PROBEmer: a web-based software tool for selecting optimal DNA oligos. - Scott J. Emrich; Mary Lowe; Arthur L. Delcher (Nucleic Acids Res., 2003)

A comparison of evolved finite state classifiers and interpolated Markov models for improving PCR primer design. - Daniel A. Ashlock; Scott J. Emrich; Kenneth Mark Bryden; Steven M. Corns; Tsui-Jung Wen; Patrick S. Schnable (CIBCB, 2004)

A strategy for assembling the maize (Zea mays L.) genome. - Scott J. Emrich; Srinivas Aluru; Yan Fu; Tsui-Jung Wen; Mahesh Narayanan; Ling Guo; Daniel A. Ashlock; Patrick S. Schnable (Bioinform., 2004)

Massively parallel expressed sequence tag clustering. - Scott J. Emrich; Anantharaman Kalyanaraman; Srinivas Aluru (PDCS, 2007)

Assembling genomes on large-scale parallel computers. - Anantharaman Kalyanaraman; Scott J. Emrich; Patrick S. Schnable; Srinivas Aluru (J. Parallel Distributed Comput., 2007)

Alignment and Analysis of Closely Related Genomes. - Allison Regier; Michael Olson; Scott J. Emrich (BICoB, 2009)

Harnessing parallelism in multicore clusters with the all-pairs and wavefront abstractions. - Li Yi; Christopher Moretti; Scott J. Emrich; Kenneth Judd; Douglas Thain (HPDC, 2009)

Highly scalable genome assembly on campus grids. - Christopher Moretti; Michael Olson; Scott J. Emrich; Douglas Thain (SC-MTAGS, 2009)

A supervised learning approach to the unsupervised clustering of genes. - Andrew K. Rider; Geoffrey Siwo; Scott J. Emrich; Michael T. Ferdig; Nitesh V. Chawla (BIBM, 2010)

A two-stage machine learning approach for pathway analysis. - Wei Zhang 175; Scott J. Emrich; Erliang Zeng (BIBM, 2010)

Biocompute: towards a collaborative workspace for data intensive bio-science. - Rory Carmichael; Patrick Braga-Henebry; Douglas Thain; Scott J. Emrich (HPDC, 2010)

A statistical approach to finding overlooked genetic associations. - Andrew K. Rider; Geoffrey Siwo; Nitesh V. Chawla; Michael T. Ferdig; Scott J. Emrich (BMC Bioinform., 2010)

Harnessing parallelism in multicore clusters with the All-Pairs, Wavefront, and Makeflow abstractions. - Li Yu; Christopher Moretti; Andrew Thrasher; Scott J. Emrich; Kenneth Judd; Douglas Thain (Clust. Comput., 2010)

Robust haplotype reconstruction of eukaryotic read data with Hapler. - Shawn T. O'Neil; Scott J. Emrich (ICCABS, 2011)

Biocompute 2.0: an improved collaborative workspace for data intensive bio-science. - Rory Carmichael; Patrick Braga-Henebry; Douglas Thain; Scott J. Emrich (Concurr. Comput. Pract. Exp., 2011)

Workshop: Opportunities and challenges of non-model ecoinformatics. - Scott J. Emrich (ICCABS, 2012)

Shifting the bioinformatics computing paradigm: A case study in parallelizing genome annotation using MAKER and Work Queue. - Andrew Thrasher; Douglas Thain; Scott J. Emrich; Zachary Musgrave (ICCABS, 2012)

A machine learning framework for trait based genomics. - Wei Zhang 175; Erliang Zeng; Dan Liu; Stuart E. Jones; Scott J. Emrich (ICCABS, 2012)

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. - 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; et al. (Nucleic Acids Res., 2012)

A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids. - Christopher Moretti; Andrew Thrasher; Li Yu; Michael Olson; Scott J. Emrich; Douglas Thain (IEEE Trans. Parallel Distributed Syst., 2012)

Case Studies in Designing Elastic Applications. - Dinesh Rajan; Andrew Thrasher; Badi Abdul-Wahid; Jesús A. Izaguirre; Scott J. Emrich; Douglas Thain (CCGRID, 2013)

