2024
| 86. | Ogoniak L, Steffen R, Grundmann N, Stöver B, Müller K, Schmitz J | NewickTreeModifier: a simple web tool to prune and modify Newick trees | Journal of Heredity 2024 |
2023
| 85. | Doronina L, Ogoniak L, Schmitz J | Homoplasy of retrotransposon insertions in toothed whales | Genes 14: 1830, 2023 | ||
| 84. | Churakov G, Kuritzin A, Chukharev K, Zhang F, Wünnemann F, Ulyantsev V, Schmitz J | 4-lineage statistics with simulations for large-scale retroposon insertion data | Systematic Biology 72: 649-661, 2023 | Cover |
2022
| 83. | Zhang F, Raabe CA, Cardoso-Moreira M, Brosius J, Kaessmann H, Schmitz J | ExoPLOT: represenation of alternative splicing in human tissues and developmental stages with transposed element (TE) involvement | Genomics, 114: 110424, 2022 | ||
| 82. | Doronina L, Feigin CY, Schmitz J | Reunion of Australasian Possums by Shared SINE Insertions | Systematic Biology 71:1045-1053, 2022 | Cover | |
| 81. | Steffen R, Ogoniak L, Grundmann N, Pawluchin A, Soehnlein O, Schmitz J | paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences | Genes 13:1090, 2022 | ||
| 80. | Doronina L, Hughes GH, Moreno-Santillan D, Lawless C, Lonergan T, Ryan L, Jebb d, Kirilenko BM, KorstianJM, Davolos LM, Vernes SC, Myers EW, Teeling EC, Hiller M, Jermiin LS, Schmitz J, Springer MS, Ray DA | Contradictory phylogenetic signals in the Laurasiatheria anomaly zone; | Genes 13:766, 2022 | Cover | |
| 79. | Doronina L, Reising O, Clawson H, Churakov G, Schmitz J | Euarchontoglires challenged by incomplete lineage sorting | Genes 13:774, 2022 |
2021
| 78. | Müller D, Schmitz J, Fischer K, Granado D, Groh A-C, Krausel V, Lüttgenau SM, Amelung TM, Pavenstädt H, Weide T | Evolution of renal-disease factor APOL1 results in cis and trans orientations at the endoplasmic reticulum that both show cytotoxic effects | Molecular Biology and Evolutoin 38:4962-4976, 2021 | |
| 77. | Doronna L, Reising O, Schmitz J | Gene conversion amongst Alu SINE elements | Genes 12:905, 2021 | |
| 76. | Dongl Y, Blanchard TS, Noll A, Vasquez P, Schmitz J, Kelly SP, Wright PA, Whitehead A | Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish; | Journal of Experimental Biology 224:jeb235515, 2021 |
2020
| 75. | Churakov G, Zhang F, Grundmann N, Makalowski W, Noll A,Doronina L, Schmitz J | The multi-comparative 2-n-way genome suite | Genome Research Genome Res 30:1508-1516, 2020 |
2019
| 74. | Doronina L, Reising O, Clawson H, Ray DA, Schmitz J | True Homoplasy of Retrotransposon Insertions in Primates | Systematic Biology 63:482-493 | |
| 73. | Schrader L, Schmitz J | The impact of transposable elements in adaptive evolution | Molecular Ecology 28:1537-1549, 2019 | |
| 72. | Sparwel M, Doronina L, Churakov G, Stegemann A, Brosius J, Robinson TJ, Schmitz J | The Volcano Rabbit in the Phylogenetic Network of Lagomorphs | Genome Biology and Evolution 11:11-16, 2019 |
2024
2018
| 71. | Schmitz J, Doronina L | How ancient sex drove mammalian lineage evolution | BioEssays 40:1800064, 2018 | |
| 70. | Feigin CY, Newton AH, Doronina L, Schmitz J, Hipsley CA, Mitchell KJ, Gower G, Llamas B, Soubrier J, Heider TN, Menzies BR, Cooper A, O’Neill RJ, Pask AJ | Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore | Nat Ecol & Evol 2:182-192, 2018 |
2017
| 69. | Suh A, BachgS, Donnellan S, Joseph L, Brosius J, Kriegs JO, Schmitz J | De-novo emergence and template switching of SINE retroposons during the early evolution of passerine birds | Mobile DNA 8:21, 2017 | |
