Search Results - "Sokhansanj, Bahrad A"

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

“…We propose an efficient framework for genetic subtyping of SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. Efficient viral subtyping…”
Get full text

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

“…Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term…”
Get full text

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

“…Machine learning algorithms can learn mechanisms of antimicrobial resistance from the data of DNA sequence without any a priori information. Interpreting a…”
Get full text

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

“…Through the COVID-19 pandemic, SARS-CoV-2 has gained and lost multiple mutations in novel or unexpected combinations. Predicting how complex mutations affect…”
Get full text

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

“…A major challenge for clustering algorithms is to balance the trade-off between homogeneity, , the degree to which an individual cluster includes only related…”
Get full text

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 Briefs by Sokhansanj, Bahrad A., Rosen, Gail L.

“…A key challenge for artificial intelligence in the legal field is to determine from the text of a party’s litigation brief whether, and why, it will succeed or…”
Get full text

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

“…Next-generation sequencing has been essential to the global response to the COVID-19 pandemic. As of January 2022, nearly 7 million severe acute respiratory…”
Get full text

Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening by Chandraghatgi, Rohan, Ji, Hai-Feng, Rosen, Gail L., Sokhansanj, Bahrad A.

“…Recent advances in computational methods provide the promise of dramatically accelerating drug discovery. While mathematical modeling and machine learning have…”
Get full text

Temporal Global Changes in Gene Expression during Temperature Transition in Yersinia pestis by MOTIN, Vladimir L, GEORGESCU, Anca M, ELLIOTT, Jeffrey M, KEGELMEYER, Laura M, WYROBEK, Andrew J, SLEZAK, Thomas R, BRUBAKER, Robert R, GARCIA, Emilio, FITCH, Joseph P, GU, Pauline P, NELSON, David O, MABERY, Shalini L, GARNHAM, Janine B, SOKHANSANJ, Bahrad A, OTT, Linda L, COLEMAN, Matthew A

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
Get full text

Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning by Sokhansanj, Bahrad A., Rosen, Gail L.

“…Epidemiological studies show that COVID-19 variants-of-concern, like Delta and Omicron, pose different risks for severe disease, but they typically lack…”
Get full text

Accelerated search for biomolecular network models to interpret high-throughput experimental data by Datta, Suman, Sokhansanj, Bahrad A

“…The functions of human cells are carried out by biomolecular networks, which include proteins, genes, and regulatory sites within DNA that encode and control…”
Get full text

Estimating the Effect of Human Base Excision Repair Protein Variants on the Repair of Oxidative DNA Base Damage by SOKHANSANJ, Bahrad A, WILSON, David M

“…Epidemiologic studies have revealed a complex association between human genetic variance and cancer risk. Quantitative biological modeling based on…”
Get full text

Fragment databases from screened ligands for drug discovery (FDSL-DD) by Wilson, Jerica, Sokhansanj, Bahrad A, Chong, Wei Chuen, Chandraghatgi, Rohan, Rosen, Gail L, Ji, Hai-Feng

“…Fragment-based drug design (FBDD) is one major drug discovery method employed in computer-aided drug discovery. Due to its inherent limitations, this process…”
Get full text

Genetic Variability of Yersinia pestis Isolates as Predicted by PCR-Based IS100 Genotyping and Analysis of Structural Genes Encoding Glycerol-3-Phosphate Dehydrogenase (glpD) by Motin, Vladimir L, Georgescu, Anca M, Elliott, Jeffrey M, Hu, Ping, Worsham, Patricia L, Ott, Linda L, Slezak, Tomas R, Sokhansanj, Bahrad A, Regala, Warren M, Brubaker, Robert R, Garcia, Emilio

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
Get full text

Linear fuzzy gene network models obtained from microarray data by exhaustive search by Sokhansanj, Bahrad A, Fitch, J Patrick, Quong, Judy N, Quong, Andrew A

“…Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole…”
Get full text

Discovering the Unknown : Improving Detection of Novel Species and Genera from Short Reads by Rosen, Gail L., Polikar, Robi, Caseiro, Diamantino A., Essinger, Steven D., Sokhansanj, Bahrad A.

“…High-throughput sequencing technologies enable metagenome profiling, simultaneous sequencing of multiple microbial species present within an environmental…”
Get full text

Systems approaches to the networks of aging by Kriete, Andres, Sokhansanj, Bahrad A, Coppock, Donald L, West, Geoffrey B

“…The aging of an organism is the result of complex changes in structure and function of molecules, cells, tissues, and whole body systems. To increase our…”
Get full text

Semi-Supervised and Incremental Sequence Analysis for Taxonomic Classification by Fasino, Adriana, Ozdogan, Emrecan, Sokhansanj, Bahrad A., Rosen, Gail, Polikar, Robi

“…Metagenomic analysis is vital in determining what organisms are present in a microbial sample and why they are present. In this study, we explore the utility…”
Get full text

Integrated modeling methodology for microtubule dynamics and Taxol kinetics with experimentally identifiable parameters by Zhao, He, Sokhansanj, Bahrad A

“…Abstract Microtubule dynamics play a critical role in cell function and stress response, modulating mitosis, morphology, signaling, and transport. Drugs such…”
Get full text

A quantitative model of human DNA base excision repair. I. mechanistic insights by Sokhansanj, Bahrad A., Rodrigue, Garry R., Fitch, J. Patrick, III, David M. Wilson

“…Base excision repair (BER) is a multistep process involving the sequential activity of several proteins that cope with spontaneous and environmentally induced…”
Get full text