SE
Scott Emrich
bioinformaticsGenome, InsectSoftwareGenome, PlantgenomicsPolymorphism, Single NucleotideAnopheles gambiaeEvolution, MolecularGenomeProtein Folding
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
100 papers in the corpus · 2002–2025Reduced uptake through clathrin down-regulation is associated with resistance to dsRNA in a population of the Colorado potato beetle (Leptinotarsa decemlineata, Say).41326120 · Mishra, Swati, Lamour, Kurt, Emrich, Scott et al.2025 · 6 citationsPesticide biochemistry and physiology. 2026;216(Pt 1):106783
Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production.39190361 · Rodriguez, Anabel, Diehl, Jacob D, Wright, Gabriel S et al.2024 · 18 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(36):e2405510121
The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes.38273363 · Ryazansky, Sergei S, Chen, Chujia, Potters, Mark et al.2024 · 31 citationsBMC biology. 2024;22(1):16
Profiling Expression Strategies for a Type III Polyketide Synthase in a Lysate-Based, Cell-free System.38077034 · Sword, Tien T, Dinglasan, Jaime Lorenzo N, Abbas, Ghaeath S K et al.2024 · 12 citationsbioRxiv : the preprint server for biology. 2023
Screening for resistance alleles to Cry1 proteins through targeted sequencing in the native and invasive range of Spodoptera frugiperda (Lepidoptera: Noctuidae).37311017 · Tandy, Peter, Lamour, Kurt, Placidi de Bortoli, Caroline et al.2023 · 16 citationsJournal of economic entomology. 2023;116(3):935-944
Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World.37043542 · Labbé, Frédéric, Abdeladhim, Maha, Abrudan, Jenica et al.2023 · 25 citationsPLoS neglected tropical diseases. 2023;17(4):e0010862
Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito.36881629 · Small, Scott T, Costantini, Carlo, Sagnon, N'Fale et al.2023 · 19 citationsProceedings of the National Academy of Sciences of the United States of America. 2023;120(11):e2219835120
Deep Learning for Reference-Free Geolocation for Poplar Trees2301.13387v1 · Cai W. John, Owen Queen, Wellington Muchero et al.2023 · 0 citationsarXiv
Rapid plant trait evolution can alter coastal wetland resilience to sea level rise.36701449 · Vahsen, M L, Blum, M J, Megonigal, J P et al.2023 · 57 citationsScience (New York, N.Y.). 2023;379(6630):393-398
Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria vector10.1101/2022.11.21.517335v2 · Small, S. T., Costantini, C., Sagnon, N. et al.2022 · 0 citationsbioRxiv
Synonymous codon substitutions regulate transcription and translation of an upstream gene10.1101/2022.08.05.502938v1 · Rodriguez, A., Wright, G. S., Lundgren, T. et al.2022 · 2 citationsbioRxiv
Multi-layer sequential network analysis improves protein 3D structural classification.35441395 · Newaz, Khalique, Piland, Jacob, Clark, Patricia L et al.2022 · 7 citationsProteins. 2022;90(9):1721-1731
Fast, low-memory detection and localization of large, polymorphic inversions from SNPs.35116204 · Nowling, Ronald J, Fallas-Moya, Fabian, Sadovnik, Amir et al.2023 · 8 citationsPeerJ. 2022;10:e12831
CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern.34738275 · Wright, Gabriel, Rodriguez, Anabel, Li, Jun et al.2022 · 31 citationsProtein science : a publication of the Protein Society. 2022;31(1):221-231
Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.34325695 · Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M et al.2021 · 7 citationsBMC biology. 2021;19(1):150
Genetic Screening to Identify Candidate Resistance Alleles to Cry1F Corn in Fall Armyworm Using Targeted Sequencing.34357278 · Schlum, Katrina, Lamour, Kurt, Tandy, Peter et al.2021 · 16 citationsInsects. 2021;12(7)
The power and promise of genetic mapping from Plasmodium falciparum crosses utilizing human liver-chimeric mice.34127785 · Button-Simons, Katrina A, Kumar, Sudhir, Carmago, Nelly et al.2021 · 27 citationsCommunications biology. 2021;4(1):734
Dynamic network analysis improves protein 3D structural classification2105.07079v1 · Khalique Newaz, Jacob Piland, Patricia L. Clark et al.2021 · 0 citationsarXiv
Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations.33711916 · Schlum, Katrina A, Lamour, Kurt, de Bortoli, Caroline Placidi et al.2021 · 78 citationsBMC genomics. 2021;22(1):179
The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.33750380 · Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M et al.2021 · 46 citationsBMC biology. 2021;19(1):41
PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map.33509290 · Nowling, Ronald J, Behura, Susanta K, Halfon, Marc S et al.2021 · 2 citationsHereditas. 2021;158(1):7
Network analysis of synonymous codon usage.32609328 · Newaz, Khalique, Wright, Gabriel, Piland, Jacob et al.2021 · 10 citationsBioinformatics (Oxford, England). 2020;36(19):4876-4884
Detecting inversions with PCA in the presence of population structure.33119626 · Nowling, Ronald J, Manke, Krystal R, Emrich, Scott J2020 · 24 citationsPloS one. 2020;15(10):e0240429
Author Correction: GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison.32778675 · Faisal, Fazle E, Newaz, Khalique, Chaney, Julie L et al.2021 · 1 citationScientific reports. 2020;10(1):13455
