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Selected Papers based on Research Topics 

1. Studies on the evolution of bicoid and embryonic axis specification in true flies (Diptera):

Emerging developmental genetic model systems in holometabolous insects
Schmidt-Ott U. and Lynch J.
Current Opinion in Genetics & Development. 2016
PMID: 27399647

A cysteine-clamp gene drives embryo polarity in the midge Chironomus
Klomp J, Athy D, Kwan CW, Bloch NI, Sandmann T, Lemke S., Schmidt-Ott U.
Science. 2015
PMID: 25953821
>>Read the blog! (link)<<
[This study reveals unexpectedly frequent evolutionary changes of body axis determinants in dipteran insects and establishes a molecular model for head-tail axis specification for the mosquito-related harlequin fly Chironomus riparius. It also establishes this species as an experimental system for molecular-developmental studies in lower dipterans.]

Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita.
Wotton KR, Jiménez-Guri E, Crombach A, Janssens H, Alcaine-Colet A, Lemke S, Schmidt-Ott U, Jaeger J.
eLife. 2015; 4.
PMID: 25560971

Maternal activation of gap genes in the hover fly Episyrphus.
Lemke S, Busch SE, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U.
Development (Cambridge, England). 2010; 137(10):1709-19.
PMID: 20430746

Evidence for a composite anterior determinant in the hover fly Episyrphus balteatus (Syrphidae), a cyclorrhaphan fly with an anterodorsal serosa anlage.
Lemke S, Schmidt-Ott U.
Development (Cambridge, England). 2009; 136(1):117-27.
PMID: 19060334
[This study introduces the hover or marmalade fly Episyrphus balteatus (Syrphidae) as an experimental system for functional developmental studies in flies.  This and the following studies examine the mechanism of axis specification in bicoid-containing fly species that are only distantly related to Drosophila.]

A single Hox3 gene with composite bicoid and zerknullt expression characteristics in non-cyclorrhaphan flies.
Stauber M, Prell A, Schmidt-Ott U.
Proceedings of the National Academy of Sciences of the United States of America. 2002; 99(1):274-9.
PMID: 11773616

Function of bicoid and hunchback homologs in the basal cyclorrhaphan fly Megaselia (Phoridae).
Stauber M, Taubert H, Schmidt-Ott U.
Proceedings of the National Academy of Sciences of the United States of America. 2000; 97(20):10844-9.
PMID: 10995461

The anterior determinant bicoid of Drosophila is a derived Hox class 3 gene.
Stauber M, Jäckle H, Schmidt-Ott U.
Proceedings of the National Academy of Sciences of the United States of America. 1999; 96(7):3786-9.
PMID: 10097115
[This and the following study provide the first evidence that bicoid, a global pattern organizer gene and axis determinant in the Drosophila embryo, originated in higher flies and newly acquired its characteristic functions. The studies take advantage of a newly established experimental system, the scuttle fly Megasselia abdita (Phoridae) and the mothmidge Clogmia albipunctata (Psychodidae).]  

2. Studies on the evolution of extraembryonic tissues in flies:

Functional evolution of a morphogenetic gradient 
Kwan CW, Gavin-Smyth J, Ferguson E.L, Schmidt-Ott U. 
eLife. (2016) 
PMID: 28005004
>>Read the blog! (Link)<<
[This manuscript reports evidence that the spatiotemporal dynamics of the embryonic BMP gradient diverged between two species thorugh a postive feedback mechanism and thereby altered tissue complexity]

Morphogenetic functions of extraembryonic membranes in insects
Schmidt-Ott U and Kwan CW
Current Opinion in Insect Science. 2016; 13(1):86-92.
[Review paper] 

Evolutionary origin of the amnioserosa in cyclorrhaphan flies correlates with spatial and temporal expression changes of zen.
Rafiqi AM, Lemke S, Ferguson S, Stauber M, Schmidt-Ott U.
Proceedings of the National Academy of Sciences of the United States of America. 2008; 105(1):234-9.
PMID: 18172205
[This study examines the evolution of extraembryonic tissues in flies. A genetic mechanism for the origin of the amnioserosa is proposed based on functional and comparative data from three fly species and other insects. The study includes the first report of distinct serosa and amnion tissues in phorid and syrphid flies and explores (together with the next study) the broader question of how to reconstruct and test genetic mechanisms of evolutionary change that occurred many million years ago. ]

Postgastrular zen expression is required to develop distinct amniotic and serosal epithelia in the scuttle fly Megaselia.
Rafiqi AM, Lemke S, Schmidt-Ott U.
Developmental biology. 2010; 341(1):282-90.
PMID: 20144604

BMP-dependent serosa and amnion specification in the scuttle fly Megaselia abdita.
Rafiqi AM, Park CH, Kwan CW, Lemke S, Schmidt-Ott U.
Development (Cambridge, England). 2012; 139(18):3373-82.
PMID: 22874914
[This study examines amnion and serosa specification in flies, and addresses the broader question of how BMP-signaling specifies tissues and affects their evolution.]

3. Phylogenetic and genomic contributions:

Episodic radiations in the fly tree of life.
Wiegmann BM, Trautwein MD, Winkler IS, Barr NB, Kim JW, Lambkin C, Bertone MA, Cassel BK, Bayless KM, Heimberg AM, Wheeler BM, Peterson KJ, Pape T, Sinclair BJ, Skevington JH, Blagoderov V, Caravas J, Kutty SN, Schmidt-Ott U, Kampmeier GE, Thompson FC, Grimaldi DA, Beckenbach AT, Courtney GW, Friedrich M, Meier R, Yeates DK.
Proceedings of the National Academy of Sciences of the United States of America. 2011; 108(14):5690-5.
PMID: 21402926

Extremely small genomes in two unrelated dipteran insects with shared early developmental traits.
Schmidt-Ott U, Rafiqi AM, Sander K, Johnston JS.
Development genes and evolution. 2009; 219(4):207-10.
PMID: 19308443

BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae).
Lemke S, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U.
BMC genomics. 2011; 12:278.
PMID: 21627820

4. A comparative study on subcellular transcript localization:

Differential cytoplasmic mRNA localization adjusts pair-rule transcription factor activity to cytoarchitecture in dipteran evolution.
Bullock SL, Stauber M, Prell A, Hughes JR, Ish-Horowicz D, Schmidt-Ott U.
Development (Cambridge, England). 2004; 131(17):4251-61.
PMID: 15280214
[This study reveals the evolutionary lability of mRNA localization signals and their impact gene regulation in the blastoderm of Drosophila.]

Studies on segmentation of the insect head:

Number, identity, and sequence of the Drosophila head segments as revealed by neural elements and their deletion patterns in mutants.
Schmidt-Ott U, González-Gaitán M, Jäckle H, Technau GM.
Proceedings of the National Academy of Sciences of the United States of America. 1994; 91(18):8363-7.
PMID: 7915837
[This and the following paper provide a detailed description of the developing peripheral nervous system of the first instar larva of Drosophila and deletions patterns in head gap gene mutants. This analysis reveals an anterior-posterior sequence of neural elements and defines their anterior-posterior sequence.]

Expression of en and wg in the embryonic head and brain of Drosophila indicates a refolded band of seven segment remnants.
Schmidt-Ott U, Technau GM.
Development (Cambridge, England). 1992; 116(1):111-25.
PMID: 1483381
[This paper examines the expression of segment polarity genes in the Drosophila head in the light of morphogenetic movements and arthropod head segmentation models. The study revised assumptions about the anterior pole of the insect head and revived the debate about arthropod head segmentation.]