| 68. | Stolle, A.-S, Norkowski S, Körner B, Schmitz J, Lüken L, Frankenberg M, Rüter C, Schmidt MA | T3SS-independent uptake of the short-trip toxin-related recombinant NleC effector of enteropathogenic Escherichia coli leads to NF-kB p65 cleavage | Front. Cell Infect Microbiol 7:119, 2017 | |
| 67. | Doronina L, Churakov G, Kuritzin A, Shi J, Baertsch R, Clawson H, Schmitz J | Speciation network in Laurasiatheria: retrophylogenomic signals | Genome Res 27:997-1003, 2017 | |
| 66. | Doronina L, Matzke A, Churakov G, Stoll M, Huge A, Schmitz J | The beaver's phylogenetic lineage illuminated by retroposon reads | Sci Rep 7:43562, 2017 |
2016
| 65. | Schmitz J, Noll A, Raabe C, Churakov G, Voss R, Kiefmann M, Rozhdestvensky T, Brosius J, Baertsch R, Clawson H, Roos C, Zimin A, Minx P, Montague MJ, Wilson RK, Warren WC | Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions | Nat Commun 7:12997, 2016 | |
| 64. | Mason VC, Li G, Minx P, Schmitz J, Churakov G, Doronina L, Melin AD, Dominy NJ, Lim NT-L, Springer MS, Wilson RK, Warren WC, Helgen KM, Murphy WJ | Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates | Sci Adv 2:e1600633, 2016 | |
| 63. | Kuritzin A, Kischka T, Schmitz J, Churakov G | Incomplete lineage sorting and hybridization statistics for large-scale retroposon insertion data | PLoS Computation Biol 12:e1004812, 2016 |
2015
| 62. | Warren WC, Jasinska AJ, Garcia-perez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LDW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Wang Y, Ramensky V, Choi O, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O’Connor DH, Redmond E, Nisbett A, Jacquelin B, Müller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GWC, Hahn MW, Raney B, Aken B, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB | The genome of the vervet (Chlorocebus aethiops sabaeus) | Genome Res 25:1921-1933, 2015 | ||
| 61. | Doronina L, Churakov G, Shi J, Brosius J, Baertsch R, Clawson H, Schmitz J | Exploring massive incomplete lineage sorting in arctoids (Laurasiatheria, Carnivora) | Mol Biol Evol 32:3194-3204, 2015 | ||
| 60. | Catania F, Schmitz J | On the path to genetic novelties: insights from RNA splicing and programmed DNA elimination | WIREs RNA 6:547-561, 2015 | ||
| 59. | Noll A, Raabe C, Churakov G, Brosius J, Schmitz J | Ancient traces of tailless retropseudogenes in therian genomes | Genome Biol Evol 7:889-900, 2015 | ||
| 58. | Suh A, Churakov G, Ramakodi MP, Platt II RN, Jurka J, Kojima KK, Caballero J, Smit A, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J | Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes | Genome Biol Evol 7:205-217, 2015 | ||
| 57. | Noll A, Grundmann N, Churakov G, Brosius J, Makalowski W, Schmitz J | GPAC - Genome Presence/Absence Compiler: a web application to comparatively visualize multiple genome-level changes | Mol Biol Evol 32:275-286, 2015 | Cover |
2014
| 56. | Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger Jr. JW, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock PD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, and Ray DA | Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs | Science 346:1254449, 2014 | Cover | |
| 55. | Wennmann DO, Schmitz J, Wehr MC, Krahn MP, Koschmal N, Gromnitza S, Schulze U, Weide T, Chekuri A, Skryabin BV, Gerke V, Pavenstädt H, Duning K, Kremerskothen J | Evolutionary and molecular facts link the WWC protein family to Hippo signaling | Mol Biol Evol 31:1710-1723, 2014 |
