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 pdf  

2023

85. Doronina L, Ogoniak L, Schmitz J Homoplasy of retrotransposon insertions in toothed whales  Genes 14: 1830, 2023 pdf  
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 pdf 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
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82. Doronina L, Feigin CY, Schmitz J Reunion of Australasian Possums by Shared SINE Insertions  Systematic Biology 71:1045-1053, 2022
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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 pdf  
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 pdfCover
79. Doronina L, Reising O, Clawson H, Churakov G, Schmitz J Euarchontoglires challenged by incomplete lineage sorting  Genes 13:774, 2022 pdf  

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
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77. Doronna L, Reising O, Schmitz J Gene conversion amongst Alu SINE elements Genes 12:905, 2021 pdf
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 pdf

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 pdf

2019

74. Doronina L, Reising O, Clawson H, Ray DA, Schmitz J True Homoplasy of Retrotransposon Insertions in Primates  Systematic Biology 63:482-493
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73. Schrader L, Schmitz J The impact of transposable elements in adaptive evolution Molecular Ecology 28:1537-1549, 2019 pdf
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 pdf

2024

2018

71. Schmitz J, Doronina L How ancient sex drove mammalian lineage evolutionBioEssays 40:1800064, 2018 pdf
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 carnivoreNat Ecol & Evol 2:182-192, 2018 pdf

2017

69. Suh A, BachgS, Donnellan S, Joseph L, Brosius J, Kriegs JO, Schmitz JDe-novo emergence and template switching of SINE retroposons during the early evolution of passerine birds Mobile DNA 8:21, 2017 pdf
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 pdf
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 pdf
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 pdf

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 pdf
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 pdf
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 pdf

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 pdf  
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 pdf  
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 pdf  
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 pdf  
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 pdf  
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 pdfCover

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 pdfCover
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 pdf  

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 pdf
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 pdf
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 pdf

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 pdf
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 pdf
49. Schmitz J SINEs as driving forces in genome evolution Genome Dynamics. Repetitive DNA 7:91-107, 2012 pdf
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 pdf
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 pdf

2011

46. Schmitz J, Brosius J Exonization of transposed elements: A challenge and opportunity for evolution Biochimie 93:1928-1934, 2011 pdf
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 pdf
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 pdf

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 pdf
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 pdf
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 pdf
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 pdf

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 pdf

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 pdf  
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 pdfCover
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 pdfCover
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 pdf  

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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf

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 pdf  
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 pdf 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 pdf  
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 pdf  

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 pdf
23. Krull M, Brosius J, Schmitz J Alu-SINE exonization: en route to protein-coding function Mol Biol Evol 22:1702-1711, 2005 pdf
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 pdf
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 pdf
20. Kriegs JO, Schmitz J, Makalowski W, Brosius J Does the AD7c-NTP locus encode a protein? BBA 1727:1-4, 2005 pdf
19. Schmitz J, Roos C, Zischler H Primate phylogeny: Molecular evidence from retroposons Cyt Genome Res 108:26-37, 2005 pdf

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 pdf
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 pdf
16. Roos C, Schmitz J, Zischler H Primate jumping genes elucidate strepsirrhine phylogeny Proc Natl Acad Sci USA 101:10650-10654, 2004 pdf
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 pdf

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 pdf
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 pdf
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 pdf

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 pdf
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 pdf
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 pdf

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 pdf

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 pdf
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 pdf
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 pdf

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 pdf
3. Schmitz J, Moritz RFA Molecular phylogeny of Vespidae (Hymenoptera) and the evolution of sociality in wasps Mol Phyl Evol 9:183-19, 1998 pdf

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 pdf

1990

1. Schmitz J, Moritz RFA Mitochondrial DNA variation in social wasps (Hymenoptera, Vespidae) Experientia 46:1068-1072, 1990 pdf