, Philip J.R, Brumme, Zabrina L, Hunter, Eric, Goepfert, Paul A

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Probabilistic matrix factorization for automated machine learning von Fusi, Nicolo

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Feature Gradients: Scalable Feature Selection via Discrete Relaxation von Sheth, Rishit, Fusi, Nicolo

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Dataset Dynamics via Gradient Flows in Probability Space von Alvarez-Melis, David, Fusi, Nicolò

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