☰

Manyuan Long - Publications

Affiliations: 
Pritzker School of Medicine and The Division of Biological Sciences University of Chicago, Chicago, IL 
Area:
Molecular evolution, population genetics
Website:
http://pondside.uchicago.edu/ecol-evol/faculty/long_m.html
Tree Info Grants Similar researchers PubMed Report error

134 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
2023 Flynn JM, Ahmed-Braimah YH, Long M, Wing RA, Clark AG. High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the Drosophila virilis sub-group. Genome Biology and Evolution. PMID 38159044 DOI: 10.1093/gbe/evad238  0.686
2023 Chen J, Landback P, Arsala D, Guzzetta A, Xia S, Atlas J, Dong C, Sosa D, Zhang YE, Cheng J, Shen B, Long M. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. Biorxiv : the Preprint Server For Biology. PMID 38045239 DOI: 10.1101/2023.11.14.567139  0.842
2023 Flynn JM, Ahmed-Braimah YH, Long M, Wing RA, Clark AG. High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the sub-group. Biorxiv : the Preprint Server For Biology. PMID 37645834 DOI: 10.1101/2023.08.13.553086  0.689
2023 Zhang L, Park JJ, Dong MB, Arsala D, Xia S, Chen J, Sosa D, Atlas JE, Long M, Chen S. Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system. Genome Biology and Evolution. PMID 37170918 DOI: 10.1093/gbe/evad081  0.853
2022 Lee U, Mortola EN, Kim EJ, Long M. Evolution and maintenance of phenotypic plasticity. Bio Systems. 222: 104791. PMID 36244511 DOI: 10.1016/j.biosystems.2022.104791  0.781
2022 Betrán E, Long M. Evolutionary New Genes in a Growing Paradigm. Genes. 13. PMID 36140774 DOI: 10.3390/genes13091605  0.788
2022 Miller D, Chen J, Liang J, Betrán E, Long M, Sharakhov IV. Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes. Genes. 13. PMID 35741730 DOI: 10.3390/genes13060968  0.828
2022 Zhou Y, Zhang C, Zhang L, Ye Q, Liu N, Wang M, Long G, Fan W, Long M, Wing RA. Gene fusion as an important mechanism to generate new genes in the genus Oryza. Genome Biology. 23: 130. PMID 35706016 DOI: 10.1186/s13059-022-02696-w  0.865
2021 Krinsky BH, Arthur RK, Xia S, Sosa D, Arsala D, White KP, Long M. Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in . Genes. 13. PMID 35052398 DOI: 10.3390/genes13010057  0.856
2021 Huang Y, Chen J, Dong C, Sosa D, Xia S, Ouyang Y, Fan C, Li D, Mortola E, Long M, Bergelson J. Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. The Plant Cell. PMID 34875081 DOI: 10.1093/plcell/koab291  0.847
2021 Xia S, Ventura IM, Blaha A, Sgromo A, Han S, Izaurralde E, Long M. Rapid Gene evolution in an ancient post-transcriptional and translational regulatory system compensates for meiotic X chromosomal inactivation. Molecular Biology and Evolution. PMID 34626117 DOI: 10.1093/molbev/msab296  0.824
2021 Jin G, Ma PF, Wu X, Gu L, Long M, Zhang C, Li DZ. New Genes Interacted with Recent Whole Genome Duplicates in the Fast Stem Growth of Bamboos. Molecular Biology and Evolution. PMID 34581782 DOI: 10.1093/molbev/msab288  0.76
2021 Xia S, VanKuren NW, Chen C, Zhang L, Kemkemer C, Shao Y, Jia H, Lee U, Advani AS, Gschwend A, Vibranovski MD, Chen S, Zhang YE, Long M. Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development. Plos Genetics. 17: e1009654. PMID 34242211 DOI: 10.1371/journal.pgen.1009654  0.875
2021 Long M. A zebrafish-specific chimeric gene evolved essential developmental functions: discussion of conceptual significance. Science China. Life Sciences. PMID 33580430 DOI: 10.1007/s11427-021-1884-2  0.434
