Scott J. Emrich

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 30

Top Topics

Comparative Genomics

Data Partitioning

Dimensionality Reduction Methods

Feature Ranking

Top Venues

Publications

Cai W. John, Owen Queen, Wellington Muchero, Scott J. Emrich
Deep Learning for Reference-Free Geolocation for Poplar Trees. CoRR (2023)
Ashley Babjac, Owen Queen, Shawn-Patrick Barhorst, Kambiz Kalhor, Andrew D. Steen, Scott J. Emrich
Adapting Protein Language Models for Explainable Fine-Grained Evolutionary Pattern Discovery. BIBM (2023)
Ashley Nicole Babjac, Zhixiu Lu, Scott J. Emrich
CodonBERT: Using BERT for Sentiment Analysis to Better Predict Genes with Low Expression. BCB (2023)
Ashley Babjac, Taylor M. Royalty, Andrew D. Steen, Scott J. Emrich
A comparison of dimensionality reduction methods for large biological data. BCB (2022)
Owen Queen, Scott J. Emrich
LASSO-based feature selection for improved microbial and microbiome classification. BIBM (2021)
Khalique Newaz, Gabriel Wright, Jacob Piland, Jun Li, Patricia L. Clark, Scott J. Emrich, Tijana Milenkovic
Network analysis of synonymous codon usage. Bioinform. 36 (19) (2020)
Ronald J. Nowling, Christopher R. Beal, Scott J. Emrich, Susanta K. Behura, Marc S. Halfon, Molly Duman-Scheel
PeakMatcher: Matching Peaks Across Genome Assemblies. BCB (2020)
Hongyu Guo, Khalique Newaz, Scott J. Emrich, Tijana Milenkovic, Jun Li
Weighted graphlets and deep neural networks for protein structure classification. CoRR (2019)
Olivia Choudhury, Ankush Chakrabarty, Scott J. Emrich
Highly Accurate and Efficient Data-Driven Methods for Genotype Imputation. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (4) (2019)
Shenglong Zhu, Scott J. Emrich, Danny Z. Chen
Inversion detection using PacBio long reads. Int. J. Data Min. Bioinform. 20 (3) (2018)
Gabriel Wright, Anabel Rodriguez, Patricia L. Clark, Scott J. Emrich
HarMinMax: Harmonizing Codon Usage to Replicate Local Host Translation. BCB (2018)
Ronald J. Nowling, Scott J. Emrich
Detecting Chromosomal Inversions from Dense SNPs by Combining PCA and Association Tests. BCB (2018)
Shenglong Zhu, Scott J. Emrich, Danny Z. Chen
Predicting Local Inversions Using Rectangle Clustering and Representative Rectangle Prediction. BIBM (2018)
David C. Molik, Michael E. Pfrender, Scott J. Emrich
Effects from structure of Metabarcode Sequences on Lossy Analysis of Microbiome Data. BIBM (2018)
DeAndre A. Tomlinson, David C. Molik, Michael E. Pfrender, Scott J. Emrich
The Effects of Normalization, Transformation, and Rarefaction on Clustering of OTU Abundance. BIBM (2018)
Ronald J. Nowling, Scott J. Emrich
Adjusted likelihood-ratio test for variants with unknown genotypes. J. Bioinform. Comput. Biol. 16 (5) (2018)
Nicholas L. Hazekamp, Nathaniel Kremer-Herman, Benjamín Tovar, Haiyan Meng, Olivia Choudhury, Scott J. Emrich, Douglas Thain
Combining Static and Dynamic Storage Management for Data Intensive Scientific Workflows. IEEE Trans. Parallel Distributed Syst. 29 (2) (2018)
Ronald J. Nowling, Scott J. Emrich
Stable feature ranking with logistic regression ensembles. BIBM (2017)
Shenglong Zhu, Scott J. Emrich, Danny Z. Chen
Inversion detection using PacBio long reads. BIBM (2017)
Julie L. Chaney, Aaron Steele, Rory Carmichael, Anabel Rodriguez, Alicia T. Specht, Kim Ngo, Jun Li, Scott J. Emrich, Patricia L. Clark
