Scott J. Emrich

64 papers A 3B 4C 2Journal 24Unranked 31

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Transformer-based Prediction of Microbial Growth Rates from Genomic Data. BCB Iyanu Oduwole, Mengling He, Ratish Kumar Chandrakant Jha, Adrienne Hoarfrost, Andrew D. Steen, Scott J. Emrich
2024	—	`conf`	CodonT5: A Multi-task Codon Language Model to Perform Generative Codon Optimization. BIBM Ashley Babjac, Scott J. Emrich
2023	—	`conf`	Adapting Protein Language Models for Explainable Fine-Grained Evolutionary Pattern Discovery. BIBM Ashley Babjac, Owen Queen, Shawn-Patrick Barhorst, Kambiz Kalhor, Andrew D. Steen, Scott J. Emrich
2023	—	`conf`	CodonBERT: Using BERT for Sentiment Analysis to Better Predict Genes with Low Expression. BCB Ashley Nicole Babjac, Zhixiu Lu, Scott J. Emrich
2023	J	`jnl`	Deep Learning for Reference-Free Geolocation for Poplar Trees. CoRR Cai W. John, Owen Queen, Wellington Muchero, Scott J. Emrich
2022	—	`conf`	A comparison of dimensionality reduction methods for large biological data. BCB Ashley Babjac, Taylor M. Royalty, Andrew D. Steen, Scott J. Emrich
2021	—	`conf`	Fine-Grained Synonymous Codon Usage Patterns and their Potential Role in Functional Protein Production. BIBM Ashley Babjac, Jun Li, Scott J. Emrich
2021	—	`conf`	LASSO-based feature selection for improved microbial and microbiome classification. BIBM Owen Queen, Scott J. Emrich
2020	—	`conf`	Extreme Phenotype Sampling Improves LASSO and Random Forest Marker Selection for Complex Traits. BIBM Cai W. John, Wellington Muchero, Scott J. Emrich
2020	J	`jnl`	Network analysis of synonymous codon usage. Bioinform. Khalique Newaz, Gabriel Wright, Jacob Piland, Jun Li, Patricia L. Clark, Scott J. Emrich, Tijana Milenkovic
2020	—	`conf`	PeakMatcher: Matching Peaks Across Genome Assemblies. BCB Ronald J. Nowling, Christopher R. Beal, Scott J. Emrich, Susanta K. Behura, Marc S. Halfon, Molly Duman-Scheel
2019	J	`jnl`	Highly Accurate and Efficient Data-Driven Methods for Genotype Imputation. IEEE ACM Trans. Comput. Biol. Bioinform. Olivia Choudhury, Ankush Chakrabarty, Scott J. Emrich
2019	J	`jnl`	Weighted graphlets and deep neural networks for protein structure classification. CoRR Hongyu Guo, Khalique Newaz, Scott J. Emrich, Tijana Milenkovic, Jun Li
2018	J	`jnl`	Adjusted likelihood-ratio test for variants with unknown genotypes. J. Bioinform. Comput. Biol. Ronald J. Nowling, Scott J. Emrich
2018	J	`jnl`	Combining Static and Dynamic Storage Management for Data Intensive Scientific Workflows. IEEE Trans. Parallel Distributed Syst. Nicholas L. Hazekamp, Nathaniel Kremer-Herman, Benjamín Tovar, Haiyan Meng, Olivia Choudhury, Scott J. Emrich, Douglas Thain
2018	—	`conf`	Detecting Chromosomal Inversions from Dense SNPs by Combining PCA and Association Tests. BCB Ronald J. Nowling, Scott J. Emrich
2018	—	`conf`	Effects from structure of Metabarcode Sequences on Lossy Analysis of Microbiome Data. BIBM David C. Molik, Michael E. Pfrender, Scott J. Emrich
2018	—	`conf`	HarMinMax: Harmonizing Codon Usage to Replicate Local Host Translation. BCB Gabriel Wright, Anabel Rodriguez, Patricia L. Clark, Scott J. Emrich
2018	J	`jnl`	Inversion detection using PacBio long reads. Int. J. Data Min. Bioinform. Shenglong Zhu, Scott J. Emrich, Danny Z. Chen
2018	—	`conf`	Predicting Local Inversions Using Rectangle Clustering and Representative Rectangle Prediction. BIBM Shenglong Zhu, Scott J. Emrich, Danny Z. Chen
2018	—	`conf`	The Effects of Normalization, Transformation, and Rarefaction on Clustering of OTU Abundance. BIBM DeAndre A. Tomlinson, David C. Molik, Michael E. Pfrender, Scott J. Emrich
2017	—	`conf`	Inversion detection using PacBio long reads. BIBM Shenglong Zhu, Scott J. Emrich, Danny Z. Chen
2017	—	`conf`	Stable feature ranking with logistic regression ensembles. BIBM Ronald J. Nowling, Scott J. Emrich
