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In Print: Sep 2, 2011

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Bioinformatics Tool-Related Papers of Note, August 2011

Lee B, Meyer CA, Shin H, et al.
Cistrome: an integrative platform for transcriptional regulation studies.
Genome Biol. 2011 Aug 22;12(8):R83. [Epub ahead of print]


Chinnaiyan AM, Maher CA, Iyer MK.
ChimeraScan: A tool for identifying chimeric transcription in sequencing data.
Bioinformatics. 2011 Aug 11. [Epub ahead of print]


Weigel D, Huson DH, Klein JD, Schneeberger K, Ossowski S.
LOCAS — A Low Coverage Assembly Tool for Resequencing Projects.
PLoS One. 2011;6(8):e23455. Epub 2011 Aug 15.


Pugalenthi G, Kandaswamy KK, Kalies KU, Hazrati MK, Martinetz T.
BLProt: Prediction of bioluminescent proteins based on Support Vector Machine and ReliefF feature selection.
BMC Bioinformatics. 2011 Aug 17;12(1):345. [Epub ahead of print].


McCampbell A, Holder DJ, Toolan DM, et al.
cSSMD: Assessing Collective Activity for Addressing Off-Target Effects in Genome-Scale RNA Interference Screens.
Bioinformatics. 2011 Aug 16. [Epub ahead of print]


McDonald K, Jung SK.
Visual Gene Developer: a fully programmable bioinformatics software for synthetic gene optimization.
BMC Bioinformatics. 2011 Aug 16;12(1):340. [Epub ahead of print]


Hirschman L, Colosimo ME, Peterson MW, Mardis S.
Nephele: Genotyping via Complete Composition Vectors and MapReduce.
Source Code Biol Med. 2011 Aug 18;6(1):13. [Epub ahead of print]


Schmidt B, Maskell DL, Liu Y.
Parallelized short read assembly of large genomes using de Bruijn graphs.
BMC Bioinformatics. 2011 Aug 25;12(1):354. [Epub ahead of print]


Essam D, Naznin F, Sarker R.
Vertical Decomposition with Genetic Algorithm for Multiple Sequence Alignment.
BMC Bioinformatics. 2011 Aug 25;12(1):353. [Epub ahead of print]


Margulies EH, Ozel Abaan H, Goldfeder RL, Parker SC, Ajay SS.
A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data.
PLoS One. 2011;6(8):e23683. Epub 2011 Aug 17.


Murphy JR, Hum RC, Wade TD.
A Dimensional Bus model for integrating clinical and research data.
J Am Med Inform Assoc. 2011 Aug 19. [Epub ahead of print]


Schweizer L, Lei M, Siemers NO, Bruccoleri RE, Ji RR.
SDRS — an algorithm for analyzing large-scale dose response data.
Bioinformatics. 2011 Aug 24. [Epub ahead of print]


Jaramillo A, Rodrigo G, Carrera J.
Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors.
Nucleic Acids Res. 2011 Aug 24. [Epub ahead of print]


King BL, Walton DO, Howell GR, Libby RT, John SW.
Datgan, a reusable software system for facile interrogation and visualization of complex transcription profiling data.
BMC Genomics. 2011 Aug 24;12(1):429. [Epub ahead of print]


Di Camillo B, Cobelli C, Toffolo G, Falda M.
SimBioNeT: A Simulator of Biological Network Topology.
IEEE/ACM Trans Comput Biol Bioinform. 2011 Aug 18. [Epub ahead of print]


Stumpf MP, Kelly WP.
Assessing Coverage of Protein Interaction Data Using Capture-Recapture Models.
Bull Math Biol. 2011 Aug 26. [Epub ahead of print]


Stojmirovic A, Yu YK.
ppiTrim: constructing non-redundant and up-to-date interactomes.
Database (Oxford). 2011 Aug 27;2011:bar036. Print 2011.


Fu G, Li J, Wu R, Wang Z.
A mathematical framework for functional mapping of complex phenotypes using delay differential equations.
J Theor Biol. 2011 Aug 22. [Epub ahead of print].


Rokhsar DS, Schroth GP, Ho I, Chapman JA, Luo S, Sunkara S.
Meraculous: de novo genome assembly with short paired-end reads.
PLoS One. 2011;6(8):e23501. Epub 2011 Aug 18.


Darling A, Tritt A, Eisen JA, Facciotti MT.
Mauve Assembly Metrics.
Bioinformatics. 2011 Aug 2. [Epub ahead of print].


Peng B, Amos CI, Fu Y, Xu Y.
Genome-wide algorithm for detecting CNV associations with diseases.
BMC Bioinformatics. 2011 Aug 9;12(1):331. [Epub ahead of print]


Szilagyi A, Wu S, Zhang Y.
Improving protein structure prediction using multiple sequence-based contact predictions.
Structure. 2011 Aug 10;19(8):1182-91.


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