2013
| 54. | Hartig G, Churakov G, Warren W, Brosius J, Makalowski W, Schmitz J | Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids | Sci Rep 3:1756, 2013 | |
| 53. | Suh A, Brosius J, Schmitz J, Kriegs JO | The genome of a Mesozoic paleovirus reveal the ancient evolution of hepatitis B viruses | Nat Commun 4:1791, 2013 | |
| 52. | Zemann A, Churakov G, Donellan S, Grützner F, Fangquing Z, Borsius J, Schmitz J | Ancestry of the Australian termitivorous numbat | Mol Biol Evol 30:1041-1045, 2013 |
2012
| 51. | Arkhipova IR, Batzer MA, Brosius J, Feschotte C, Moran JV, Schmitz J, Jurka J | Genomic impact of eukaryotic transposable elements | Mobile DNA 3:19, 2012 | |
| 50. | Suh A, Kriegs JO, Donnellan S, Brosius J, Schmitz J | A universal method for the study of CR1 retroposons in non-model bird genomes | Mol Biol Evol 29:2899-2903, 2012 | |
| 49. | Schmitz J | SINEs as driving forces in genome evolution | Genome Dynamics. Repetitive DNA 7:91-107, 2012 | |
| 48. | Matzke A, Churakov G, Berkes P, Arms E, Kelsey D, Brosius J, Kriegs JO, Schmitz J | Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era | Mol Biol Evol 29:1497-1501, 2012 | |
| 47. | Erpenbeck D, Schmitz J, Churakov G, Huchon D, Wöhrheide G, Degnan BM | First evidence of miniature transposable elements in Porifera | Hydrobiology 687:43-47, 2012 |
2011
| 46. | Schmitz J, Brosius J | Exonization of transposed elements: A challenge and opportunity for evolution | Biochimie 93:1928-1934, 2011 | |
| 45. | Suh A, Paus M, Kiefmann M, Churakov G, Franke FA, Brosius J, Kriegs JO, Schmitz J | Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds | Nat Commun 2:443, 2011 | |
| 44. | Suh A, Kriegs JO, Brosius J, Schmitz J | Retroposon insertions and the chronology of avian sex chromosome evolution | Mol Biol Evol, 28:2993-2997, 2011 |
2010
| 43. | Churakov G, Grundmann N, Kuritzin A, Brosius J, Makałowski W, Schmitz J | A novel web-based TinT application and the chronology of the primate Alu retroposon activity | BMC Evol Biol, 10:376, 2010 | |
| 42. | Kriegs JO, Zemann A, Churakov G, Matzke A, Ohme M, Zischler H, Brosius J, Kryger U, Schmitz J | Retroposon insertions provide insights into deep lagomorph evolution | Mol Biol Evol, 27:2678-2681, 2010 | |
| 41. | Nilsson M, Churakov G, Sommer M, Ngoc Van T, Zemann A, Brosius J, Schmitz J | Tracking marsupial evolution using archaic genomic retroposon insertions | PLoS Biol 8:e1000436, 2010 | |
| 40. | Churakov G, Sadasivuni M, Rosenbool K, Huchon D, Brosius J, Schmitz J | Rodent Evolution: Back to the Root | Mol Biol Evol 27:1315-1326, 2010 |
2009
| 39. | Churakov G, Kriegs JO, Baertsch R, Zemann A, Brosius J, Schmitz J | Mosaic retroposon insertion patterns in placental mammals | Genome Res 19:868-875, 2009 |
2008
| 38. | Moeller-Krull M, Zemann A, Roos C, Brosius J, Schmitz J | Beyond DNA: RNA-editing and steps toward Alu-exonization in primates | J Mol Biol 382:601-609, 2008 | ||
| 37. | Warren WC, Hillier LW, Graves JAM, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang S-P, Heager A, Clarke D, Miethke P, Waters P, Veyrunes F, Fulton L, Graves T, Puente X, Lopez-Otin C, Ordonez GR, Eichler EE, Deakin JE, Thompson K, Kirby P, Papenfuss AT, Wakefield M, Olender T, Lancet D, Huttley GA, Smit AFA, Renfree M, Temple-Smith P, Batzer MA, Jerilyn A, Walker JA, Konkel MK, Harris RS, Taylor J, Whittington CM, Gemmell N, Buschiazzo E, Jentzsch IV, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison E, Sachidanandam R, Smith C, Stark A, Hannon G, Rens W, Ferguson-Smith M, Lefevre C, Sharp J, Nicholas KR, Ray D, Kube M, Reinhardt R, Pringle TH, Flicek P, Washington University Genome Sequencing Center, Mardis ER, Wilson RK | Genome analysis of the platypus reveals unique signatures of evolution | Nature 453:175-184, 2008 | Cover | |
