Scott J. Emrich - Publications

Affiliations: 
Computer Science and Engineering University of Notre Dame, Notre Dame, IN, United States 
Area:
Computer Science, Bioinformatics Biology, Information Technology

63 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Behura SK, Sarro J, Li P, Mysore K, Severson DW, Emrich SJ, Duman-Scheel M. High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti. Bmc Genomics. 17: 341. PMID 27161480 DOI: 10.1186/S12864-016-2468-X  0.92
2016 Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, ... ... Emrich SJ, et al. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proceedings of the National Academy of Sciences of the United States of America. PMID 27035980 DOI: 10.1073/Pnas.1525164113  0.92
2015 Mesquita RD, Vionette-Amaral RJ, Lowenberger C, Rivera-Pomar R, Monteiro FA, Minx P, Spieth J, Carvalho AB, Panzera F, Lawson D, Torres AQ, Ribeiro JM, Sorgine MH, Waterhouse RM, Montague MJ, ... ... Emrich SJ, et al. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection. Proceedings of the National Academy of Sciences of the United States of America. 112: 14936-14941. PMID 26627243 DOI: 10.1073/Pnas.1506226112  0.92
2015 Ramalho-Ortigão M, Coutinho-Abreu IV, Balbino VQ, Figueiredo CA, Mukbel R, Dayem H, Hanafi HA, El-Hossary SS, Fawaz Eel-D, Abo-Shehada M, Hoel DF, Stayback G, Wadsworth M, Shoue DA, Abrudan J, ... ... Emrich SJ, et al. Phlebotomus papatasi SP15: mRNA expression variability and amino acid sequence polymorphisms of field populations. Parasites & Vectors. 8: 298. PMID 26022221 DOI: 10.1186/S13071-015-0914-2  0.92
2015 Mbengue A, Bhattacharjee S, Pandharkar T, Liu H, Estiu G, Stahelin RV, Rizk SS, Njimoh DL, Ryan Y, Chotivanich K, Nguon C, Ghorbal M, Lopez-Rubio JJ, Pfrender M, Emrich S, et al. A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria. Nature. 520: 683-7. PMID 25874676 DOI: 10.1038/Nature14412  0.92
2015 Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, Madey G, Collins FH, Lawson D. VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Research. 43: D707-13. PMID 25510499 DOI: 10.1093/Nar/Gku1117  0.92
2015 Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, ... ... Emrich SJ, et al. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science (New York, N.Y.). 347: 1258524. PMID 25431491 DOI: 10.1126/Science.1258524  0.92
2015 Choudhury O, Hazekamp NL, Thain D, Emrich SJ. Accelerating comparative genomics workflows in a distributed environment with optimized data partitioning and workflow fusion Scalable Computing. 16: 53-69. DOI: 10.12694/Scpe.V16I1.1060  0.92
2015 Assour LA, Emrich SJ. Global maximum-parsimony based ancestral reconstruction with non-universal genes 2015 Ieee 5th International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2015. DOI: 10.1109/ICCABS.2015.7344716  0.92
2015 Hazekamp N, Sarro J, Choudhury O, Gesing S, Emrich S, Thain D. Scaling up bioinformatics workflows with dynamic job expansion: A case study using galaxy and makeflow Proceedings - 11th Ieee International Conference On Escience, Escience 2015. 332-341. DOI: 10.1109/eScience.2015.39  0.92
2015 Choudhury O, Rajan D, Hazekamp N, Gesing S, Thain D, Emrich S. Balancing thread-level and task-level parallelism for data-intensive workloads on clusters and clouds Proceedings - Ieee International Conference On Cluster Computing, Iccc. 2015: 390-393. DOI: 10.1109/CLUSTER.2015.60  0.92
2015 Aganezov S, Sitdykova N, Alekseyev MA, Neafsey DE, Christophides GK, Collins FH, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Howell PI, Kafatos FC, Lawson D, Muskavitch MAT, Waterhouse R, et al. Scaffold assembly based on genome rearrangement analysis Computational Biology and Chemistry. 57: 46-53. DOI: 10.1016/j.compbiolchem.2015.02.005  0.92
2015 Assour LA, Emrich SJ. Multi-genome synteny for assembly improvement Proceedings of the 7th International Conference On Bioinformatics and Computational Biology, Bicob 2015. 193-198.  0.92
