Computational Biology |
[Youssef et al., 2024] | Ahmed Youssef, Indranil Paul, Mark Crovella and Andrew Emili (2024). DESP: Demixing Cell State Profiles from Dynamic Bulk Molecular Measurements. In: Cell Reports Methods, . doi:10.1016/j.crmeth.2024.100729 |
[Kewalramani et al., 2023] | Neal Kewalramani, Andrew Emili and Mark Crovella (2023). State-of-the-Art Computational Methods to Predict Protein-Protein Interactions with High Accuracy and Coverage. In: Proteomics, (e2200292). doi:10.1002/pmic.202200292 |
[Youssef et al., 2023] | Ahmed Youssef, Fei Bian, Pierre Havugimana, Mark Crovella and Andrew Emili (2023). Dynamic Remodeling of Escherichia coli Interactome in Response to Environmental Perturbations. In: Proteomics, . doi:10.1002/pmic.202200404 |
[Youssef et al., 2023] | Ahmed Youssef, Indranil Paul, Mark Crovella and Andrew Emili (2023). DESP: Demixing Cell State Profiles from Dynamic Bulk Molecular Measurements. In: bioRxiv, . doi:10.1101/2023.01.19.524460 |
[Jung et al., 2022] | J. Jung, M. Guo, M. Crovella, J. G. McDaniel, K. M. Warkentin (2022). Frog embryos use multiple levels of temporal pattern in risk assessment for vibration-cued hatching. In: Animal Cognition, . doi:10.1007/s10071-022-01634-4 |
[Law et al., 2021] | Jeffrey N. Law, Kyle Akers, Nure Tasnina, Catherine M. Della-Santina, Shay Deutsch, Meghana Kshirsagar, Judith Klein-Seetharaman, Mark Crovella, Padmavathy Rajagopalan, Simon Kasif, T. M. Murali (2021). Interpretable Network Propagation with Application to Expanding the Repertoire of Human Proteins that Interact with SARS-CoV-2. In: GigaScience, 10(12). doi:10.1093/gigascience/giab082 |
[Lancour et al., 2020] | Dan Lancour, Josee Dupuis, Richard Mayeux, Jonathan Haines, Margaret Pericak-Vance, Gerard Schellenberg, Mark Crovella, Lindsay Farrer and Simon Kasif (2020). Analysis of Brain Region-Specific Co-Expression Networks Reveals Clustering of Established and Novel Genes Associated with Alzheimer Disease. In: Alzheimer's Research and Therapy, 12. doi:10.1186/s13195-020-00674-7 |
[Fan et al., 2020] | Jason Fan, Xuan Cindy Li, Mark Crovella, Mark D. M. Leiserson (2020). Matrix (Factorization) Reloaded: Flexible Methods for Imputing Genetic Interactions with Cross-Species and Side Information. In: Proceedings of the 19th European Conference on Computational Biology. Online. Also appears in OUP Bioinformatics Special Issue, 2020. doi:10.1093/bioinformatics/btaa818 |
[Law et al., 2020] | Jeffrey N. Law, Nure Tasnina, Meghana Kshirsagar, Judith Klein-Seetharaman, Mark Crovella, Padmavathy Rajagopalan, Simon Kasif, T. M. Murali (2020). Identifying Human Interactors of SARS-CoV-2 Proteins and Drug Targets for COVID-19 using Network-Based Label Propagation. Technical Report Nr. arXiv:2006.01968. |
[Ramirez et al., 2020] | Alfred Ramirez, Simon Dankel, Bashir Rastegarpanah, Weikang Cai, Ruidan Xue, Mark Crovella, Yu-Hua Tseng, C. Ronald Kahn and Simon Kasif (2020). Single-Cell Transcriptional Networks in Differentiating Preadipocytes Suggest Drivers Associated with Tissue Heterogeneity. In: Nature Communications, 11. doi:10.1038/s41467-020-16019-9 |
[Fan et al., 2019] | Jason Fan, Anthony Cannistra, Inbar Fried, Tim Lim, Thomas Schaffner, Mark Crovella, Benjamin Hescott, Mark D. M. Leiserson (2019). Functional Protein Representations from Biological Networks Enable Diverse Cross-Species Inference. In: Nucleic Acids Research, 47(9). doi:10.1186/s13195-020-00674-7 |
[Lancour et al., 2018] | Daniel Lancour, Adam Naj, Richard Mayeux, Jonathan L. Haines, Margaret A. Pericak-Vance, Gerard C. Schellenberg, Mark Crovella, Lindsay A. Farrer and Simon Kasif (2018). One for all and all for One: Improving replication of genetic studies through network diffusion. In: PLoS Genetics, 14(4):1--20. doi:10.1371/journal.pgen.1007306 |
[Leiserson et al., 2018] | Mark D. M. Leiserson, Jason Fan, Anthony Cannistra, Inbar Fried, Tim Lim, Thomas Schaffner, Mark Crovella and Benjamin Hescott (2018). A Multi-Species Functional Embedding Integrating Sequence and Network Structure. In: Proceedings of RECOMB: Lecture Notes in Bioinformatics. Volume 10812. Paris, France. Published by Springer. Code and demo for this method are available at links below. doi:10.1007/978-3-319-89929-9 |
[Leiserson et al., 2017] | Mark D. M. Leiserson, Jason Fan, Anthony Cannistra, Inbar Fried, Tim Lim, Thomas Schaffner, Mark Crovella and Benjamin Hescott (2017). A Multi-Species Functional Embedding Integrating Sequence and Network Structure. Technical Report. bioRxiv. Code and demo for this method are available at links below. doi:10.1101/229211 |
[Cao et al., 2013] | Mengfei Cao, Hao Zhang, Jisoo Park, Noah Daniels, Mark Crovella, Lenore Cowen and Benjamin Hescott (2013). Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks. In: PLOS One, 8(10):e76339. doi:10.1371/journal.pone.0076339 |