2017	J	`jnl`	Widespread position-specific conservation of synonymous rare codons within coding sequences. PLoS Comput. Biol. Julie L. Chaney, Aaron Steele, Rory Carmichael, Anabel Rodriguez, Alicia T. Specht, Kim Ngo, Jun Li, Scott J. Emrich, Patricia L. Clark
2016	—	`conf`	HAPI-Gen: Highly Accurate Phasing and Imputation of Genotype Data. BCB Olivia Choudhury, Ankush Chakrabarty, Scott J. Emrich
2016	J	`jnl`	Prediction of fine-tuned promoter activity from DNA sequence. F1000Research Geoffrey Siwo, Andrew K. Rider, Asako Tan, Richard S. Pinapati, Scott J. Emrich, Nitesh V. Chawla, Michael T. Ferdig
2016	—	`conf`	Single molecule sequencing-guided scaffolding and correction of draft assemblies. ICCABS Shenglong Zhu, Danny Z. Chen, Scott J. Emrich
2015	—	`conf`	A computational framework for integrative analysis of large microbial genomics data. BIBM Erliang Zeng, Wei Zhang, Scott J. Emrich, Dan Liu, Joshua Livermore, Stuart E. Jones
2015	J	`jnl`	Accelerating Comparative Genomics Work ows in a Distributed Environment with Optimized Data Partitioning and Workflow Fusion. Scalable Comput. Pract. Exp. Olivia Choudhury, Nicholas L. Hazekamp, Douglas Thain, Scott J. Emrich
2015	C	`conf`	Balancing Thread-Level and Task-Level Parallelism for Data-Intensive Workloads on Clusters and Clouds. CLUSTER Olivia Choudhury, Dinesh Rajan, Nicholas L. Hazekamp, Sandra Gesing, Douglas Thain, Scott J. Emrich
2015	—	`conf`	Global maximum-parsimony based ancestral reconstruction with non-universal genes. ICCABS Lauren A. Assour, Scott J. Emrich
2015	J	`jnl`	RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. Bioinform. Andrew S. Warren, Cristina Aurrecoechea, Brian P. Brunk, Prerak Desai, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Deborah Hix, Daniel Lawson, Dustin Machi, Chunhong Mao, Michael McClelland, Eric K. Nordberg, Maulik Shukla, Leslie B. Vosshall, Alice R. Wattam, Rebecca Will, Hyun Seung Yoo, Bruno W. S. Sobral
2015	B	`conf`	Scaling Up Bioinformatics Workflows with Dynamic Job Expansion: A Case Study Using Galaxy and Makeflow. e-Science Nicholas L. Hazekamp, Joseph Sarro, Olivia Choudhury, Sandra Gesing, Scott J. Emrich, Douglas Thain
2015	J	`jnl`	VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res. Gloria I. Giraldo-Calderón, Scott J. Emrich, Robert M. MacCallum, Gareth Maslen, Emmanuel Dialynas, Pantelis Topalis, Nicholas Ho, Sandra Gesing, Gregory R. Madey, Frank H. Collins, Daniel Lawson
2014	J	`jnl`	A supervised learning approach to the ensemble clustering of genes. Int. J. Data Min. Bioinform. Andrew K. Rider, Geoffrey Siwo, Scott J. Emrich, Michael T. Ferdig, Nitesh V. Chawla
2014	B	`conf`	Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning. CCGRID Olivia Choudhury, Nicholas L. Hazekamp, Douglas Thain, Scott J. Emrich
2014	J	`jnl`	Adapting bioinformatics applications for heterogeneous systems: a case study. Concurr. Comput. Pract. Exp. Irena Lanc, Peter Bui, Douglas Thain, Scott J. Emrich
2014	B	`conf`	Expanding Tasks of Logical Workflows Into Independent Workflows for Improved Scalability. CCGRID Nicholas L. Hazekamp, Olivia Choudhury, Sandra Gesing, Scott J. Emrich, Douglas Thain
2014	J	`jnl`	Mapping genomic features to functional traits through microbial whole genome sequences. Int. J. Bioinform. Res. Appl. Wei Zhang, Erliang Zeng, Dan Liu, Stuart E. Jones, Scott J. Emrich
2014	J	`jnl`	Scaling up genome annotation using MAKER and work queue. Int. J. Bioinform. Res. Appl. Andrew Thrasher, Zachary Musgrave, Brian Kachmarck, Douglas Thain, Scott J. Emrich
2013	—	`conf`	An unsupervised learning approach to assembly validation. ICCABS Irena Lanc, Scott J. Emrich
2013	B	`conf`	Case Studies in Designing Elastic Applications. CCGRID Dinesh Rajan, Andrew Thrasher, Badi Abdul-Wahid, Jesús A. Izaguirre, Scott J. Emrich, Douglas Thain