2015 Steele A, Emrich SJ. PbSandwich: Scaffolding draft genomes with long reads Proceedings of the 7th International Conference On Bioinformatics and Computational Biology, Bicob 2015. 155-160.  0.92
2014 Tomchaney M, Mysore K, Sun L, Li P, Emrich SJ, Severson DW, Duman-Scheel M. Examination of the genetic basis for sexual dimorphism in the Aedes aegypti (dengue vector mosquito) pupal brain. Biology of Sex Differences. 5: 10. PMID 25729562 DOI: 10.1186/S13293-014-0010-X  0.92
2014 Zhang W, Zeng E, Liu D, Jones SE, Emrich S. Mapping genomic features to functional traits through microbial whole genome sequences. International Journal of Bioinformatics Research and Applications. 10: 461-78. PMID 24989863 DOI: 10.1504/Ijbra.2014.062995  0.92
2014 Thrasher A, Musgrave Z, Kachmarck B, Thain D, Emrich S. Scaling up genome annotation using MAKER and work queue International Journal of Bioinformatics Research and Applications. 10: 447-460. PMID 24989862 DOI: 10.1504/Ijbra.2014.062994  0.92
2014 Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, et al. Standardized metadata for human pathogen/vector genomic sequences. Plos One. 9: e99979. PMID 24936976 DOI: 10.1371/Journal.Pone.0099979  0.92
2014 Rider AK, Siwo G, Emrich SJ, Ferdig MT, Chawla NV. A supervised learning approach to the ensemble clustering of genes. International Journal of Data Mining and Bioinformatics. 9: 199-219. PMID 24864378 DOI: 10.1504/IJDMB.2014.059062  0.92
2014 O'Neil ST, Dzurisin JD, Williams CM, Lobo NF, Higgins JK, Deines JM, Carmichael RD, Zeng E, Tan JC, Wu GC, Emrich SJ, Hellmann JJ. Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world. Molecular Ecology. 23: 2686-98. PMID 24766086 DOI: 10.1111/Mec.12773  0.92
2014 Livermore JA, Emrich SJ, Tan J, Jones SE. Freshwater bacterial lifestyles inferred from comparative genomics. Environmental Microbiology. 16: 746-58. PMID 23889754 DOI: 10.1111/1462-2920.12199  0.92
2014 Hazekamp N, Choudhury O, Gesing S, Emrich S, Thain D. Expanding tasks of logical workflows into independent workflows for improved scalability Proceedings - 14th Ieee/Acm International Symposium On Cluster, Cloud, and Grid Computing, Ccgrid 2014. 548-549. DOI: 10.1109/CCGrid.2014.84  0.92
2014 Choudhury O, Hazekamp NL, Thain D, Emrich S. Accelerating comparative genomics workflows in a distributed environment with optimized data partitioning Proceedings - 14th Ieee/Acm International Symposium On Cluster, Cloud, and Grid Computing, Ccgrid 2014. 711-719. DOI: 10.1109/CCGrid.2014.79  0.92
2014 Lanc I, Bui P, Thain D, Emrich S. Adapting bioinformatics applications for heterogeneous systems: A case study Concurrency Computation Practice and Experience. 26: 866-877. DOI: 10.1002/Cpe.2927  0.92
2013 Rinker DC, Zhou X, Pitts RJ, Rokas A, Zwiebel LJ. Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. Bmc Genomics. 14: 749. PMID 24182346 DOI: 10.1186/1471-2164-14-749  0.92
2013 Evans JD, Brown SJ, Hackett KJJ, Robinson G, Richards S, Lawson D, Elsik C, Coddington J, Edwards O, Emrich S, Gabaldon T, Goldsmith M, Hanes G, Misof B, Muñoz-Torres M, et al. The i5K initiative: Advancing arthropod genomics for knowledge, human health, agriculture, and the environment Journal of Heredity. 104: 595-600. PMID 23940263 DOI: 10.1093/Jhered/Est050  0.92
2013 O'Neil ST, Emrich SJ. Assessing De Novo transcriptome assembly metrics for consistency and utility. Bmc Genomics. 14: 465. PMID 23837739 DOI: 10.1186/1471-2164-14-465  0.92
2013 Neafsey DE, Christophides GK, Collins FH, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Howell PI, Kafatos FC, Lawson D, Muskavitch MA, Waterhouse RM, Williams LJ, Besansky NJ. The evolution of the Anopheles 16 genomes project. G3 (Bethesda, Md.). 3: 1191-4. PMID 23708298 DOI: 10.1534/G3.113.006247  0.92
2013 Abrudan J, Ramalho-Ortigão M, O'Neil S, Stayback G, Wadsworth M, Bernard M, Shoue D, Emrich S, Lawyer P, Kamhawi S, Rowton ED, Lehane MJ, Bates PA, Valenzeula JG, Tomlinson C, et al. The characterization of the Phlebotomus papatasi transcriptome. Insect Molecular Biology. 22: 211-32. PMID 23398403 DOI: 10.1111/Imb.12015  0.92
