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Items: 11


Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly.

Sameith K, Roscito JG, Hiller M.

Brief Bioinform. 2016 Feb 10. pii: bbw003.


A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions.

Sameith K, Amini S, Groot Koerkamp MJ, van Leenen D, Brok M, Brabers N, Lijnzaad P, van Hooff SR, Benschop JJ, Lenstra TL, Apweiler E, van Wageningen S, Snel B, Holstege FC, Kemmeren P.

BMC Biol. 2015 Dec 23;13:112. doi: 10.1186/s12915-015-0222-5.


Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.

Kemmeren P, Sameith K, van de Pasch LA, Benschop JJ, Lenstra TL, Margaritis T, O'Duibhir E, Apweiler E, van Wageningen S, Ko CW, van Heesch S, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ, Bouwmeester D, van Hooff SR, van Bakel H, Sluiters E, Bakker LV, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Holstege FC.

Cell. 2014 Apr 24;157(3):740-52. doi: 10.1016/j.cell.2014.02.054.


A central role for TFIID in the pluripotent transcription circuitry.

Pijnappel WW, Esch D, Baltissen MP, Wu G, Mischerikow N, Bergsma AJ, van der Wal E, Han DW, Bruch Hv, Moritz S, Lijnzaad P, Altelaar AF, Sameith K, Zaehres H, Heck AJ, Holstege FC, Schöler HR, Timmers HT.

Nature. 2013 Mar 28;495(7442):516-9. doi: 10.1038/nature11970.


Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis.

Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker LV, van Leenen D, Holstege FC, Kemmeren P.

BMC Genomics. 2012 Jun 14;13:239. doi: 10.1186/1471-2164-13-239.


The specificity and topology of chromatin interaction pathways in yeast.

Lenstra TL, Benschop JJ, Kim T, Schulze JM, Brabers NA, Margaritis T, van de Pasch LA, van Heesch SA, Brok MO, Groot Koerkamp MJ, Ko CW, van Leenen D, Sameith K, van Hooff SR, Lijnzaad P, Kemmeren P, Hentrich T, Kobor MS, Buratowski S, Holstege FC.

Mol Cell. 2011 May 20;42(4):536-49. doi: 10.1016/j.molcel.2011.03.026.


Functional overlap and regulatory links shape genetic interactions between signaling pathways.

van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJ, Ko CW, Miles AJ, Brabers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, van de Pasch LA, van Hooff SR, Bakker LV, Krogan NJ, Snel B, Holstege FC.

Cell. 2010 Dec 10;143(6):991-1004. doi: 10.1016/j.cell.2010.11.021.


Stratification of pediatric ALL by in vitro cellular responses to DNA double-strand breaks provides insight into the molecular mechanisms underlying clinical response.

Marston E, Weston V, Jesson J, Maina E, McConville C, Agathanggelou A, Skowronska A, Mapp K, Sameith K, Powell JE, Lawson S, Kearns P, Falciani F, Taylor M, Stankovic T.

Blood. 2009 Jan 1;113(1):117-26. doi: 10.1182/blood-2008-03-142950.


Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage.

Sameith K, Antczak P, Marston E, Turan N, Maier D, Stankovic T, Falciani F.

Bioinformatics. 2008 Nov 15;24(22):2602-7. doi: 10.1093/bioinformatics/btn489.


Models and computational strategies linking physiological response to molecular networks from large-scale data.

Ortega F, Sameith K, Turan N, Compton R, Trevino V, Vannucci M, Falciani F.

Philos Trans A Math Phys Eng Sci. 2008 Sep 13;366(1878):3067-89. doi: 10.1098/rsta.2008.0085.


Fragrep: an efficient search tool for fragmented patterns in genomic sequences.

Mosig A, Sameith K, Stadler P.

Genomics Proteomics Bioinformatics. 2006 Feb;4(1):56-60.

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