2020 Cheng Y, Shang D, Luo M, Huang C, Lai F, Wang X, Xu X, Ying R, Wang L, Zhao Y, Zhang L, Long M, Cheng H, Zhou R. Whole genome-wide chromosome fusion and new gene birth in the genome. Cell & Bioscience. 10: 67. PMID 32477490 DOI: 10.1186/s13578-020-00432-0  0.446
2020 Flynn JM, Long M, Wing RA, Clark AG. Evolutionary dynamics of abundant 7 bp satellites in the genome of Drosophila virilis. Molecular Biology and Evolution. PMID 31960929 DOI: 10.1093/Molbev/Msaa010  0.723
2019 Lee YCG, Ventura IM, Rice GR, Chen DY, Colmenares SU, Long M. Rapid evolution of gained essential developmental functions of a young gene via interactions with other essential genes. Molecular Biology and Evolution. PMID 31187122 DOI: 10.1093/molbev/msz137  0.619
2019 Long M, Shen B. Evolution of genes and genomes: an emerging paradigm in life science. Science China. Life Sciences. PMID 30929192 DOI: 10.1007/s11427-018-9448-x  0.692
2019 Zhang W, Gao Y, Long M, Shen B. Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans. Science China. Life Sciences. PMID 30919281 DOI: 10.1007/s11427-019-9482-0  0.824
2019 Zu J, Gu Y, Li Y, Li C, Zhang W, Zhang YE, Lee U, Zhang L, Long M. Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors. Science China. Life Sciences. PMID 30919280 DOI: 10.1007/s11427-019-9483-6  0.699
2019 Shao Y, Chen C, Shen H, He BZ, Yu D, Jiang S, Zhao S, Gao Z, Zhu Z, Chen X, Fu Y, Chen H, Gao G, Long M, Zhang YE. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Research. PMID 30862647 DOI: 10.1101/gr.238733.118  0.815
2019 Zhang L, Ren Y, Yang T, Li G, Chen J, Gschwend AR, Yu Y, Hou G, Zi J, Zhou R, Wen B, Zhang J, Chougule K, Wang M, Copetti D, ... ... Long M, et al. Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution. PMID 30858588 DOI: 10.1038/S41559-019-0822-5  0.856
2019 Gao G, Vibranovski MD, Zhang L, Li Z, Liu M, Zhang YE, Li X, Zhang W, Fan Q, VanKuren NW, Long M, Wei L. Corrigendum: A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster Genome Research. 29: 1566_1-1566_1. DOI: 10.1101/Gr.255315.119  0.765
2018 Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, ... ... Long M, et al. Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics. PMID 30291357 DOI: 10.1038/S41588-018-0261-2  0.78
2018 VanKuren NW, Long M. Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. Nature Ecology & Evolution. PMID 29459709 DOI: 10.1038/s41559-018-0471-0  0.808
2018 Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, ... ... Long M, et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics. PMID 29358651 DOI: 10.1038/S41588-018-0040-0  0.832
2017 Long M, Emerson JJ. Meiotic Sex Chromosome Inactivation: Compensation by Gene Traffic. Current Biology : Cb. 27: R659-R661. PMID 28697367 DOI: 10.1016/J.Cub.2017.05.077  0.739
2017 Chwen Y, Lee G, Yang Q, Chi W, Turkson SA, Du WA, Kemkemer C, Zeng ZB, Long M, Zhuang X. Genetic architecture of natural variation underlying adult foraging behavior that is essential for survival of Drosophila melanogaster. Genome Biology and Evolution. PMID 28472322 DOI: 10.1093/Gbe/Evx089  0.363
2017 Chen ZX, Oliver B, Zhang YE, Gao G, Long M. Expressed Structurally-stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. Genome Biology and Evolution. PMID 28338961 DOI: 10.1093/gbe/evx054  0.703
2016 Tan S, Cardoso-Moreira M, Shi W, Zhang D, Huang J, Mao Y, Jia H, Zhang Y, Chen C, Shao Y, Leng L, Liu Z, Huang X, Long M, Zhang YE. LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans. Genome Research. 26: 1663-1675. PMID 27934698 DOI: 10.1101/Gr.204925.116  0.569