2013 Zhang W, Zeng E, Emrich SJ, Livermore J, Liu D, Jones SE. Predicting bacterial functional traits from whole genome sequences using random forest 2013 Ieee 3rd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2013. DOI: 10.1109/ICCABS.2013.6629212  0.92
2013 Rajan D, Thrasher A, Abdul-Wahid B, Izaguirre JA, Emrich S, Thain D. Case studies in designing elastic applications Proceedings - 13th Ieee/Acm International Symposium On Cluster, Cloud, and Grid Computing, Ccgrid 2013. 466-473. DOI: 10.1109/CCGrid.2013.46  0.92
2013 Rider AK, Chawla NV, Emrich SJ. A survey of current integrative network algorithms for systems biology Systems Biology. 1: 479-495. DOI: 10.1007/978-94-007-6803-1_17  0.92
2012 O'Neil ST, Emrich SJ. Haplotype and minimum-chimerism consensus determination using short sequence data. Bmc Genomics. 13: S4. PMID 22537299 DOI: 10.1186/1471-2164-13-S2-S4  0.92
2012 Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, Maccallum RM, Redmond SN, Sheehan A, Topalis P, Wilson D. VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Research. 40: D729-34. PMID 22135296 DOI: 10.1093/Nar/Gkr1089  0.92
2012 Moretti C, Thrasher A, Yu L, Olson M, Emrich S, Thain D. A framework for scalable genome assembly on clusters, clouds, and grids Ieee Transactions On Parallel and Distributed Systems. 23: 2189-2197. DOI: 10.1109/Tpds.2012.80  0.92
2012 Zhang W, Zeng E, Liu D, Jones S, Emrich S. A machine learning framework for trait based genomics 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182648  0.92
2012 Thrasher A, Thain D, Emrich S, Musgrave Z. Shifting the bioinformatics computing paradigm: A case study in parallelizing genome annotation using MAKER and Work Queue 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182647  0.92
2011 Samarakoon U, Regier A, Tan A, Desany BA, Collins B, Tan JC, Emrich SJ, Ferdig MT. High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum. Bmc Genomics. 12: 116. PMID 21324207 DOI: 10.1186/1471-2164-12-116  0.92
2011 O'Neil ST, Emrich SJ. Robust haplotype reconstruction of eukaryotic read data with Hapler 2011 Ieee 1st International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2011. 141-146. DOI: 10.1109/ICCABS.2011.5729869  0.92
2011 Carmichael R, Braga-Henebry P, Thain D, Emrich S. Biocompute 2.0: An improved collaborative workspace for data intensive bio-science Concurrency Computation Practice and Experience. 23: 2305-2314. DOI: 10.1002/Cpe.1782  0.92
2010 Lobo NF, Sangaré DM, Regier AA, Reidenbach KR, Bretz DA, Sharakhova MV, Emrich SJ, Traore SF, Costantini C, Besansky NJ, Collins FH. Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion. Malaria Journal. 9: 293. PMID 20974007 DOI: 10.1186/1475-2875-9-293  0.92
2010 Lawniczak MK, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang SP, Minx P, Nelson J, et al. Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science (New York, N.Y.). 330: 512-4. PMID 20966253 DOI: 10.1126/Science.1195755  0.92
2010 Rider AK, Siwo G, Chawla NV, Ferdig M, Emrich SJ. A statistical approach to finding overlooked genetic associations. Bmc Bioinformatics. 11: 526. PMID 20964847 DOI: 10.1186/1471-2105-11-526  0.92
2010 O'Neil ST, Dzurisin JD, Carmichael RD, Lobo NF, Emrich SJ, Hellmann JJ. Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. Bmc Genomics. 11: 310. PMID 20478048 DOI: 10.1186/1471-2164-11-310  0.92
2010 Liu S, Chen HD, Makarevitch I, Shirmer R, Emrich SJ, Dietrich CR, Barbazuk WB, Springer NM, Schnable PS. High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing. Genetics. 184: 19-26. PMID 19884313 DOI: 10.1534/Genetics.109.107557  0.92
2010 Carmichael R, Braga-Henebry P, Thain D, Emrich S. Biocompute: Towards a collaborative workspace for data intensive bio-science Hpdc 2010 - Proceedings of the 19th Acm International Symposium On High Performance Distributed Computing. 489-498. DOI: 10.1145/1851476.1851547  0.92
2010 Thrasher A, Carmichael R, Bui P, Yu L, Thain D, Emrich S. Taming complex bioinformatics workflows with weaver, makeflow, and starch 2010 5th Workshop On Workflows in Support of Large-Scale Science, Works 2010. DOI: 10.1109/WORKS.2010.5671858  0.92