An unsupervised learning approach to assembly validation. - Irena Lanc; Scott J. Emrich (ICCABS, 2013)

Predicting bacterial functional traits from whole genome sequences using random forest. - Wei Zhang 175; Erliang Zeng; Scott J. Emrich; Joshua Livermore; Dan Liu; Stuart E. Jones (ICCABS, 2013)

Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning. - Olivia Choudhury; Nicholas L. Hazekamp; Douglas Thain; Scott J. Emrich (CCGRID, 2014)

Expanding Tasks of Logical Workflows Into Independent Workflows for Improved Scalability. - Nicholas L. Hazekamp; Olivia Choudhury; Sandra Gesing; Scott J. Emrich; Douglas Thain (CCGRID, 2014)

Adapting bioinformatics applications for heterogeneous systems: a case study. - Irena Lanc; Peter Bui; Douglas Thain; Scott J. Emrich (Concurr. Comput. Pract. Exp., 2014)

Scaling up genome annotation using MAKER and work queue. - Andrew Thrasher; Zachary Musgrave; Brian Kachmarck; Douglas Thain; Scott J. Emrich (Int. J. Bioinform. Res. Appl., 2014)

Mapping genomic features to functional traits through microbial whole genome sequences. - Wei Zhang 175; Erliang Zeng; Dan Liu; Stuart E. Jones; Scott J. Emrich (Int. J. Bioinform. Res. Appl., 2014)

A supervised learning approach to the ensemble clustering of genes. - Andrew K. Rider; Geoffrey Siwo; Scott J. Emrich; Michael T. Ferdig; Nitesh V. Chawla (Int. J. Data Min. Bioinform., 2014)

A computational framework for integrative analysis of large microbial genomics data. - Erliang Zeng; Wei Zhang 175; Scott J. Emrich; Dan Liu; Joshua Livermore; Stuart E. Jones (BIBM, 2015)

Balancing Thread-Level and Task-Level Parallelism for Data-Intensive Workloads on Clusters and Clouds. - Olivia Choudhury; Dinesh Rajan; Nicholas L. Hazekamp; Sandra Gesing; Douglas Thain; Scott J. Emrich (CLUSTER, 2015)

Scaling Up Bioinformatics Workflows with Dynamic Job Expansion: A Case Study Using Galaxy and Makeflow. - Nicholas L. Hazekamp; Joseph Sarro; Olivia Choudhury; Sandra Gesing; Scott J. Emrich; Douglas Thain (e-Science, 2015)

Global maximum-parsimony based ancestral reconstruction with non-universal genes. - Lauren A. Assour; Scott J. Emrich (ICCABS, 2015)

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. - 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; et al. (Bioinform., 2015)

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. - 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 (Nucleic Acids Res., 2015)

Accelerating Comparative Genomics Work ows in a Distributed Environment with Optimized Data Partitioning and Workflow Fusion. - Olivia Choudhury; Nicholas L. Hazekamp; Douglas Thain; Scott J. Emrich (Scalable Comput. Pract. Exp., 2015)

HAPI-Gen: Highly Accurate Phasing and Imputation of Genotype Data. - Olivia Choudhury; Ankush Chakrabarty; Scott J. Emrich (BCB, 2016)

Single molecule sequencing-guided scaffolding and correction of draft assemblies. - Shenglong Zhu; Danny Z. Chen; Scott J. Emrich (ICCABS, 2016)

Prediction of fine-tuned promoter activity from DNA sequence. - Geoffrey Siwo; Andrew K. Rider; Asako Tan; Richard S. Pinapati; Scott J. Emrich; Nitesh V. Chawla; Michael T. Ferdig (F1000Research, 2016)

Stable feature ranking with logistic regression ensembles. - Ronald J. Nowling; Scott J. Emrich (BIBM, 2017)

Widespread position-specific conservation of synonymous rare codons within coding sequences. - Julie L. Chaney; Aaron Steele; Rory Carmichael; Anabel Rodriguez; Alicia T. Specht; Kim Ngo; Jun Li 052; Scott J. Emrich; Patricia L. Clark (PLoS Comput. Biol., 2017)

