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1

inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons

by Dandekar Thomas, Liang Chunguang
Published in BMC Bioinformatics (2006)

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2

Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE

by Dandekar Thomas, Müller Tobias, Seibel Philipp N, Wolf Matthias
Published in BMC Research Notes (2008)

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3

Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)

by Rahmann Sven, Müller Tobias, Dandekar Thomas, Wolf Matthias
Published in BMC Evolutionary Biology (2004)

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4

Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation

by Dandekar Thomas, Geiger Jörg, Hubertus Katharina, Mark Regina, Butt Elke, Wangorsch Gaby, Dittrich Marcus
Published in BMC Systems Biology (2011)

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5

Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling

by Dandekar Thomas, Goebel Werner, Liang Chunguang, Geginat Gernot, Schauer Kristina, Fuchs Thilo M
Published in BMC Genomics (2010)

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6

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays

by Brazma Alvis, Sanchez Mayka, Vainshtein Yevhen, Hentze Matthias W, Dandekar Thomas, Muckenthaler Martina U
Published in BMC Bioinformatics (2010)

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7

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

by Dandekar Thomas, Müller Tobias, Förster Frank, Keller Alexander, Schultz Jörg, Wolf Matthias
Published in Biology Direct (2010)

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8

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes

by López-Sánchez María, Moya Andres, Bernhardt Jörg, Gross Roy, Liang Chunguang, Schmid Alexander, Dandekar Thomas
Published in BMC Bioinformatics (2009)

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9

ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)

by Dandekar Thomas, Ruderisch Benjamin, Förster Frank, Schleicher Tina, Keller Alexander, Müller Tobias, Wolf Matthias
Published in BMC Evolutionary Biology (2008)

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10

Exonization of active mouse L1s: a driver of transcriptome evolution?

by Badge Richard, Dandekar Thomas, Schultz Jörg, Penzkofer Tobias, Zemojtel Tomasz, Vingron Martin
Published in BMC Genomics (2007)

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11

Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus

by Moya Andres, Silva Francisco J, Zientz Evelyn, Vogl Ina, Gaudermann Peter, Gross Roy, Dandekar Thomas
Published in BMC Microbiology (2006)

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12

4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

by Schultz Jörg, Dandekar Thomas, Müller Tobias, Seibel Philipp N, Wolf Matthias
Published in BMC Bioinformatics (2006)

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E-Article

13

YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities

by Engels Bernd, von Kamp Axel, Musch Patrick, Schwarz Roland, Schirmer Heiner, Schuster Stefan, Dandekar Thomas
Published in BMC Bioinformatics (2005)

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14

Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer

by Reuter Dirk, Wełnicz Weronika, Schnölzer Martina, Dandekar Thomas, Förster Frank, Grohme Markus A, Mali Brahim, Schill Ralph O, Frohme Marcus
Published in BMC Genomics (2010)

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15

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection

by Timmer Jens, Sawodny Oliver, Ederer Michael, Ferreira Karine, Schlatter Rebekka, Walter Dorothee, Philippi Nicole, Borner Christoph, Dandekar Thomas
Published in BMC Systems Biology (2009)

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16

Modelling phagosomal lipid networks that regulate actin assembly

by Schwarz Roland, Thakar Juilee, Dandekar Thomas, Mayorga Luis S, Kühnel Mark, Anes Elsa, Griffiths Gareth, Reich Jens
Published in BMC Systems Biology (2008)

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17

The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'

by Migdoll Alexander M, Heitmann Katja, Dandekar Thomas, Kuhl Heiner, Schneider Bernd, Kube Michael, Reinhardt Richard, Seemüller Erich
Published in BMC Genomics (2008)

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18

Integrated network reconstruction, visualization and analysis using YANAsquare

by Hecker Michael, Kuznetsov Sergei, Hoffmann Eik, Kühnel Mark, Kaleta Christoph, Liang Chunguang, Schwarz Roland, Griffiths Gareth, Schuster Stefan, Dandekar Thomas
Published in BMC Bioinformatics (2007)

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19

XML schemas for common bioinformatic data types and their application in workflow systems

by Mersch Henning, Löwenthal Kai, Schwarzer Knut, Hartmeier Sven, Krüger Jan, Seibel Philipp N, Dandekar Thomas, Giegerich Robert
Published in BMC Bioinformatics (2006)

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20

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum

by Beisser Daniela, Grohme Markus A, Kopka Joachim, Frohme Marcus, Schill Ralph O, Hengherr Steffen, Dandekar Thomas, Klau Gunnar W, Dittrich Marcus, Müller Tobias
Published in BMC Systems Biology (2012)

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