2010 Rider A, Siwo G, Emrich S, Ferdig M, Chawla NV. A supervised learning approach to the unsupervised clustering of genes Proceedings - 2010 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2010. 323-328. DOI: 10.1109/BIBM.2010.5706585  0.92
2010 Zhang W, Emrich S, Zeng E. A two-stage machine learning approach for pathway analysis Proceedings - 2010 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2010. 274-279. DOI: 10.1109/BIBM.2010.5706576  0.92
2010 Yu L, Moretti C, Thrasher A, Emrich S, Judd K, Thain D. Harnessing parallelism in multicore clusters with the All-Pairs, Wavefront, and Makeflow abstractions Cluster Computing. 13: 243-256. DOI: 10.1007/S10586-010-0134-7  0.92
2009 Moretti C, Olson M, Emrich S, Thain D. Highly scalable genome assembly on campus grids Proceedings of the 2nd Acm Workshop On Many-Task Computing On Grids and Supercomputers 2009, Mtags '09. DOI: 10.1145/1646468.1646480  0.92
2009 Yu L, Moretti C, Emrich S, Judd K, Thain D. Harnessing parallelism in multicore clusters with the all-pairs and wavefront abstractions Proc. 18th Acm International Symposium On High Performance Distributed Computing, Hpdc 09, Co-Located With the 2009 International Symposium On High Performance Distributed Computing Conf., Hpdc'09. 1-10. DOI: 10.1145/1551609.1551613  0.92
2009 Regier A, Olson M, Emrich SJ. Alignment and analysis of closely related genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5462: 343-352. DOI: 10.1007/978-3-642-00727-9_32  0.92
2007 Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MC, Beck J, Buckner B, Janick-Buckner D, Nettleton D, Scanlon MJ, Schnable PS. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). The Plant Journal : For Cell and Molecular Biology. 52: 391-404. PMID 17764504 DOI: 10.1111/J.1365-313X.2007.03244.X  0.92
2007 Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS. SNP discovery via 454 transcriptome sequencing. The Plant Journal : For Cell and Molecular Biology. 51: 910-8. PMID 17662031 DOI: 10.1111/J.1365-313X.2007.03193.X  0.92
2007 Emrich SJ, Li L, Wen TJ, Yandeau-Nelson MD, Fu Y, Guo L, Chou HH, Aluru S, Ashlock DA, Schnable PS. Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution. Genetics. 175: 429-39. PMID 17110490 DOI: 10.1534/Genetics.106.064006  0.92
2007 Emrich SJ, Barbazuk WB, Li L, Schnable PS. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Research. 17: 69-73. PMID 17095711 DOI: 10.1101/Gr.5145806  0.92
2007 Kalyanaraman A, Emrich SJ, Schnable PS, Aluru S. Assembling genomes on large-scale parallel computers Journal of Parallel and Distributed Computing. 67: 1240-1255. DOI: 10.1016/J.Jpdc.2007.05.014  0.92
2005 Fu Y, Emrich SJ, Guo L, Wen TJ, Ashlock DA, Aluru S, Schnable PS. Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. Proceedings of the National Academy of Sciences of the United States of America. 102: 12282-7. PMID 16103354 DOI: 10.1073/Pnas.0503394102  0.92
2005 Yao H, Guo L, Fu Y, Borsuk LA, Wen TJ, Skibbe DS, Cui X, Scheffler BE, Cao J, Emrich SJ, Ashlock DA, Schnable PS. Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Molecular Biology. 57: 445-60. PMID 15830133 DOI: 10.1007/S11103-005-0271-1  0.92
2004 Emrich SJ, Aluru S, Fu Y, Wen TJ, Narayanan M, Guo L, Ashlock DA, Schnable PS. A strategy for assembling the maize (Zea mays L.) genome. Bioinformatics (Oxford, England). 20: 140-7. PMID 14734303 DOI: 10.1093/Bioinformatics/Bth017  0.92
2004 Ashlock DA, Emrich SJ, Bryden KM, Corns SM, Wen TJ, Schnable PS. A comparison of evolved finite state classifiers and interpolated Markov models for improving PCR primer design Proceedings of the 2004 Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology, Cibcb'04. 190-197.  0.92
2003 Emrich SJ, Lowe M, Delcher AL. PROBEmer: A web-based software tool for selecting optimal DNA oligos. Nucleic Acids Research. 31: 3746-50. PMID 12824409 DOI: 10.1093/Nar/Gkg569  0.92
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