Detecting Chromosomal Inversions from Dense SNPs by Combining PCA and Association Tests. - Ronald J. Nowling; Scott J. Emrich (BCB, 2018)

HarMinMax: Harmonizing Codon Usage to Replicate Local Host Translation. - Gabriel Wright; Anabel Rodriguez; Patricia L. Clark; Scott J. Emrich (BCB, 2018)

Effects from structure of Metabarcode Sequences on Lossy Analysis of Microbiome Data. - David C. Molik; Michael E. Pfrender; Scott J. Emrich (BIBM, 2018)

The Effects of Normalization, Transformation, and Rarefaction on Clustering of OTU Abundance. - DeAndre A. Tomlinson; David C. Molik; Michael E. Pfrender; Scott J. Emrich (BIBM, 2018)

Predicting Local Inversions Using Rectangle Clustering and Representative Rectangle Prediction. - Shenglong Zhu; Scott J. Emrich; Danny Z. Chen (BIBM, 2018)

Inversion detection using PacBio long reads. - Shenglong Zhu; Scott J. Emrich; Danny Z. Chen (Int. J. Data Min. Bioinform., 2018)

Adjusted likelihood-ratio test for variants with unknown genotypes. - Ronald J. Nowling; Scott J. Emrich (J. Bioinform. Comput. Biol., 2018)

Combining Static and Dynamic Storage Management for Data Intensive Scientific Workflows. - Nicholas L. Hazekamp; Nathaniel Kremer-Herman; Benjamín Tovar; Haiyan Meng; Olivia Choudhury; Scott J. Emrich; Douglas Thain (IEEE Trans. Parallel Distributed Syst., 2018)

Weighted graphlets and deep neural networks for protein structure classification. - Hongyu Guo; Khalique Newaz; Scott J. Emrich; Tijana Milenkovic; Jun Li 052 (CoRR, 2019)

Highly Accurate and Efficient Data-Driven Methods for Genotype Imputation. - Olivia Choudhury; Ankush Chakrabarty; Scott J. Emrich (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

PeakMatcher: Matching Peaks Across Genome Assemblies. - Ronald J. Nowling; Christopher R. Beal; Scott J. Emrich; Susanta K. Behura; Marc S. Halfon; Molly Duman-Scheel (BCB, 2020)

Extreme Phenotype Sampling Improves LASSO and Random Forest Marker Selection for Complex Traits. - Cai W. John; Wellington Muchero; Scott J. Emrich (BIBM, 2020)

Network analysis of synonymous codon usage. - Khalique Newaz; Gabriel Wright; Jacob Piland; Jun Li 052; Patricia L. Clark; Scott J. Emrich; Tijana Milenkovic (Bioinform., 2020)

Fine-Grained Synonymous Codon Usage Patterns and their Potential Role in Functional Protein Production. - Ashley Babjac; Jun Li 052; Scott J. Emrich (BIBM, 2021)

LASSO-based feature selection for improved microbial and microbiome classification. - Owen Queen; Scott J. Emrich (BIBM, 2021)

A comparison of dimensionality reduction methods for large biological data. - Ashley Babjac; Taylor M. Royalty; Andrew D. Steen; Scott J. Emrich (BCB, 2022)

CodonBERT: Using BERT for Sentiment Analysis to Better Predict Genes with Low Expression. - Ashley Nicole Babjac; Zhixiu Lu; Scott J. Emrich (BCB, 2023)

Adapting Protein Language Models for Explainable Fine-Grained Evolutionary Pattern Discovery. - Ashley Babjac; Owen Queen; Shawn-Patrick Barhorst; Kambiz Kalhor; Andrew D. Steen; Scott J. Emrich (BIBM, 2023)

Deep Learning for Reference-Free Geolocation for Poplar Trees. - Cai W. John; Owen Queen; Wellington Muchero; Scott J. Emrich (CoRR, 2023)

CodonT5: A Multi-task Codon Language Model to Perform Generative Codon Optimization. - Ashley Babjac; Scott J. Emrich (BIBM, 2024)