Widespread position-specific conservation of synonymous rare codons within coding sequences. PLoS Comput. Biol. 13 (5) (2017)
Olivia Choudhury, Ankush Chakrabarty, Scott J. Emrich
HAPI-Gen: Highly Accurate Phasing and Imputation of Genotype Data. BCB (2016)
Geoffrey Siwo, Andrew K. Rider, Asako Tan, Richard S. Pinapati, Scott J. Emrich, Nitesh V. Chawla, Michael T. Ferdig
Prediction of fine-tuned promoter activity from DNA sequence. F1000Research 5 (2016)
Shenglong Zhu, Danny Z. Chen, Scott J. Emrich
Single molecule sequencing-guided scaffolding and correction of draft assemblies. ICCABS (2016)
Nicholas L. Hazekamp, Joseph Sarro, Olivia Choudhury, Sandra Gesing, Scott J. Emrich, Douglas Thain
Scaling Up Bioinformatics Workflows with Dynamic Job Expansion: A Case Study Using Galaxy and Makeflow. e-Science (2015)
Erliang Zeng, Wei Zhang, Scott J. Emrich, Dan Liu, Joshua Livermore, Stuart E. Jones
A computational framework for integrative analysis of large microbial genomics data. BIBM (2015)
Olivia Choudhury, Nicholas L. Hazekamp, Douglas Thain, Scott J. Emrich
Accelerating Comparative Genomics Work ows in a Distributed Environment with Optimized Data Partitioning and Workflow Fusion. Scalable Comput. Pract. Exp. 16 (1) (2015)
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
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. Bioinform. 31 (9) (2015)
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
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res. 43 (Database-Issue) (2015)
Olivia Choudhury, Dinesh Rajan, Nicholas L. Hazekamp, Sandra Gesing, Douglas Thain, Scott J. Emrich
Balancing Thread-Level and Task-Level Parallelism for Data-Intensive Workloads on Clusters and Clouds. CLUSTER (2015)
Lauren A. Assour, Scott J. Emrich
Global maximum-parsimony based ancestral reconstruction with non-universal genes. ICCABS (2015)
Andrew K. Rider, Geoffrey Siwo, Scott J. Emrich, Michael T. Ferdig, Nitesh V. Chawla
A supervised learning approach to the ensemble clustering of genes. Int. J. Data Min. Bioinform. 9 (2) (2014)
Andrew Thrasher, Zachary Musgrave, Brian Kachmarck, Douglas Thain, Scott J. Emrich
Scaling up genome annotation using MAKER and work queue. Int. J. Bioinform. Res. Appl. 10 (4/5) (2014)
Wei Zhang, Erliang Zeng, Dan Liu, Stuart E. Jones, Scott J. Emrich
Mapping genomic features to functional traits through microbial whole genome sequences. Int. J. Bioinform. Res. Appl. 10 (4/5) (2014)
Olivia Choudhury, Nicholas L. Hazekamp, Douglas Thain, Scott J. Emrich
Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning. CCGRID (2014)
Irena Lanc, Peter Bui, Douglas Thain, Scott J. Emrich
Adapting bioinformatics applications for heterogeneous systems: a case study. Concurr. Comput. Pract. Exp. 26 (4) (2014)
Nicholas L. Hazekamp, Olivia Choudhury, Sandra Gesing, Scott J. Emrich, Douglas Thain
Expanding Tasks of Logical Workflows Into Independent Workflows for Improved Scalability. CCGRID (2014)
Wei Zhang, Erliang Zeng, Scott J. Emrich, Joshua Livermore, Dan Liu, Stuart E. Jones
Predicting bacterial functional traits from whole genome sequences using random forest. ICCABS (2013)
Dinesh Rajan, Andrew Thrasher, Badi Abdul-Wahid, Jesús A. Izaguirre, Scott J. Emrich, Douglas Thain
Case Studies in Designing Elastic Applications. CCGRID (2013)
Irena Lanc, Scott J. Emrich
An unsupervised learning approach to assembly validation. ICCABS (2013)