| 36. | Schmitz J, Zemann A, Churakov G, Kuhl H, Grützner F, Reinhardt R, Brosius J | Retroposed SNOfall – A mammalian-wide comparison of platypus snoRNAs | Genome Res 18:1005-1010, 2008 | Cover | |
| 35. | Qiu H, Taudien S, Herlyn H, Schmitz J, Zhou Y, Chen G, Roberto R, Rocchi M, Platzer M, Wojnowski L | CYP3 phylogenomics: Evidence for positive selection of CYP3A4 and CYP3A7 | Pharmacogenetics and Genomics 18:53-66, 2008 |
2007
| 34. | Kriegs JO, Matzke A, Churakov G, Kuritzin A, Mayr G, Brosius J, Schmitz J | Waves of genomic hitchhikers characterize the evolution of gamebirds (Aves: Galliformes) | BMC Evol Biol 7:190, 2007 | |
| 33. | Möller-Krull M, Delsuc F, Churakov G, Marker C, Superina M, Brosius J, Douzery EJP, Schmitz J | Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters and sloths) | Mol Biol Evol 24:2573-2582, 2007 | |
| 32. | Chen X, Collins L, Rozhdestvensky TS, Schmitz J, Penny D | Combined experimental and computional approach to identify non-protein-coding RNAs in the deep branching eukaryote Giardia intestinalis | Nucleic Acids Res 35:4619-4628, 2007 | |
| 31. | Krull M, Petrusma M, Makalowski W, Brosius J, Schmitz J | Functional persistence of exonized Mammalian-wide Interspersed Repeat elements (MIRs) | Genome Res 17:1139-1145, 2007 | |
| 30. | Huchon D, Chevret P, Jordan U, Kilpatrick CW, Ranwez V, Jenkins PD, Brosius J, Schmitz J | Multiple molecular evidence for a living mammalian fossil | Proc Natl Acad Sci USA 104:7495-7499 , 2007 | |
| 29. | Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J | Evolutionary history of 7SL RNA-derived SINEs in Supraprimates - Glires and Euarchonta Phylogeny - | Trends Genet 23:158-161, 2007 |
2006
| 28. | Farwick A, Jordan U, Fuellen G, Huchon D, Catzeflis F, Brosius J, Schmitz J | Automated scanning for phylogenetically informative transposed elements in rodents | Sys Biol 55:936-948, 2006 | ||
| 27. | Kuryshev VY, Vorobyov E, Zink D, Schmitz J, Rozhdestvensky TS, Münstermann E, Ernst U, Wellenreuther R, Moosmayer P, Bechtel S, Schupp I, Hort J, Korn B, Poustka A, Wiemann S | An anthropoid-specific segmental duplication on human chromosome 1q22: Structure and evolution of the affected genes | Genomics 88:143-151, 2006 | Cover | |
| 26. | Zemann A, op de Bekke A, Kiefmann M, Brosius J, Schmitz J | Evolution of small nucleolar RNAs in nematodes | Nucleic Acids Res 34:2676-2685, 2006 | ||
| 25. | Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J | Retropsosed elements as archives for the evolutionary history of placental mammals | PLoS Biol 4:e91, 2006 |
2005
| 24. | Schmitz J, Piskurek O, Zischler H | Forty million years of independent evolution: a mitochondrial gene and its corresponding nuclear pseudogene in primates | J Mol Evol 61:1-11, 2005 | |
| 23. | Krull M, Brosius J, Schmitz J | Alu-SINE exonization: en route to protein-coding function | Mol Biol Evol 22:1702-1711, 2005 | |
| 22. | Churakov G, Smit A, Brosius J, Schmitz J | A novel abundant family of transposable elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus) | Mol Biol Evol 22:886-893, 2005 | |
