Lehr- und Forschungseinheit Bioinformatik



Weitere Literatur

Ausgewählte aktuelle Bücher

  1. Somnath Datta, Dan Nettleton (Eds.: Statistical analysis of Next Generation Sequencing Data, Springer 2014
  2. Eija Korpelainen, Jarno Tuimala, Panu Somervuo, Mikael Huss, and Gary Wong: RNA-seq Data Analysis - A practical approach, Chapman&Hall/CRC Press 2015

Ausgewählte Paper


Anders, Simon, and Wolfgang Huber. 2010
Differential Expression Analysis for Sequence Count Data.
Genome Biology 11(10): R106


Bolstad, B.M., F. Collin, J. Brettschneider, K. Simpson, L. Cope, R.A. Irizarry, and T.P. Speed. 2013
Quality Assessment of Affymetrix GeneChip Data.
In Bioinformatics and Computational Biology Solutions Using R and Bioconductor.


Bolstad, B.M., R.A. Irizarry, L. Gautier, and Z. Wu. 2013.
Preprocessing High-density Oligonucleotide Arrays.
In Bioinformatics and Computational Biology Solutions Using R and Bioconductor.


Cox, Jürgen, and Matthias Mann. 2008.
MaxQuant Enables High Peptide Identification Rates, Individualized P.p.b.-range Mass Accuracies and Proteome-wide Protein Quantification.
Nature Biotechnology 26 (12): 1367\u20131372


Cox, Jürgen, Nadin Neuhauser, Annette Michalski, Richard A Scheltema, Jesper V Olsen, and Matthias Mann. 2011.
Andromeda: a Peptide Search Engine Integrated into the MaxQuant Environment.
Journal of Proteome Research 10 (4): 1794\u20131805


Goeman, Jelle J., and Peter Bühlmann. 2007.
Analyzing Gene Expression Data in Terms of Gene Sets: Methodological Issues.
Bioinformatics 23 (8): 980\u2013987


Hafner, Markus, Markus Landthaler, Lukas Burger, Mohsen Khorshid, Jean Hausser, Philipp Berninger, Andrea Rothballer, et al. 2010.
Transcriptome-wide Identification of RNA-binding Protein and microRNA Target Sites by PAR-CLIP.
Cell 141 (1): 129\u2013141


Langmead, Ben, Cole Trapnell, Mihai Pop, and Steven L. Salzberg. 2009.
Ultrafast and Memory-efficient Alignment of Short DNA Sequences to the Human Genome.
Genome Biology 10 (3): R25.


Li, Jun, Hui Jiang, and Wing H. Wong. 2010.
Modeling Non-uniformity in Short-read Rates in RNA-Seq Data.
Genome Biology 11 (5): R50.


Mortazavi, Ali, Brian A Williams, Kenneth McCue, Lorian Schaeffer, and Barbara Wold. 2008.
Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq.
Nature Methods 5 (7): 621\u2013628.


Nam, Dougu, and Seon-Young Kim. 2008.
Gene-set Approach for Expression Pattern Analysis.
Briefings in Bioinformatics 9 (3): 189\u2013197.


Neph, Shane, Jeff Vierstra, Andrew B Stergachis, Alex P Reynolds, Eric Haugen, Benjamin Vernot, Robert E Thurman, et al. 2012.
An Expansive Human Regulatory Lexicon Encoded in Transcription Factor Footprints.
Nature 489 (7414): 83\u201390.


Pollard, K.S., and A. van der Laan. 2013.
Cluster Analysis of Genomic Data.
In Bioinformatics and Computational Biology Solutions Using R and Bioconductor. New York: Springer.


Rozowsky, Joel, Ghia Euskirchen, Raymond K. Auerbach, Zhengdong D. Zhang, Theodore Gibson, Robert Bjornson, Nicholas Carriero, Michael Snyder, and Mark B. Gerstein. 2009.
PeakSeq Enables Systematic Scoring of ChIP-seq Experiments Relative to Controls.
Nature Biotechnology 27 (1): 66\u201375.


Scholtens, D., and A. von Heydebreck. 2013.
Analysis of Differential Gene Expression Studies.
In Bioinformatics and Computational Biology Solutions Using R and Bioconductor. New York: Springer.


Subramanian, Aravind, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, et al. 2005.
Gene Set Enrichment Analysis: A Knowledge-based Approach for Interpreting Genome-wide Expression Profiles.
Proceedings of the National Academy of Sciences of the United States of America 102 (43): 15545\u201315550.


Ulitsky, Igor, and Ron Shamir. 2007.
Identification of Functional Modules Using Network Topology and High-throughput Data.
BMC Systems Biology 1 (1): 8.


Valouev, Anton, David S. Johnson, Andreas Sundquist, Catherine Medina, Elizabeth Anton, Serafim Batzoglou, Richard M. Myers, and Arend Sidow. 2008.
Genome-wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data.
Nature Methods 5 (9): 829\u2013834.


Trapnell, C, Pachter, L, Salzberg, SL. 2009.
TopHat: discovering splice junctions with RNA-Seq.
Bioinformatics, 25, 9:1105-11.


Harrow, J, Frankish, A, Gonzalez, JM, Tapanari, E, Diekhans, M, Kokocinski, F, Aken, BL, Barrell, D, Zadissa, A, Searle, S, Barnes, I, Bignell, A, Boychenko, V, Hunt, T, Kay, M, Mukherjee, G, Rajan, J, Despacio-Reyes, G, Saunders, G, Steward, C, Harte, R, Lin, M, Howald, C, Tanzer, A, Derrien, T, Chrast, J, Walters, N, Balasubramanian, S, Pei, B, Tress, M, Rodriguez, JM, Ezkurdia, I, van Baren, J, Brent, M, Haussler, D, Kellis, M, Valencia, A, Reymond, A, Gerstein, M, Guigo, R, Hubbard, TJ. 2012.
GENCODE: the reference human genome annotation for The ENCODE Project.
Genome Res., 22, 9:1760-74.


Trapnell, C, Hendrickson, DG, Sauvageau, M, Goff, L, Rinn, JL, Pachter, L. 2013.
Differential analysis of gene regulation at transcript resolution with RNA-seq.
Nat. Biotechnol., 31, 1:46-53.


Wang, J, Zhuang, J, Iyer, S, Lin, X, Whitfield, TW, Greven, MC, Pierce, BG, Dong, X, Kundaje, A, Cheng, Y, Rando, OJ, Birney, E, Myers, RM, Noble, WS, Snyder, M, Weng, Z. 2012.
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Genome Res., 22, 9:1798-812.


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