Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization von Zhao, Zhengqiao, Sokhansanj, Bahrad A, Malhotra, Charvi, Zheng, Kitty, Rosen, Gail L

Volltext

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses von Woloszynek, Stephen, Zhao, Zhengqiao, Chen, Jian, Rosen, Gail L

Volltext

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers von McIntyre, Alexa B R, Ounit, Rachid, Afshinnekoo, Ebrahim, Prill, Robert J, Hénaff, Elizabeth, Alexander, Noah, Minot, Samuel S, Danko, David, Foox, Jonathan, Ahsanuddin, Sofia, Tighe, Scott, Hasan, Nur A, Subramanian, Poorani, Moffat, Kelly, Levy, Shawn, Lonardi, Stefano, Greenfield, Nick, Colwell, Rita R, Rosen, Gail L, Mason, Christopher E

Volltext

Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms von Lan, Yemin, Wang, Qiong, Cole, James R, Rosen, Gail L

Volltext

Emerging Priorities for Microbiome Research von Cullen, Chad M, Aneja, Kawalpreet K, Beyhan, Sinem, Cho, Clara E, Woloszynek, Stephen, Convertino, Matteo, McCoy, Sophie J, Zhang, Yanyan, Anderson, Matthew Z, Alvarez-Ponce, David, Smirnova, Ekaterina, Karstens, Lisa, Dorrestein, Pieter C, Li, Hongzhe, Sen Gupta, Ananya, Cheung, Kevin, Powers, Jennifer Gloeckner, Zhao, Zhengqiao, Rosen, Gail L

Volltext

Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network von Zhao, Zhengqiao, Woloszynek, Stephen, Agbavor, Felix, Mell, Joshua Chang, Sokhansanj, Bahrad A, Rosen, Gail L

Volltext

Teaching Microbiome Analysis: From Design to Computation Through Inquiry von Rosen, Gail L, Hammrich, Penny

Volltext

Exploring thematic structure and predicted functionality of 16S rRNA amplicon data von Woloszynek, Stephen, Mell, Joshua Chang, Zhao, Zhengqiao, Simpson, Gideon, O'Connor, Michael P, Rosen, Gail L

Volltext

Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights von ValizadehAslani, Taha, Zhao, Zhengqiao, Sokhansanj, Bahrad A, Rosen, Gail L

Volltext

Interpretable and Predictive Deep Neural Network Modeling of the SARS-CoV-2 Spike Protein Sequence to Predict COVID-19 Disease Severity von Sokhansanj, Bahrad A, Zhao, Zhengqiao, Rosen, Gail L

Volltext

Complet+: a computationally scalable method to improve completeness of large-scale protein sequence clustering von Nguyen, Rachel, Sokhansanj, Bahrad A, Polikar, Robi, Rosen, Gail L

Volltext

Predicting Institution Outcomes for Inter Partes Review (IPR) Proceedings at the United States Patent Trial & Appeal Board by Deep Learning of Patent Owner Preliminary Response Bri... von Sokhansanj, Bahrad A., Rosen, Gail L.

Volltext

Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing von Demidova, Elena V, Serebriiskii, Ilya G, Vlasenkova, Ramilia, Kelow, Simon, Andrake, Mark D, Hartman, Tiffiney R, Kent, Tatiana, Virtucio, James, Rosen, Gail L, Pomerantz, Richard T, Dunbrack, Jr, Roland L, Golemis, Erica A, Hall, Michael J, Chen, David Y T, Daly, Mary B, Arora, Sanjeevani

Volltext

Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing von Demidova, Elena V, Serebriiskii, Ilya G, Vlasenkova, Ramilia, Kelow, Simon, Andrake, Mark D, Hartman, Tiffiney R, Kent, Tatiana, Virtucio, James, Rosen, Gail L, Pomerantz, Richard T, Dunbrack, Jr, Roland L, Golemis, Erica A, Hall, Michael J, Chen, David Y T, Daly, Mary B, Arora, Sanjeevani

Volltext

Mapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences von Sokhansanj, Bahrad A, Rosen, Gail L

Volltext

Combining gene prediction methods to improve metagenomic gene annotation von Yok, Non G, Rosen, Gail L

Volltext

MetaMutationalSigs: comparison of mutational signature refitting results made easy von Pandey, Palash, Arora, Sanjeevani, Rosen, Gail L

Volltext

Healthcare Shift Workers' Temporal Habits for Eating, Sleeping, and Light Exposure: A Multi-Instrument Pilot Study von Chen, Chiahui, ValizadehAslani, Taha, Rosen, Gail L, Anderson, Laura M, Jungquist, Carla R

Volltext

Opportunities and obstacles for deep learning in biology and medicine von Ching, Travers, Himmelstein, Daniel S., Beaulieu-Jones, Brett K., Kalinin, Alexandr A., Do, Brian T., Way, Gregory P., Ferrero, Enrico, Agapow, Paul-Michael, Zietz, Michael, Hoffman, Michael M., Xie, Wei, Rosen, Gail L., Lengerich, Benjamin J., Israeli, Johnny, Lanchantin, Jack, Woloszynek, Stephen, Carpenter, Anne E., Shrikumar, Avanti, Xu, Jinbo, Cofer, Evan M., Lavender, Christopher A., Turaga, Srinivas C., Alexandari, Amr M., Lu, Zhiyong, Harris, David J., DeCaprio, Dave, Qi, Yanjun, Kundaje, Anshul, Peng, Yifan, Wiley, Laura K., Segler, Marwin H. S., Boca, Simina M., Swamidass, S. Joshua, Huang, Austin, Gitter, Anthony, Greene, Casey S.

Volltext

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis von SULLAM, KAREN E., ESSINGER, STEVEN D., LOZUPONE, CATHERINE A., O'CONNOR, MICHAEL P., ROSEN, GAIL L., KNIGHT, ROB, KILHAM, SUSAN S., RUSSELL, JACOB A.

Volltext