2015 Zhang W, Landback P, Gschwend AR, Shen B, Long M. New genes drive the evolution of gene interaction networks in the human and mouse genomes. Genome Biology. 16: 202. PMID 26424194 DOI: 10.1186/S13059-015-0772-4  0.848
2015 Long MD, van den Berg PR, Russell JL, Singh PK, Battaglia S, Campbell MJ. Integrative genomic analysis in K562 chronic myelogenous leukemia cells reveals that proximal NCOR1 binding positively regulates genes that govern erythroid differentiation and Imatinib sensitivity. Nucleic Acids Research. PMID 26117541 DOI: 10.1093/nar/gkv642  0.446
2014 Zhang YE, Long M. New genes contribute to genetic and phenotypic novelties in human evolution. Current Opinion in Genetics & Development. 29: 90-6. PMID 25218862 DOI: 10.1016/j.gde.2014.08.013  0.64
2014 Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, ... ... Long M, et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics. 46: 982-8. PMID 25064006 DOI: 10.1038/Ng.3044  0.828
2014 Kemkemer C, Long M. New genes important for development. Embo Reports. 15: 460-1. PMID 24723687 DOI: 10.1002/embr.201438787  0.655
2014 Zhang C, Gschwend AR, Ouyang Y, Long M. Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes. Plant Physiology. 165: 412-23. PMID 24520158 DOI: 10.1104/Pp.113.231696  0.86
2014 Gao G, Vibranovski MD, Zhang L, Li Z, Liu M, Zhang YE, Li X, Zhang W, Fan Q, VanKuren NW, Long M, Wei L. A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. Genome Research. 24: 629-38. PMID 24407956 DOI: 10.1101/Gr.165837.113  0.827
2013 Long M, VanKuren NW, Chen S, Vibranovski MD. New gene evolution: little did we know. Annual Review of Genetics. 47: 307-33. PMID 24050177 DOI: 10.1146/Annurev-Genet-111212-133301  0.872
2013 Chen S, Krinsky BH, Long M. New genes as drivers of phenotypic evolution. Nature Reviews. Genetics. 14: 645-60. PMID 23949544 DOI: 10.1038/Nrg3521  0.872
2013 Zhang C, Wang J, Marowsky NC, Long M, Wing RA, Fan C. High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. Genome Biology and Evolution. 5: 1038-48. PMID 23651622 DOI: 10.1093/Gbe/Evt071  0.873
2013 Zhang C, Wang J, Long M, Fan C. gKaKs: the pipeline for genome-level Ka/Ks calculation. Bioinformatics (Oxford, England). 29: 645-6. PMID 23314322 DOI: 10.1093/Bioinformatics/Btt009  0.809
2013 Long M. Society for molecular biology and evolution, council and business meetings, 2012, Dublin, Ireland Molecular Biology and Evolution. 30: 234-235. DOI: 10.1093/molbev/mss244  0.323
2013 Chen S, Krinsky BH, Long M. Erratum: New genes as drivers of phenotypic evolution Nature Reviews Genetics. 14: 744-744. DOI: 10.1038/Nrg3584  0.855
2012 Long M, Zhang L. Why rodent pseudogenes refuse to retire. Genome Biology. 13: 178. PMID 23167957 DOI: 10.1186/gb4060  0.38
2012 Ni X, Zhang YE, Nègre N, Chen S, Long M, White KP. Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome. Plos Biology. 10: e1001420. PMID 23139640 DOI: 10.1371/Journal.Pbio.1001420  0.718
2012 Zhang YE, Landback P, Vibranovski M, Long M. New genes expressed in human brains: implications for annotating evolving genomes. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 34: 982-91. PMID 23001763 DOI: 10.1002/Bies.201200008  0.872
2012 Vibranovski MD, Zhang YE, Kemkemer C, VanKuren NW, Lopes HF, Karr TL, Long M. Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes. Bmc Evolutionary Biology. 12: 169. PMID 22950647 DOI: 10.1186/1471-2148-12-169  0.847
2012 Chen S, Spletter M, Ni X, White KP, Luo L, Long M. Frequent recent origination of brain genes shaped the evolution of foraging behavior in Drosophila. Cell Reports. 1: 118-32. PMID 22832161 DOI: 10.1016/J.Celrep.2011.12.010  0.704
