Aakrosh Ratan, Ph.D. - Publications

Affiliations: 
2009 Pennsylvania State University, State College, PA, United States 

41 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
2020 Fry E, Kim SK, Chigurapti S, Mika KM, Ratan A, Dammermann A, Mitchell BJ, Miller W, Lynch VJ. Functional architecture of deleterious genetic variants in the genome of a Wrangel Island mammoth. Genome Biology and Evolution. PMID 32031213 DOI: 10.1093/gbe/evz279  0.52
2020 Wang TT, Yang J, Dighe S, Schmachtenberg MW, Leigh NT, Farber E, Onengut-Gumuscu S, Feith DJ, Ratan A, Loughran TP, Olson TL. Whole Genome Sequencing of Spontaneously Occurring Rat Natural Killer Large Granular Lymphocyte Leukemia Identifies JAK1 Somatic Activating Mutation. Cancers. 12. PMID 31947841 DOI: 10.3390/cancers12010126  0.4
2020 Suryamohan K, Krishnankutty SP, Guillory J, Jevit M, Schröder MS, Wu M, Kuriakose B, Mathew OK, Perumal RC, Koludarov I, Goldstein LD, Senger K, Dixon MD, Velayutham D, Vargas D, ... ... Ratan A, et al. The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. Nature Genetics. PMID 31907489 DOI: 10.1038/s41588-019-0559-8  0.36
2019 Moosic KB, Paila U, Olson KC, Dziewulska K, Wang TT, Xing JC, Ratan A, Feith DJ, Loughran TP, Olson TL. Genomics of LGL leukemia and select other rare leukemia/lymphomas. Best Practice & Research. Clinical Haematology. 32: 196-206. PMID 31585620 DOI: 10.1016/j.beha.2019.06.003  0.4
2019 Kitchen SA, Ratan A, Bedoya-Reina OC, Burhans R, Fogarty ND, Miller W, Baums IB. Genomic Variants Among Threatened Corals. G3 (Bethesda, Md.). PMID 30914426 DOI: 10.1534/g3.119.400125  0.52
2017 Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, et al. The microbiomes of blowflies and houseflies as bacterial transmission reservoirs. Scientific Reports. 7: 16324. PMID 29176730 DOI: 10.1038/s41598-017-16353-x  0.48
2017 Kistler L, Johnson SM, Irwin MT, Louis EE, Ratan A, Perry GH. A massively parallel strategy for STR marker development, capture, and genotyping. Nucleic Acids Research. PMID 28666376 DOI: 10.1093/nar/gkx574  0.48
2016 Agaba M, Ishengoma E, Miller WC, McGrath BC, Hudson CN, Bedoya Reina OC, Ratan A, Burhans R, Chikhi R, Medvedev P, Praul CA, Wu-Cavener L, Wood B, Robertson H, Penfold L, et al. Giraffe genome sequence reveals clues to its unique morphology and physiology. Nature Communications. 7: 11519. PMID 27187213 DOI: 10.1038/ncomms11519  0.52
2016 Carpi G, Kitchen A, Kim HL, Ratan A, Drautz-Moses DI, McGraw JJ, Kazimirova M, Rizzoli A, Schuster SC. Mitogenomes reveal diversity of the European Lyme borreliosis vector Ixodes ricinus in Italy. Molecular Phylogenetics and Evolution. PMID 27165938 DOI: 10.1016/j.ympev.2016.05.009  0.52
2016 Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C. Data characterizing the chloroplast genomes of extinct and endangered Hawaiian endemic mints (Lamiaceae) and their close relatives. Data in Brief. 7: 900-22. PMID 27077093 DOI: 10.1016/j.dib.2016.03.037  0.48
2016 Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C. The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). Molecular Phylogenetics and Evolution. PMID 26953739 DOI: 10.1016/j.ympev.2016.02.024  0.52
2016 Junqueira AC, Azeredo-Espin AM, Paulo DF, Marinho MA, Tomsho LP, Drautz-Moses DI, Purbojati RW, Ratan A, Schuster SC. Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity. Scientific Reports. 6: 21762. PMID 26912394 DOI: 10.1038/srep21762  0.52
