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In Print: Last Week's Sequencing-Related Papers of Note: Mar 5, 2013


ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data.
Wu G, Yustein JT, McCall MN, Zilliox M, et al.
Bioinformatics. 2013 Mar 1. [Epub ahead of print]

EBARDenovo: Highly accurate de novo assembly of RNA-seq with efficient chimera-detection.
Chu HT, Hsiao WW, Chen JC, Yeh TJ, et al.
Bioinformatics. 2013 Mar 1. [Epub ahead of print]

A Y2H-seq approach defines the human protein methyltransferase interactome.
Weimann M, Grossmann A, Woodsmith J, Ozkan Z, et al.
Nat Methods. 2013 Mar 3. [Epub ahead of print]

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.
Li Y, Zhao DY, Greenblatt JF, Zhang Z.
Nucleic Acids Res. 2013 Feb 28. [Epub ahead of print]

Sequencing of hippocampal and cerebellar transcriptomes provides new insights into the complexity of gene regulation in the human brain.
Twine NA, Janitz C, Wilkins MR, Janitz M.
Neurosci Lett. 2013 Feb 27. [Epub ahead of print]

Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.
Tilgner H, Raha D, Habegger L, Mohiuddin M, et al.
G3 (Bethesda). 2013 Mar;3(3):387-97.

PolyCat: a resource for genome categorization of sequencing reads from allopolyploid organisms.
Page JT, Gingle AR, Udall JA.
G3 (Bethesda). 2013 Mar;3(3):517-25.

SplicingCompass: differential splicing detection using RNA-seq data.
Aschoff M, Hotz-Wagenblatt A, Glatting KH, Fischer M, et al.
Bioinformatics. 2013 Feb 28. [Epub ahead of print]

Identification of radiation-induced microRNA transcriptome by next-generation massively parallel sequencing.
Chaudhry MA, Omaruddin RA, Brumbaugh CD, Tariq MA, Pourmand N.
J Radiat Res. 2013 Feb 26. [Epub ahead of print]

Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing.
Zhang L, Szulwach KE, Hon GC, Song CX, et al.
Nat Commun. 2013 Feb 26;4:1517.

Accurate indel prediction using paired-end short reads.
Grimm D, Hagmann J, Koenig D, Weigel D, Borgwardt K.
BMC Genomics. 2013 Feb 27;14(1):132.

A tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics.
Izawa A, Sese J.
Source Code Biol Med. 2013 Feb 26;8(1):6.

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.
Sepúlveda N, Campino SG, Assefa SA, Sutherland CJ, et al.
BMC Genomics. 2013 Feb 26;14(1):128.

Copynumber: efficient algorithms for single- and multi-track copy number segmentation.
Nilsen G, Liestøl K, Loo PV, Moen Vollan HK, et al.
BMC Genomics. 2012 Nov 4;13:591.

FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets.
Pope BJ, Nguyen-Dumont T, Odefrey F, Bell R, et al.
BMC Bioinformatics. 2013 Feb 25;14(1):65.

Metaseq: privacy preserving meta-analysis of sequencing-based association studies.
Singh AP, Zafer S, Pe'er I.
Pac Symp Biocomput. 2013:356-67.

Detecting highly differentiated copy-number variants from pooled population sequencing.
Schrider DR, Begun DJ, Hahn MW.
Pac Symp Biocomput. 2013:344-55.

Chipmodule: systematic discovery of transcription factors and their cofactors from ChIP-seq data.
Ding J, Cai X, Wang Y, Hu H, Li X.
Pac Symp Biocomput. 2013:320-31.

Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-seq data.
Perez-Rathke A, Li H, Lussier YA.
Pac Symp Biocomput. 2013:159-70.

CNVeM: copy number variation detection using uncertainty of read mapping.
Wang Z, Hormozdiari F, Yang WY, Halperin E, Eskin E.
J Comput Biol. 2013 Feb 19. [Epub ahead of print]

The Scan

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.