2012 Vibranovski MD, Zhang YE, Kemkemer C, Lopes HF, Karr TL, Long M. Re-analysis of the larval testis data on meiotic sex chromosome inactivation revealed evidence for tissue-specific gene expression related to the drosophila X chromosome. Bmc Biology. 10: 49; author reply 50. PMID 22691264 DOI: 10.1186/1741-7007-10-49  0.818
2012 Chen S, Ni X, Krinsky BH, Zhang YE, Vibranovski MD, White KP, Long M. Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene. The Embo Journal. 31: 2798-809. PMID 22543869 DOI: 10.1038/Emboj.2012.108  0.871
2012 Wang J, Long M, Vibranovski MD. Retrogenes moved out of the z chromosome in the silkworm. Journal of Molecular Evolution. 74: 113-26. PMID 22535494 DOI: 10.1007/s00239-012-9499-y  0.791
2012 Cardoso-Moreira M, Long M. The origin and evolution of new genes. Methods in Molecular Biology (Clifton, N.J.). 856: 161-86. PMID 22399459 DOI: 10.1007/978-1-61779-585-5_7  0.606
2011 Cardoso-Moreira M, Emerson JJ, Clark AG, Long M. Drosophila duplication hotspots are associated with late-replicating regions of the genome. Plos Genetics. 7: e1002340. PMID 22072977 DOI: 10.1371/Journal.Pgen.1002340  0.742
2011 Zhang YE, Landback P, Vibranovski MD, Long M. Accelerated recruitment of new brain development genes into the human genome. Plos Biology. 9: e1001179. PMID 22028629 DOI: 10.1371/Journal.Pbio.1001179  0.841
2011 Chen S, Yang H, Krinsky BH, Zhang A, Long M. Roles of young serine-endopeptidase genes in survival and reproduction revealed rapid evolution of phenotypic effects at adult stages. Fly. 5: 345-51. PMID 21946255 DOI: 10.4161/Fly.5.4.17808  0.84
2011 Chen M, Zou M, Fu B, Li X, Vibranovski MD, Gan X, Wang D, Wang W, Long M, He S. Evolutionary patterns of RNA-based duplication in non-mammalian chordates. Plos One. 6: e21466. PMID 21779328 DOI: 10.1371/Journal.Pone.0021466  0.804
2011 Zhang YE, Vibranovski MD, Krinsky BH, Long M. A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes. Bioinformatics (Oxford, England). 27: 1749-53. PMID 21551137 DOI: 10.1093/bioinformatics/btr280  0.869
2011 Chen ZX, Zhang YE, Vibranovski M, Luo J, Gao G, Long M. Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Molecular Biology and Evolution. 28: 2823-32. PMID 21546357 DOI: 10.1093/Molbev/Msr101  0.831
2011 Chen Y, Dai H, Chen S, Zhang L, Long M. Highly tissue specific expression of Sphinx supports its male courtship related role in Drosophila melanogaster. Plos One. 6: e18853. PMID 21541324 DOI: 10.1371/Journal.Pone.0018853  0.784
2011 Zhang C, Wang J, Xie W, Zhou G, Long M, Zhang Q. Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method. Proceedings of the National Academy of Sciences of the United States of America. 108: 7860-5. PMID 21521791 DOI: 10.1073/Pnas.1018621108  0.593
2010 Chen S, Zhang YE, Long M. New genes in Drosophila quickly become essential. Science (New York, N.Y.). 330: 1682-5. PMID 21164016 DOI: 10.1126/Science.1196380  0.794
2010 Fu B, Chen M, Zou M, Long M, He S. The rapid generation of chimerical genes expanding protein diversity in zebrafish. Bmc Genomics. 11: 657. PMID 21106061 DOI: 10.1186/1471-2164-11-657  0.666
2010 Zhang YE, Vibranovski MD, Landback P, Marais GA, Long M. Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome. Plos Biology. 8. PMID 20957185 DOI: 10.1371/Journal.Pbio.1000494  0.854