2015 Fuller ZL, Niño EL, Patch HM, Bedoya-Reina OC, Baumgarten T, Muli E, Mumoki F, Ratan A, McGraw J, Frazier M, Masiga D, Schuster S, Grozinger CM, Miller W. Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools. Bmc Genomics. 16: 518. PMID 26159619 DOI: 10.1186/s12864-015-1712-0  0.52
2015 Lynch VJ, Bedoya-Reina OC, Ratan A, Sulak M, Drautz-Moses DI, Perry GH, Miller W, Schuster SC. Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Cell Reports. 12: 217-28. PMID 26146078 DOI: 10.1016/j.celrep.2015.06.027  0.52
2015 Ratan A, Olson TL, Loughran TP, Miller W. Identification of indels in next-generation sequencing data. Bmc Bioinformatics. 16: 42. PMID 25879703 DOI: 10.1186/s12859-015-0483-6  0.52
2015 Kistler L, Ratan A, Godfrey LR, Crowley BE, Hughes CE, Lei R, Cui Y, Wood ML, Muldoon KM, Andriamialison H, McGraw JJ, Tomsho LP, Schuster SC, Miller W, Louis EE, et al. Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs. Journal of Human Evolution. 79: 45-54. PMID 25523037 DOI: 10.1016/j.jhevol.2014.06.016  0.52
2015 Fuller ZL, Niño EL, Patch HM, Bedoya-Reina OC, Baumgarten T, Muli E, Mumoki F, Ratan A, McGraw J, Frazier M, Masiga D, Schuster S, Grozinger CM, Miller W. Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools Bmc Genomics. DOI: 10.1186/s12864-015-1712-0  0.52
2015 Lynch VJ, Bedoya-Reina OC, Ratan A, Sulak M, Drautz-Moses DI, Perry GH, Miller W, Schuster SC. Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic Cell Reports. DOI: 10.1016/j.celrep.2015.06.027  0.52
2014 Kim HL, Ratan A, Perry GH, Montenegro A, Miller W, Schuster SC. Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history. Nature Communications. 5: 5692. PMID 25471224 DOI: 10.1038/ncomms6692  0.52
2013 Bedoya-Reina OC, Ratan A, Burhans R, Kim HL, Giardine B, Riemer C, Li Q, Olson TL, Loughran TP, Vonholdt BM, Perry GH, Schuster SC, Miller W. Galaxy tools to study genome diversity. Gigascience. 2: 17. PMID 24377391 DOI: 10.1186/2047-217X-2-17  0.52
2013 Perry GH, Louis EE, Ratan A, Bedoya-Reina OC, Burhans RC, Lei R, Johnson SE, Schuster SC, Miller W. Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar. Proceedings of the National Academy of Sciences of the United States of America. 110: 5823-8. PMID 23530231 DOI: 10.1073/pnas.1211990110  0.52
2013 Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC. Comparison of sequencing platforms for single nucleotide variant calls in a human sample. Plos One. 8: e55089. PMID 23405114 DOI: 10.1371/journal.pone.0055089  0.52
2012 Giardine BM, Riemer C, Burhans R, Ratan A, Miller W. Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit15.2. PMID 22948727 DOI: 10.1002/0471250953.bi1502s39  0.52
2012 Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte AJ, Schuster SC, Seshagiri S, Thomas G. Sequencing and analysis of a South Asian-Indian personal genome. Bmc Genomics. 13: 440. PMID 22938532 DOI: 10.1186/1471-2164-13-440  0.52
2012 Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE, Tomsho LP, Ibarra-Laclette E, Herrera-Estrella L, Peacock E, Farley S, et al. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences of the United States of America. 109: E2382-90. PMID 22826254 DOI: 10.1073/pnas.1210506109  0.52
2012 Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE, Pritchard JK, Mason CE, Gilad Y. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biology and Evolution. 4: 126-35. PMID 22155688 DOI: 10.1093/gbe/evr132  0.52
2012 Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, et al. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil) (Proceedings of the National Academy of Sciences of the United States of America (2011) 108, 30 (12348-12353) DOI: 10.1073/pnas.1102838108) Proceedings of the National Academy of Sciences of the United States of America. 109: 18625. DOI: 10.1073/pnas.1217345109  0.52
