| Year |
Citation |
Score |
| 2023 |
Jun G, English A, Metcalf G, Yang J, Chaisson M, Pankratz N, Menon V, Salerno W, Krasheninina O, Smith A, Lane J, Blackwell T, Kang HM, Salvi S, Meng Q, ... ... Ratan A, et al. Structural variation across 138,134 samples in the TOPMed consortium. Research Square. PMID 36778386 DOI: 10.21203/rs.3.rs-2515453/v1 |
0.342 |
|
| 2023 |
Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, ... ... Ratan A, et al. Structural variation across 138,134 samples in the TOPMed consortium. Biorxiv : the Preprint Server For Biology. PMID 36747810 DOI: 10.1101/2023.01.25.525428 |
0.343 |
|
| 2023 |
Kim HL, Li T, Kalsi N, Nguyen HTT, Shaw TA, Ang KC, Cheng KC, Ratan A, Peltier WR, Samanta D, Pratapneni M, Schuster SC, Horton BP. Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise. Communications Biology. 6: 150. PMID 36739308 DOI: 10.1038/s42003-023-04510-0 |
0.309 |
|
| 2022 |
Wheeler MM, Stilp AM, Rao S, Halldórsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, ... ... Ratan A, et al. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nature Communications. 13: 7592. PMID 36481753 DOI: 10.1038/s41467-022-35354-7 |
0.466 |
|
| 2022 |
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. Author Correction: Comparative and demographic analysis of orang-utan genomes. Nature. PMID 35962045 DOI: 10.1038/s41586-022-04799-7 |
0.665 |
|
| 2021 |
Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM, Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, Gupta N, Gabriel S, Blackwell TW, Ratan A, Taylor KD, et al. Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science (New York, N.Y.). 374: abg8871. PMID 34914532 DOI: 10.1126/science.abg8871 |
0.46 |
|
| 2020 |
Fang C, Wang Z, Han C, Safgren SL, Helmin KA, Adelman ER, Serafin V, Basso G, Eagen KP, Gaspar-Maia A, Figueroa ME, Singer BD, Ratan A, Ntziachristos P, Zang C. Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation. Genome Biology. 21: 247. PMID 32933554 DOI: 10.1186/S13059-020-02152-7 |
0.428 |
|
| 2020 |
Grabski DF, Ratan A, Gray LR, Bekiranov S, Rekosh D, Hammarskjold ML, Rasmussen SK. Upregulation of human endogenous retrovirus-K (HML-2) mRNAs in hepatoblastoma: Identification of potential new immunotherapeutic targets and biomarkers. Journal of Pediatric Surgery. PMID 32682541 DOI: 10.1016/J.Jpedsurg.2020.05.022 |
0.342 |
|
| 2020 |
Grabski DF, Ratan A, Gray LR, Bekiranov S, Rekosh D, Hammarskjold ML, Rasmussen SK. Human endogenous retrovirus-K mRNA expression and genomic alignment data in hepatoblastoma. Data in Brief. 31: 105895. PMID 32637500 DOI: 10.1016/J.Dib.2020.105895 |
0.421 |
|
| 2020 |
Kathuria K, Ratan A. SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures. Plos Computational Biology. 16: e1007737. PMID 32182236 DOI: 10.1371/Journal.Pcbi.1007737 |
0.374 |
|
| 2020 |
Chatrath A, Przanowska R, Kiran S, Su Z, Saha S, Wilson B, Tsunematsu T, Ahn JH, Lee KY, Paulsen T, Sobierajska E, Kiran M, Tang X, Li T, Kumar P, ... Ratan A, et al. The pan-cancer landscape of prognostic germline variants in 10,582 patients. Genome Medicine. 12: 15. PMID 32066500 DOI: 10.1186/S13073-020-0718-7 |
0.33 |
|
| 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 |
0.606 |
|
| 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 |
0.33 |
|
| 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 |
0.527 |
|
| 2020 |
Onengut-Gumuscu S, Paila UD, Chen W, Ratan A, Zhu Z, Steck A, Frohnert BI, Waugh K, Webb-Robertson B, Norris JM, Lange L, Rewers M, Rich SS. 107-OR: Novel Genetic Risk Factors Influence Islet Autoimmunity Progression Diabetes. 69. DOI: 10.2337/Db20-107-Or |
0.458 |
|
| 2019 |
Wall JD, Ratan A, Stawiski E. Identification of African-Specific Admixture between Modern and Archaic Humans. American Journal of Human Genetics. 105: 1254-1261. PMID 31809748 DOI: 10.1016/J.Ajhg.2019.11.005 |
0.51 |
|
| 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 |
0.308 |
|
| 2019 |
Feng J, Ratan A, Sheffield NC. Augmented Interval List: a novel data structure for efficient genomic interval search. Bioinformatics (Oxford, England). PMID 31150060 DOI: 10.1093/Bioinformatics/Btz407 |
0.519 |
|
| 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 |
0.684 |
|
| 2019 |
Chatrath A, Kiran M, Kumar P, Ratan A, Dutta A. The Germline Variants rs61757955 and rs34988193 are Predictive of Survival in Lower Grade Glioma Patients. Molecular Cancer Research : McR. PMID 30651372 DOI: 10.1158/1541-7786.Mcr-18-0996 |
0.379 |
|
| 2018 |
Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Improved molecular karyotyping in glioblastoma. Mutation Research. 811: 16-26. PMID 30055482 DOI: 10.1016/J.Mrfmmm.2018.06.002 |
0.493 |
|
| 2018 |
Kedzierska KZ, Gerber L, Cagnazzi D, Krützen M, Ratan A, Kistler L. SONiCS: PCR stutter noise correction in genome-scale microsatellites. Bioinformatics (Oxford, England). PMID 29931218 DOI: 10.1093/Bioinformatics/Bty485 |
0.491 |
|
| 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 |
0.491 |
|
| 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 |
0.543 |
|
| 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 |
0.622 |
|
| 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 |
0.527 |
|
| 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 |
0.557 |
|
| 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 |
0.575 |
|
| 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 |
0.498 |
|
| 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 |
0.67 |
|
| 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 |
0.581 |
|
| 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 |
0.653 |
|
| 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 |
0.599 |
|
| 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 |
0.602 |
|
| 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 |
0.619 |
|
| 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 |
0.622 |
|
| 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 |
0.708 |
|
| 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 |
0.659 |
|
| 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 |
0.656 |
|
| 2013 |
Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC. Venn diagram showing the overlap in the SNP calls made using data from the three sequencing technologies. Plos One. DOI: 10.1371/Journal.Pone.0055089.G003 |
0.549 |
|
| 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 |
0.643 |
|
| 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 |
0.714 |
|
| 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 |
0.669 |
|
| 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 |
0.72 |
|
| 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 |
0.491 |
|
| 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 |
0.69 |
|
| 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 |
0.74 |
|
| 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 |
0.704 |
|
| 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 |
0.593 |
|
| 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 |
0.724 |
|
| 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 |
0.324 |
|
| 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 |
0.652 |
|
| 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 |
0.681 |
|
| 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 |
0.706 |
|
| 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 |
0.684 |
|
| 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 |
0.657 |
|
| 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 |
0.739 |
|
| 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. |
0.394 |
|
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