2010 Zhang J, Yang H, Long M, Li L, Dean AM. Evolution of enzymatic activities of testis-specific short-chain dehydrogenase/reductase in Drosophila. Journal of Molecular Evolution. 71: 241-9. PMID 20809353 DOI: 10.1007/S00239-010-9384-5  0.711
2010 Zhang YE, Vibranovski MD, Krinsky BH, Long M. Age-dependent chromosomal distribution of male-biased genes in Drosophila. Genome Research. 20: 1526-33. PMID 20798392 DOI: 10.1101/Gr.107334.110  0.855
2010 Vibranovski MD, Chalopin DS, Lopes HF, Long M, Karr TL. Direct evidence for postmeiotic transcription during Drosophila melanogaster spermatogenesis. Genetics. 186: 431-3. PMID 20610406 DOI: 10.1534/Genetics.110.118919  0.732
2010 Cardoso-Moreira MM, Long M. Mutational bias shaping fly copy number variation: implications for genome evolution. Trends in Genetics : Tig. 26: 243-7. PMID 20416969 DOI: 10.1016/j.tig.2010.03.002  0.545
2010 Raleigh DR, Marchiando AM, Zhang Y, Shen L, Sasaki H, Wang Y, Long M, Turner JR. Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions. Molecular Biology of the Cell. 21: 1200-13. PMID 20164257 DOI: 10.1091/Mbc.E09-08-0734  0.327
2010 Arguello JR, Zhang Y, Kado T, Fan C, Zhao R, Innan H, Wang W, Long M. Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome. Molecular Biology and Evolution. 27: 848-61. PMID 20008457 DOI: 10.1093/Molbev/Msp291  0.771
2009 Vibranovski MD, Lopes HF, Karr TL, Long M. Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes. Plos Genetics. 5: e1000731. PMID 19936020 DOI: 10.1371/Journal.Pgen.1000731  0.809
2009 Zhang Y, Lu S, Zhao S, Zheng X, Long M, Wei L. Positive selection for the male functionality of a co-retroposed gene in the hominoids. Bmc Evolutionary Biology. 9: 252. PMID 19832993 DOI: 10.1186/1471-2148-9-252  0.664
2009 Zhu Z, Zhang Y, Long M. Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant Physiology. 151: 1943-51. PMID 19789289 DOI: 10.1104/Pp.109.142984  0.823
2009 Li Z, Liu M, Zhang L, Zhang W, Gao G, Zhu Z, Wei L, Fan Q, Long M. Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster. Nucleic Acids Research. 37: 4308-14. PMID 19451167 DOI: 10.1093/Nar/Gkp334  0.388
2009 Vibranovski MD, Zhang Y, Long M. General gene movement off the X chromosome in the Drosophila genus. Genome Research. 19: 897-903. PMID 19251740 DOI: 10.1101/Gr.088609.108  0.815
2009 Xiao W, Liu H, Li Y, Li X, Xu C, Long M, Wang S. A rice gene of de novo origin negatively regulates pathogen-induced defense response. Plos One. 4: e4603. PMID 19240804 DOI: 10.1371/journal.pone.0004603  0.592
2009 Kaessmann H, Vinckenbosch N, Long M. RNA-based gene duplication: mechanistic and evolutionary insights. Nature Reviews. Genetics. 10: 19-31. PMID 19030023 DOI: 10.1038/nrg2487  0.566
2008 Fan C, Zhang Y, Yu Y, Rounsley S, Long M, Wing RA. The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice. Molecular Plant. 1: 839-50. PMID 19825586 DOI: 10.1093/Mp/Ssn050  0.886
2008 Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M. Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science (New York, N.Y.). 320: 1629-31. PMID 18535209 DOI: 10.1126/Science.1158078  0.726
2008 Dai H, Chen Y, Chen S, Mao Q, Kennedy D, Landback P, Eyre-Walker A, Du W, Long M. The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 105: 7478-83. PMID 18508971 DOI: 10.1073/Pnas.0800693105  0.85
2008 Fan C, Chen Y, Long M. Recurrent tandem gene duplication gave rise to functionally divergent genes in Drosophila. Molecular Biology and Evolution. 25: 1451-8. PMID 18408233 DOI: 10.1093/Molbev/Msn089  0.84
2008 Shiao MS, Liao BY, Long M, Yu HT. Adaptive evolution of the insulin two-gene system in mouse. Genetics. 178: 1683-91. PMID 18245324 DOI: 10.1534/Genetics.108.087023  0.805