2011 Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, et al. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences of the United States of America. 108: 12348-53. PMID 21709235 DOI: 10.1073/pnas.1102838108  0.52
2011 Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Ratan A, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/nature09687  0.52
2010 Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W. Calling SNPs without a reference sequence. Bmc Bioinformatics. 11: 130. PMID 20230626 DOI: 10.1186/1471-2105-11-130  0.52
2010 Lindqvist C, Schuster SC, Sun Y, Talbot SL, Qi J, Ratan A, Tomsho LP, Kasson L, Zeyl E, Aars J, Miller W, Ingólfsson O, Bachmann L, Wiig O. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proceedings of the National Academy of Sciences of the United States of America. 107: 5053-7. PMID 20194737 DOI: 10.1073/pnas.0914266107  0.52
2010 Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/nature08795  0.52
2010 Lindqvist C, Schuster SC, Sun Y, Talbot SL, Qi J, Ratan A, Tomsho LP, Kasson L, Zeyl E, Aars J, Miller W, Ingólfsson O, Bachmann L, Wiig Ø. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear (Proceedings of the National Academy of Sciences of the United States of America (2010) 107 (5053-5057)10.1073/pnas.0914266107) Proceedings of the National Academy of Sciences of the United States of America. 107: 6118. DOI: 10.1073/pnas.1002801107  0.52
2009 Willerslev E, Gilbert MT, Binladen J, Ho SY, Campos PF, Ratan A, Tomsho LP, da Fonseca RR, Sher A, Kuznetsova TV, Nowak-Kemp M, Roth TL, Miller W, Schuster SC. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. Bmc Evolutionary Biology. 9: 95. PMID 19432984 DOI: 10.1186/1471-2148-9-95  0.52
2009 Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MT, Dalén L, Arsuaga JL, Ericson PG, et al. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research. 19: 213-20. PMID 19139089 DOI: 10.1101/gr.082628.108  0.52
2008 Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 456: 387-90. PMID 19020620 DOI: 10.1038/nature07446  0.52
2008 Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. The infinite sites model of genome evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 14254-61. PMID 18787111 DOI: 10.1073/pnas.0805217105  0.52
2008 Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D. DUPCAR: reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 1007-27. PMID 18774902 DOI: 10.1089/cmb.2008.0069  0.52
2008 Gilbert MT, Drautz DI, Lesk AM, Ho SY, Qi J, Ratan A, Hsu CH, Sher A, Dalén L, Götherström A, Tomsho LP, Rendulic S, Packard M, Campos PF, Kuznetsova TV, et al. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences of the United States of America. 105: 8327-32. PMID 18541911 DOI: 10.1073/pnas.0802315105  0.52
2007 Ma J, Ratan A, Zhang L, Miller W, Haussler D. A heuristic algorithm for reconstructing ancestral gene orders with duplications Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4751: 122-135.  0.52
2002 Thomas K, Lalitha MK, Steinhoff MC, Arora NK, Ratan A, Das B, Awasthi SK, Mistra PK, Amita J, Daivanayagam R, Manjula P, Jain D, Agarwal V, Ravindran P, Cherian T, et al. Are Haemophilus influenzae infections a significant problem in India? A prospective study and review Clinical Infectious Diseases. 34: 949-957. PMID 11880961 DOI: 10.1086/339327  0.68
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