Phlebotomus papatasi sand fly predicted salivary protein diversity and immune response potential based on in silico prediction in Egypt and Jordan populations.32658913 · Flanley, Catherine M, Ramalho-Ortigao, Marcelo, Coutinho-Abreu, Iliano V et al.2020 · 3 citationsPLoS neglected tropical diseases. 2020;14(7):e0007489
Analysis of computational codon usage models and their association with translationally slow codons.32352987 · Wright, Gabriel, Rodriguez, Anabel, Li, Jun et al.2020 · 13 citationsPloS one. 2020;15(4):e0232003
Uncovering Effects from the Structure of Metabarcode Sequences for Metagenetic and Microbiome Analysis.32178466 · Molik, David C, Pfrender, Michael E, Emrich, Scott J2020 · 5 citationsMethods and protocols. 2020;3(1)
Surprising variation in the outcome of two malaria genetic crosses using humanized mice: implications for genetic mapping and malaria biology10.1101/2019.12.13.871830v2 · Button-Simons, K. A., Kumar, S., Carmago, N. et al.2019 · 3 citationsbioRxiv
Genetic mapping of fitness determinants across the malaria parasite Plasmodium falciparum life cycle.31609965 · Li, Xue, Kumar, Sudhir, McDew-White, Marina et al.2020 · 53 citationsPLoS genetics. 2019;15(10):e1008453
Weighted graphlets and deep neural networks for protein structure classification1910.02594v1 · Hongyu Guo, Khalique Newaz, Scott Emrich et al.2019 · 3 citationsarXiv
Predicting Local Inversions Using Rectangle Clustering and Representative Rectangle Prediction.31180865 · Zhu, Shenglong, Emrich, Scott J, Chen, Danny Z2020 · 3 citationsIEEE transactions on nanobioscience. 2019;18(3):316-323
Functional genomics of the stable fly, Stomoxys calcitrans, reveals mechanisms underlying reproduction, host interactions, and novel targets for pest control10.1101/623009v1 · Olafson, P. U., Aksoy, S., Attardo, G. M. et al.2019 · 9 citationsbioRxiv
MIReAD, a minimum information standard for reporting arthropod abundance data.31024009 · Rund, Samuel S C, Braak, Kyle, Cator, Lauren et al.2019 · 35 citationsScientific data. 2019;6(1):40
Improved bacteria population structure analysis on thousands of genomes using unsupervised methods10.1101/599944v2 · Schlum, K. A., Jun, S.-R., Udaondo, Z. et al.2019 · 1 citationbioRxiv
A New Look at Codon Usage and Protein Expression.35342824 · Wright, Gabriel, Rodriguez, Anabel, Clark, Patricia L et al.2022 · 2 citationsEPiC series in computing. 2019;60:104-112
Adjusted likelihood-ratio test for variants with unknown genotypes.30419783 · Nowling, Ronald J, Emrich, Scott J2019 · 3 citationsJournal of bioinformatics and computational biology. 2018;16(5):1840020
Minimum Information for Reusable Arthropod Abundance Data (MIReAAD)10.1101/429142v2 · Rund, S. S. C., Braak, K., Cator, L. et al.2018 · 3 citationsbioRxiv
Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda.30081911 · Wiltshire, Rachel M, Bergey, Christina M, Kayondo, Jonathan K et al.2019 · 10 citationsMalaria journal. 2018;17(1):285
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning.29967328 · Choudhury, Olivia, Chakrabarty, Ankush, Emrich, Scott J2019 · 20 citationsScientific reports. 2018;8(1):9936
Activation of endothelial cells by extracellular vesicles derived from Mycobacterium tuberculosis infected macrophages or mice.29851993 · Li, Li, Cheng, Yong, Emrich, Scott et al.2018 · 41 citationsPloS one. 2018;13(5):e0198337
Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling.29463695 · Ryan, Sean F, Deines, Jillian M, Scriber, J Mark et al.2018 · 79 citationsProceedings of the National Academy of Sciences of the United States of America. 2018;115(10):E2284-E2291
The Effects of Normalization, Transformation, and Rarefaction on Clustering of OTU Abundance10.1101/259325v1 · Molik, D., Pfrender, M., Emrich, S.2018 · 2 citationsbioRxiv
Single molecule sequencing-guided scaffolding and correction of draft assemblies.29244003 · Zhu, Shenglong, Chen, Danny Z, Emrich, Scott J2018 · 6 citationsBMC genomics. 2017;18(Suppl 10):879
%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.29090506 · Rodriguez, Anabel, Wright, Gabriel, Emrich, Scott et al.2017 · 75 citationsProtein science : a publication of the Protein Society. 2018;27(1):356-362
GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison.29097661 · Faisal, Fazle E, Newaz, Khalique, Chaney, Julie L et al.2019 · 36 citationsScientific reports. 2017;7(1):14890
Methods in Description and Validation of Local Metagenetic Microbial Communities10.1101/198614v4 · Molik, D. C., Pfrender, M., Emrich, S.2017 · 3 citationsbioRxiv
Whole-Genome Shotgun Sequencing of Two β-Proteobacterial Species in Search of the Bulgecin Biosynthetic Cluster.28937735 · Horsman, Mark E, Marous, Daniel R, Li, Rongfeng et al.2017 · 32 citationsACS chemical biology. 2017;12(10):2552-2557
Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail.28832025 · Adema, Coen M, Hillier, LaDeana W, Jones, Catherine S et al.2019 · 19 citationsNature communications. 2017;8:16153
High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra.28558688 · Konar, Arpita, Choudhury, Olivia, Bullis, Rebecca et al.2018 · 36 citationsBMC genomics. 2017;18(1):417
Highly Accurate and Efficient Data-Driven Methods for Genotype Imputation.28574365 · Choudhury, Olivia, Chakrabarty, Ankush, Emrich, Scott J2020 · 8 citationsIEEE/ACM transactions on computational biology and bioinformatics. 2019;16(4):1107-1116
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