2008 Yang S, Arguello JR, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zhao R, Brunet F, Peng L, Long M, Wang W. Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. Plos Genetics. 4: e3. PMID 18208328 DOI: 10.1371/Journal.Pgen.0040003  0.659
2007 Arguello JR, Fan C, Wang W, Long M. Origination of chimeric genes through DNA-level recombination. Genome Dynamics. 3: 131-46. PMID 18753789 DOI: 10.1159/000107608  0.537
2007 Havlioglu N, Wang J, Fushimi K, Vibranovski MD, Kan Z, Gish W, Fedorov A, Long M, Wu JY. An intronic signal for alternative splicing in the human genome. Plos One. 2: e1246. PMID 18043753 DOI: 10.1371/Journal.Pone.0001246  0.785
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Long M, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.831
2007 Shiao MS, Khil P, Camerini-Otero RD, Shiroishi T, Moriwaki K, Yu HT, Long M. Origins of new male germ-line functions from X-derived autosomal retrogenes in the mouse. Molecular Biology and Evolution. 24: 2242-53. PMID 17646254 DOI: 10.1093/molbev/msm153  0.776
2007 Elde NC, Long M, Turkewitz AP. A role for convergent evolution in the secretory life of cells. Trends in Cell Biology. 17: 157-64. PMID 17329106 DOI: 10.1016/J.Tcb.2007.02.007  0.333
2007 Fan C, Long M. A new retroposed gene in Drosophila heterochromatin detected by microarray-based comparative genomic hybridization. Journal of Molecular Evolution. 64: 272-83. PMID 17177089 DOI: 10.1007/S00239-006-0169-9  0.823
2007 Fan C, Vibranovski MD, Chen Y, Long M. A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants: Case Analyses of Arabidopsis and Oryza Journal of Integrative Plant Biology. 49: 915-926. DOI: 10.1111/J.1744-7909.2007.00503.X  0.86
2006 Dai H, Yoshimatsu TF, Long M. Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes. Gene. 385: 96-102. PMID 17101240 DOI: 10.1016/J.Gene.2006.04.033  0.743
2006 Wang W, Zheng H, Fan C, Li J, Shi J, Cai Z, Zhang G, Liu D, Zhang J, Vang S, Lu Z, Wong GK, Long M, Wang J. High rate of chimeric gene origination by retroposition in plant genomes. The Plant Cell. 18: 1791-802. PMID 16829590 DOI: 10.1105/Tpc.106.041905  0.838
2006 Arguello JR, Chen Y, Yang S, Wang W, Long M. Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila. Plos Genetics. 2: e77. PMID 16715176 DOI: 10.1371/Journal.Pgen.0020077  0.722
2005 Zhang J, Long M, Li L. Translational effects of differential codon usage among intragenic domains of new genes in Drosophila. Biochimica Et Biophysica Acta. 1728: 135-42. PMID 15833448 DOI: 10.1016/J.Bbaexp.2005.02.004  0.629
2005 Thornton K, Long M. Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster. Molecular Biology and Evolution. 22: 273-84. PMID 15483321 DOI: 10.1093/molbev/msi015  0.697
2004 Zhang J, Dean AM, Brunet F, Long M. Evolving protein functional diversity in new genes of Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 101: 16246-50. PMID 15534206 DOI: 10.1073/Pnas.0407066101  0.772
2004 Betrán E, Emerson JJ, Kaessmann H, Long M. Sex chromosomes and male functions: where do new genes go? Cell Cycle (Georgetown, Tex.). 3: 873-5. PMID 15190200 DOI: 10.4161/Cc.3.7.960  0.858
2004 Wang W, Thornton K, Emerson JJ, Long M. Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. Genetics. 166: 1783-94. PMID 15126398 DOI: 10.1534/Genetics.166.4.1783  0.803
2004 Wang W, Yu H, Long M. Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nature Genetics. 36: 523-7. PMID 15064762 DOI: 10.1038/Ng1338  0.673