2013	—	`conf`	Predicting bacterial functional traits from whole genome sequences using random forest. ICCABS Wei Zhang, Erliang Zeng, Scott J. Emrich, Joshua Livermore, Dan Liu, Stuart E. Jones
2012	J	`jnl`	A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids. IEEE Trans. Parallel Distributed Syst. Christopher Moretti, Andrew Thrasher, Li Yu, Michael Olson, Scott J. Emrich, Douglas Thain
2012	—	`conf`	A machine learning framework for trait based genomics. ICCABS Wei Zhang, Erliang Zeng, Dan Liu, Stuart E. Jones, Scott J. Emrich
2012	—	`conf`	Shifting the bioinformatics computing paradigm: A case study in parallelizing genome annotation using MAKER and Work Queue. ICCABS Andrew Thrasher, Douglas Thain, Scott J. Emrich, Zachary Musgrave
2012	J	`jnl`	VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res. Karine Megy, Scott J. Emrich, Daniel Lawson, David Campbell, Emmanuel Dialynas, Daniel S. T. Hughes, Gautier Koscielny, Christos Louis, Robert M. MacCallum, Seth Redmond, Andrew Sheehan, Pantelis Topalis, Derek Wilson
2012	—	`conf`	Workshop: Opportunities and challenges of non-model ecoinformatics. ICCABS Scott J. Emrich
2011	J	`jnl`	Biocompute 2.0: an improved collaborative workspace for data intensive bio-science. Concurr. Comput. Pract. Exp. Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, Scott J. Emrich
2011	—	`conf`	Robust haplotype reconstruction of eukaryotic read data with Hapler. ICCABS Shawn T. O'Neil, Scott J. Emrich
2010	J	`jnl`	A statistical approach to finding overlooked genetic associations. BMC Bioinform. Andrew K. Rider, Geoffrey Siwo, Nitesh V. Chawla, Michael T. Ferdig, Scott J. Emrich
2010	—	`conf`	A supervised learning approach to the unsupervised clustering of genes. BIBM Andrew K. Rider, Geoffrey Siwo, Scott J. Emrich, Michael T. Ferdig, Nitesh V. Chawla
2010	—	`conf`	A two-stage machine learning approach for pathway analysis. BIBM Wei Zhang, Scott J. Emrich, Erliang Zeng
2010	A	`conf`	Biocompute: towards a collaborative workspace for data intensive bio-science. HPDC Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, Scott J. Emrich
2010	J	`jnl`	Harnessing parallelism in multicore clusters with the All-Pairs, Wavefront, and Makeflow abstractions. Clust. Comput. Li Yu, Christopher Moretti, Andrew Thrasher, Scott J. Emrich, Kenneth Judd, Douglas Thain
2009	—	`conf`	Alignment and Analysis of Closely Related Genomes. BICoB Allison Regier, Michael Olson, Scott J. Emrich
2009	A	`conf`	Harnessing parallelism in multicore clusters with the all-pairs and wavefront abstractions. HPDC Li Yi, Christopher Moretti, Scott J. Emrich, Kenneth Judd, Douglas Thain
2009	—	`conf`	Highly scalable genome assembly on campus grids. SC-MTAGS Christopher Moretti, Michael Olson, Scott J. Emrich, Douglas Thain
2007	J	`jnl`	Assembling genomes on large-scale parallel computers. J. Parallel Distributed Comput. Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru
2007	—	`conf`	Massively parallel expressed sequence tag clustering. PDCS Scott J. Emrich, Anantharaman Kalyanaraman, Srinivas Aluru
2006	A	`conf`	Assembling genomes on large-scale parallel computers. IPDPS Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru
2004	C	`conf`	A comparison of evolved finite state classifiers and interpolated Markov models for improving PCR primer design. CIBCB Daniel A. Ashlock, Scott J. Emrich, Kenneth Mark Bryden, Steven M. Corns, Tsui-Jung Wen, Patrick S. Schnable
2004	J	`jnl`	A strategy for assembling the maize (Zea mays L.) genome. Bioinform. Scott J. Emrich, Srinivas Aluru, Yan Fu, Tsui-Jung Wen, Mahesh Narayanan, Ling Guo, Daniel A. Ashlock, Patrick S. Schnable
2003	J	`jnl`	PROBEmer: a web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res. Scott J. Emrich, Mary Lowe, Arthur L. Delcher