| 21. | Ludwig A, Rozhdestvensky TS, Kuryshev V, Schmitz J, Brosius J | An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription | J Mol Biol 350:200-214, 2005 | |
| 20. | Kriegs JO, Schmitz J, Makalowski W, Brosius J | Does the AD7c-NTP locus encode a protein? | BBA 1727:1-4, 2005 | |
| 19. | Schmitz J, Roos C, Zischler H | Primate phylogeny: Molecular evidence from retroposons | Cyt Genome Res 108:26-37, 2005 |
2004
| 18. | Schmitz J, Churakov G, Zischler H, Brosius J | A novel class of tailless retropseudogenes in mammalian genomes | Genome Res 14:1911-1015, 2004 | |
| 17. | Singer SS, Maennel, DN, Hehlgans T, Brosius J, Schmitz J | From “junk“ to Gene: Curriculum vitae of a primate receptor isoform gene | J Mol Biol 341:883-886, 2004 | |
| 16. | Roos C, Schmitz J, Zischler H | Primate jumping genes elucidate strepsirrhine phylogeny | Proc Natl Acad Sci USA 101:10650-10654, 2004 | |
| 15. | Schmitz J, Zischler H | Molecular cladistic markers and the infraordinal phylogenetic relationships of primates | In: Anthropoid Origins: New Visions, Kay, RF, Ross, C (eds), Kluwer Academic Press, NY, 2004 |
2003
| 14. | Schmitz J, Zischler H | A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates | Mol Phyl Evol 28:341-349, 2003 | |
| 13. | Singer SS, Schmitz J, Schwiegk C, Zischler H | Molecular cladistic markers in New World monkey phylogeny (Platyrrhini, Primates) | Mol Phyl Evol 26:490-501, 2003 | |
| 12. | Herlyn H, Piskurek O, Schmitz J, Ehlers U, Zischler H | The syndermatan phylogeny and the evolution of acanthocephalan endoparasitism as inferred from 18S rDNA sequences | Mol Phyl Evol 26:155-164, 2003 |
2002
| 11. | Albert S, Schmitz J | Characterization of the major royal jelly family like DNA sequences in Apis dorsata | J Apic Res 41:75-82, 2002 | |
| 10. | Schmitz J, Ohme M, Suryobroto B, Zischler H | The colugo (Cynocephalus variegatus, Dermoptera): The Primates‘ gliding sister? | Mol Biol Evol 19:2308-2312, 2002 | |
| 9. | Schmitz J, Ohme M, Zischler H | The complete mitochondrial sequence of Tarsius bancanus: evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA | Mol Biol Evol 19:544-553, 2002 |
2001
| 8. | Schmitz J, Ohme M, Zischler H | SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates | Genetics 157:777-784, 2001 |
2000
| 7. | Schmitz J, Ohme M, Zischler H | The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of Scandentia to other eutherian orders | Mol Biol Evol 17, 1334-1343, 2000 | |
| 6. | Schmitz J, Moritz RFA | Molecular evolution in social wasps. In: Hymenoptera: Evolution, biodiversity and biological control | Austin AD, Dowton M (eds) pp 84-89, CSIRO Publishing, Collingwood, 2000 | |
| 5. | Weichhardt-Kulessa K, Börner T, Schmitz J, Müller-Doblies U, Müller-Doblies D | Controversial taxonomy of Strumariinae (Amaryllidaceae) investigated by nuclear rDNA (IST) sequences | Plant Syst Evol 223:1-13, 2000 |
1998
| 4. | Schmitz J, Moritz RFA | Sociality and the rate of rDNA sequence evolution in wasps (Vespidae) and honeybees (Apis) | J Mol Evol 47, 606-612, 1998 | |
| 3. | Schmitz J, Moritz RFA | Molecular phylogeny of Vespidae (Hymenoptera) and the evolution of sociality in wasps | Mol Phyl Evol 9:183-19, 1998 |
1994
| 2. | Schmitz J, Moritz RFA | Sequence analysis of the D1 and D2 regions of 28S rDNA in the hornet (Vespa crabro, Hymenoptera, Vespinae) | Insect Mol Biol 3:273-277, 1994 |
1990
| 1. | Schmitz J, Moritz RFA | Mitochondrial DNA variation in social wasps (Hymenoptera, Vespidae) | Experientia 46:1068-1072, 1990 |