2004 Emerson JJ, Kaessmann H, Betrán E, Long M. Extensive gene traffic on the mammalian X chromosome. Science (New York, N.Y.). 303: 537-40. PMID 14739461 DOI: 10.1126/Science.1090042  0.856
2003 Long M, Betrán E, Thornton K, Wang W. The origin of new genes: glimpses from the young and old. Nature Reviews. Genetics. 4: 865-75. PMID 14634634 DOI: 10.1038/Nrg1204  0.882
2003 Betrán E, Long M. Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics. 164: 977-88. PMID 12871908  0.749
2003 Long M, Deutsch M, Wang W, Betrán E, Brunet FG, Zhang J. Origin of new genes: evidence from experimental and computational analyses. Genetica. 118: 171-82. PMID 12868607 DOI: 10.1023/A:1024153609285  0.883
2002 Betrán E, Thornton K, Long M. Retroposed new genes out of the X in Drosophila. Genome Research. 12: 1854-9. PMID 12466289 DOI: 10.1101/gr.6049  0.86
2002 Betrán E, Long M. Expansion of genome coding regions by acquisition of new genes. Genetica. 115: 65-80. PMID 12188049 DOI: 10.1023/A:1016024131097  0.792
2002 Llopart A, Comeron JM, Brunet FG, Lachaise D, Long M. Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proceedings of the National Academy of Sciences of the United States of America. 99: 8121-6. PMID 12060758 DOI: 10.1073/Pnas.122570299  0.468
2002 Thornton K, Long M. Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome. Molecular Biology and Evolution. 19: 918-25. PMID 12032248 DOI: 10.1093/Oxfordjournals.Molbev.A004149  0.701
2002 Betrán E, Wang W, Jin L, Long M. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Molecular Biology and Evolution. 19: 654-63. PMID 11961099 DOI: 10.1093/Oxfordjournals.Molbev.A004124  0.841
2002 Wang W, Brunet FG, Nevo E, Long M. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 99: 4448-53. PMID 11904380 DOI: 10.1073/Pnas.072066399  0.631
2002 Wang W, Thornton K, Berry A, Long M. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science (New York, N.Y.). 295: 134-7. PMID 11778050 DOI: 10.1126/Science.1064521  0.672
2001 Long M. Evolution of novel genes Current Opinion in Genetics and Development. 11: 673-680. PMID 11682312 DOI: 10.1016/S0959-437X(00)00252-5  0.613
2001 Long M, Thornton K. Gene duplication and evolution. Science (New York, N.Y.). 293: 1551. PMID 11533445 DOI: 10.1126/science.293.5535.1551a  0.782
2001 Long M. Adaptive Evolution of Genes and Genomes (review) Perspectives in Biology and Medicine. 44: 460-464. DOI: 10.1353/pbm.2001.0052  0.455
2000 Sakharkar MK, Kangueane P, Woon TW, Tan TW, Kolatkar PR, Long M, Souza SJd. IE-Kb: intron exon knowledge base. Bioinformatics. 16: 1151-1152. PMID 11159334 DOI: 10.1093/Bioinformatics/16.12.1151  0.42
2000 Long M. A new function evolved from gene fusion Genome Research. 10: 1655-1657. PMID 11076848 DOI: 10.1101/gr.165700  0.582
2000 Wang W, Zhang J, Alvarez C, Llopart A, Long M. The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster. Molecular Biology and Evolution. 17: 1294-301. PMID 10958846 DOI: 10.1093/Oxfordjournals.Molbev.A026413  0.755
2000 Sakharkar M, Passetti F, Souza JEd, Long M, Souza SJd. ExInt: an Exon/Intron database Nucleic Acids Research. 30: 191-194. PMID 10592222 DOI: 10.1093/Nar/28.1.191  0.302
1999 Long M, Wang W, Zhang J. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene. 238: 135-41. PMID 10570991 DOI: 10.1016/S0378-1119(99)00229-2  0.641
1999 Long M, Deutsch M. Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns. Molecular Biology and Evolution. 16: 1528-1534. PMID 10555284 DOI: 10.1093/Oxfordjournals.Molbev.A026065  0.727
