Search Results - "Crawford, Jake"

The effect of non-linear signal in classification problems using gene expression by Heil, Benjamin J, Crawford, Jake, Greene, Casey S

“…Those building predictive models from transcriptomic data are faced with two conflicting perspectives. The first, based on the inherent high dimensionality of…”
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Widespread redundancy in -omics profiles of cancer mutation states by Crawford, Jake, Christensen, Brock C, Chikina, Maria, Greene, Casey S

“…In studies of cellular function in cancer, researchers are increasingly able to choose from many -omics assays as functional readouts. Choosing the correct…”
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CAJAL enables analysis and integration of single-cell morphological data using metric geometry by Govek, Kiya W., Nicodemus, Patrick, Lin, Yuxuan, Crawford, Jake, Saturnino, Artur B., Cui, Hannah, Zoga, Kristi, Hart, Michael P., Camara, Pablo G.

“…High-resolution imaging has revolutionized the study of single cells in their spatial context. However, summarizing the great diversity of complex cell shapes…”
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SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses by Lee, Alexandra J., Mould, Dallas L., Crawford, Jake, Hu, Dongbo, Powers, Rani K., Doing, Georgia, Costello, James C., Hogan, Deborah A., Greene, Casey S.

“…Genome-wide transcriptome profiling identifies genes that are prone to differential expression (DE) across contexts, as well as genes with changes specific to…”
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Redefining Second Stage of Labor: Number of Pushing Contractions by Bok, Serin M., Carmona, Gabriela E. Pena, Crawford, Jake, Eskander, Ramy, Desai, Mina, Ross, Michael G.

“…Abstract Introduction Despite time standards for second stage labor, “delayed pushing,” uterine contraction frequency, and alternate contraction pushing may…”
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Incorporating biological structure into machine learning models in biomedicine by Crawford, Jake, Greene, Casey S

“…[Display omitted] Schematic showing the main categories of models incorporating structured biological data covered in this review. The first panel shows an…”
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MONET: a toolbox integrating top-performing methods for network modularization by Tomasoni, Mattia, Gómez, Sergio, Crawford, Jake, Zhang, Weijia, Choobdar, Sarvenaz, Marbach, Daniel, Bergmann, Sven

“…Abstract Summary We define a disease module as a partition of a molecular network whose components are jointly associated with one or several diseases or risk…”
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wenda_gpu: fast domain adaptation for genomic data by Hippen, Ariel A, Crawford, Jake, Gardner, Jacob R, Greene, Casey S

“…Domain adaptation allows for the development of predictive models even in cases with limited sample data. Weighted elastic net domain adaptation specifically…”
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Optimizer's dilemma: optimization strongly influences model selection in transcriptomic prediction by Crawford, Jake, Chikina, Maria, Greene, Casey S

“…Most models can be fit to data using various optimization approaches. While model choice is frequently reported in machine-learning-based research, optimizers…”
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Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs by 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

“…Off-target effects of the CRISPR–Cas9 system can lead to suboptimal gene-editing outcomes and are a bottleneck in its development. Here, we introduce two…”
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789: Redefining second stage of labor: number of pushes by Ross, Michael G., Bok, Serin M., Carmona, Gabriela P., Eskander, Ramy, Crawford, Jake, Desai, Mina

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504: Diagnosis of pre-eclampsia: can proteinuria be attributed to hematuria? by DiJulio, Mia, Ross, Michael G., Lee, Alex, Crawford, Jake, Han, Guang, Desai, Mina

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RETRACTED ARTICLE: Detangling PPI networks to uncover functionally meaningful clusters by Hall-Swan, Sarah, Crawford, Jake, Newman, Rebecca, Cowen, Lenore J.

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Detangling PPI networks to uncover functionally meaningful clusters by Hall-Swan, Sarah, Crawford, Jake, Newman, Rebecca, Cowen, Lenore J

“…Decomposing a protein-protein interaction network (PPI network) into non-overlapping clusters or communities, sometimes called "network modules," is an…”
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Abstract 1222: Efficient domain adaptation for cancer mutation prediction by Hippen, Ariel A., Crawford, Jake, Gardner, Jacob R., Greene, Casey S.

“…Abstract Prediction models have been widely used for many purposes in cancer research, including calling mutation status, identifying cancer subtype, and…”
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Retraction Note: detangling PPI networks to uncover functionally meaningful clusters by Hall-Swan, Sarah, Crawford, Jake, Newman, Rebecca, Cowen, Lenore J

“…The authors have retracted this article [1]. After publication they discovered a technical error in the Louvain algorithm with bounded cluster sizes…”
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Incorporating biological structure into machine learning models in biomedicine by Crawford, Jake, Greene, Casey S

“…In biomedical applications of machine learning, relevant information often has a rich structure that is not easily encoded as real-valued predictors. Examples…”
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A Smaller Tree Doesn’t Necessarily Mean Reduced Yields: Analysis of Pedestrian Peach Orchard Systems and the Relationships Between Fruit Size, Crop Load, and Light Interception by Crawford, Caleb Jake

“…Annual production costs for peaches (Prunus persica) grown in California are heavily dependent on the costs of labor for pruning, fruit thinning, and harvest,…”
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Redefining Second Stage of Labor: Number of Pushing Contractions by Bok, Serin M, Carmona, Gabriela E Pena, Crawford, Jake, Eskander, Ramy, Desai, Mina, Ross, Michael G

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