Scott J. Emrich
Workshop: Opportunities and challenges of non-model ecoinformatics. ICCABS (2012)
Wei Zhang, Erliang Zeng, Dan Liu, Stuart E. Jones, Scott J. Emrich
A machine learning framework for trait based genomics. ICCABS (2012)
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
VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res. 40 (Database-Issue) (2012)
Andrew Thrasher, Douglas Thain, Scott J. Emrich, Zachary Musgrave
Shifting the bioinformatics computing paradigm: A case study in parallelizing genome annotation using MAKER and Work Queue. ICCABS (2012)
Christopher Moretti, Andrew Thrasher, Li Yu, Michael Olson, Scott J. Emrich, Douglas Thain
A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids. IEEE Trans. Parallel Distributed Syst. 23 (12) (2012)
Shawn T. O'Neil, Scott J. Emrich
Robust haplotype reconstruction of eukaryotic read data with Hapler. ICCABS (2011)
Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, Scott J. Emrich
Biocompute 2.0: an improved collaborative workspace for data intensive bio-science. Concurr. Comput. Pract. Exp. 23 (17) (2011)
Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, Scott J. Emrich
Biocompute: towards a collaborative workspace for data intensive bio-science. HPDC (2010)
Andrew K. Rider, Geoffrey Siwo, Nitesh V. Chawla, Michael T. Ferdig, Scott J. Emrich
A statistical approach to finding overlooked genetic associations. BMC Bioinform. 11 (2010)
Andrew K. Rider, Geoffrey Siwo, Scott J. Emrich, Michael T. Ferdig, Nitesh V. Chawla
A supervised learning approach to the unsupervised clustering of genes. BIBM (2010)
Wei Zhang, Scott J. Emrich, Erliang Zeng
A two-stage machine learning approach for pathway analysis. BIBM (2010)
Li Yu, Christopher Moretti, Andrew Thrasher, Scott J. Emrich, Kenneth Judd, Douglas Thain
Harnessing parallelism in multicore clusters with the All-Pairs, Wavefront, and Makeflow abstractions. Clust. Comput. 13 (3) (2010)
Christopher Moretti, Michael Olson, Scott J. Emrich, Douglas Thain
Highly scalable genome assembly on campus grids. SC-MTAGS (2009)
Li Yi, Christopher Moretti, Scott J. Emrich, Kenneth Judd, Douglas Thain
Harnessing parallelism in multicore clusters with the all-pairs and wavefront abstractions. HPDC (2009)
Allison Regier, Michael Olson, Scott J. Emrich
Alignment and Analysis of Closely Related Genomes. BICoB (2009)
Scott J. Emrich, Anantharaman Kalyanaraman, Srinivas Aluru
Massively parallel expressed sequence tag clustering. PDCS (2007)
Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru
Assembling genomes on large-scale parallel computers. J. Parallel Distributed Comput. 67 (12) (2007)
Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru
Assembling genomes on large-scale parallel computers. IPDPS (2006)
Scott J. Emrich, Srinivas Aluru, Yan Fu, Tsui-Jung Wen, Mahesh Narayanan, Ling Guo, Daniel A. Ashlock, Patrick S. Schnable
A strategy for assembling the maize (Zea mays L.) genome. Bioinform. 20 (2) (2004)
Daniel A. Ashlock, Scott J. Emrich, Kenneth Mark Bryden, Steven M. Corns, Tsui-Jung Wen, Patrick S. Schnable
A comparison of evolved finite state classifiers and interpolated Markov models for improving PCR primer design. CIBCB (2004)
Scott J. Emrich, Mary Lowe, Arthur L. Delcher
PROBEmer: a web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res. 31 (13) (2003)