1999 Deutsch M, Long M. Intron—exon structures of eukaryotic model organisms Nucleic Acids Research. 27: 3219-3228. PMID 10454621 DOI: 10.1093/Nar/27.15.3219  0.807
1999 Cáceres M, Ranz JM, Barbadilla A, Long M, Ruiz A. Generation of a widespread Drosophila inversion by a transposable element. Science (New York, N.Y.). 285: 415-8. PMID 10411506 DOI: 10.1126/Science.285.5426.415  0.575
1998 De Souza SJ, Long M, Klein RJ, Roy S, Lin S, Gilbert W. Toward a resolution of the introns early/late debate: Only phase zero introns are correlated with the structure of ancient proteins Proceedings of the National Academy of Sciences of the United States of America. 95: 5094-5099. PMID 9560234 DOI: 10.1073/Pnas.95.9.5094  0.716
1998 Long M, De Souza SJ, Rosenberg C, Gilbert W. Relationship between "proto-splice sites" and intron phases: Evidence from dicodon analysis Proceedings of the National Academy of Sciences of the United States of America. 95: 219-223. PMID 9419356 DOI: 10.1073/Pnas.95.1.219  0.542
1997 de Souza SJ, Long M, Schoenbach L, Roy SW, Gilbert W. The correlation between introns and the three-dimensional structure of proteins. Gene. 205: 141-4. PMID 9461387 DOI: 10.1016/S0378-1119(97)00401-0  0.694
1997 Long M, de Souza SJ, Gilbert W. The yeast splice site revisited: new exon consensus from genomic analysis Cell. 91: 739-740. PMID 9413983 DOI: 10.1016/S0092-8674(00)80462-6  0.577
1997 Gilbert W, De Souza SJ, Long M. Origin of genes Proceedings of the National Academy of Sciences of the United States of America. 94: 7698-7703. PMID 9223251 DOI: 10.1073/Pnas.94.15.7698  0.602
1997 Long M, De Souza SJ, Gilbert W, Brazas R, Ganem D. Delta-interacting protein A and the origin of hepatitis delta antigen Science. 276: 824-825. PMID 9115212 DOI: 10.1126/Science.276.5313.824  0.459
1997 Richter B, Long M, Lewontin RC, Nitasaka E. Nucleotide variation and conservation at the dpp locus, a gene controlling early development in Drosophila. Genetics. 145: 311-23. PMID 9071586  0.614
1996 De Souza SJ, Long M, Gilbert W. Introns and gene evolution Genes to Cells. 1: 493-505. PMID 9078380 DOI: 10.1046/J.1365-2443.1996.D01-264.X  0.72
1996 de Souza SJ, Long M, Schoenbach L, Roy SW, Gilbert W. Intron positions correlate with module boundaries in ancient proteins. Proceedings of the National Academy of Sciences of the United States of America. 93: 14632-6. PMID 8962105 DOI: 10.1073/Pnas.93.25.14632  0.677
1996 Long M, De Souza SJ, Rosenberg C, Gilbert W. Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome cl precursor Proceedings of the National Academy of Sciences of the United States of America. 93: 7727-7731. PMID 8755543 DOI: 10.1073/Pnas.93.15.7727  0.666
1995 Long M, De Souza SJ, Gilbert W. Evolution of the intron-exon structure of eukaryotic genes Current Opinion in Genetics and Development. 5: 774-778. PMID 8745076 DOI: 10.1016/0959-437X(95)80010-3  0.692
1995 Long M, Rosenberg C, Gilbert W. Intron phase correlations and the evolution of the intron/exon structure of genes Proceedings of the National Academy of Sciences of the United States of America. 92: 12495-12499. PMID 8618928 DOI: 10.1073/Pnas.92.26.12495  0.693
1993 Long M, Langley CH. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science (New York, N.Y.). 260: 91-5. PMID 7682012 DOI: 10.1126/Science.7682012  0.758
1991 Long M, Gillespie JH. Codon usage divergence of homologous vertebrate genes and codon usage clock. Journal of Molecular Evolution. 32: 6-15. PMID 1901369 DOI: 10.1007/Bf02099923  0.447
Show low-probability matches.