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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at University of Maryland, College Park

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	1.	Research article *Evolution of cichlid vision via trans-regulatory divergence* Kelly E O’Quin, Jane E Schulte, Zil Patel, Nadia Kahn, Zan Naseer, Helena Wang, Matthew A Conte, Karen L Carleton BMC Evolutionary Biology 2012, 12:251 (26 December 2012) Abstract \| Full text \| PDF \| PubMed
	2.	Software Coral: an integrated suite of visualizations for comparing clusterings Darya Filippova, Aashish Gadani, Carl Kingsford BMC Bioinformatics 2012, 13:276 (29 October 2012) Abstract \| Full text \| PDF \| PubMed
	3.	Research article Gene expression anti-profiles as a basis for accurate universal cancer signatures Héctor Corrada Bravo, Vasyl Pihur, Matthew McCall, Rafael A Irizarry, Jeffrey T Leek BMC Bioinformatics 2012, 13:272 (22 October 2012) Abstract \| Full text \| PDF \| PubMed
	4.	Research article Graph rigidity reveals well-constrained regions of chromosome conformation embeddings Geet Duggal, Carl Kingsford BMC Bioinformatics 2012, 13:241 (21 September 2012) Abstract \| Full text \| PDF \| PubMed
	5.	Research Parsimonious reconstruction of network evolution Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford Algorithms for Molecular Biology 2012, 7:25 (19 September 2012) Abstract \| Full text \| PDF \| PubMed
	6.	Research article DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus Xiao Wang, James N Culver BMC Plant Biology 2012, 12:157 (31 August 2012) Abstract \| Full text \| PDF \| PubMed
	7.	Methodology Mass spectrometry quantification of clusterin in the human brain Junjun Chen, Meiyao Wang, Illarion V Turko Molecular Neurodegeneration 2012, 7:41 (20 August 2012) Abstract \| Full text \| PDF \| PubMed
	8.	Research Logic minimization and rule extraction for identification of functional sites in molecular sequences Raul Cruz-Cano, Mei-Ling Lee, Ming-Ying Leung BioData Mining 2012, 5:10 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
	9.	Methodology article AGORA: Assembly Guided by Optical Restriction Alignment Henry C Lin, Steve Goldstein, Lee Mendelowitz, Shiguo Zhou, Joshua Wetzel, David C Schwartz, Mihai Pop BMC Bioinformatics 2012, 13:189 (2 August 2012) Abstract \| Full text \| PDF \| PubMed
	10.	Research article *Evaluation of qPCR reference genes in two genotypes of Populus* for use in photoperiod and low-temperature studies** Emily A Pettengill, Cécile Parmentier-Line, Gary D Coleman BMC Research Notes 2012, 5:366 (23 July 2012) Abstract \| Full text \| PDF \| PubMed
	11.	Research article *Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration* Kevin G Nyberg, Matthew A Conte, Jamie L Kostyun, Alison Forde, Alexandra E Bely BMC Genomics 2012, 13:287 (29 June 2012) Abstract \| Full text \| PDF \| PubMed
	12.	Research article *Temporal patterns of genetic diversity in Kirtland’s warblers (Dendroica kirtlandii), the rarest songbird in North America* Amy S Wilson, Peter P Marra, Robert C Fleischer BMC Ecology 2012, 12:8 (22 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Loss of genetic diversity in the Kirtlands warbler, an endangered songbird specialized on jackpine forest, are congruent with historic population declines over the last century as a result of predation and habitat loss.
	13.	Research article A comparative evaluation of sequence classification programs Adam L Bazinet, Michael P Cummings BMC Bioinformatics 2012, 13:92 (10 May 2012) Abstract \| Full text \| PDF \| PubMed
	14.	Review A review of communication-oriented optical wireless systems Deva K Borah, Anthony C Boucouvalas, Christopher C Davis, Steve Hranilovic, Konstantinos Yiannopoulos EURASIP Journal on Wireless Communications and Networking 2012, 2012:91 (7 March 2012) Abstract \| Full text \| PDF
	15.	Research article Masked mRNA is stored with aggregated nuclear speckles and its asymmetric redistribution requires a homolog of mago nashi Thomas C Boothby, Stephen M Wolniak BMC Cell Biology 2011, 12:45 (13 October 2011) Abstract \| Full text \| PDF \| PubMed
	16.	Software CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke BMC Bioinformatics 2011, 12:356 (30 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Cloud Virtual Resource (CloVR) is a new desktop application for large-scale sequence analysis using remote computing resources that provides several automated pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis.
	17.	Method TopHat-Fusion: an algorithm for discovery of novel fusion transcripts Daehwan Kim, Steven L Salzberg Genome Biology 2011, 12:R72 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm
	18.	Nano Express Ultrafast nano-oscillators based on interlayer-bridged carbon nanoscrolls Zhao Zhang, Teng Li Nanoscale Research Letters 2011, 6:470 (25 July 2011) Abstract \| Full text \| PDF \| PubMed
	19.	Research article Detection of lineage-specific evolutionary changes among primate species Mihaela Pertea, Geo M Pertea, Steven L Salzberg BMC Bioinformatics 2011, 12:274 (4 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DivE (Divergence by Evolution), a new methodology for predicting both positive and negative selection in noncoding DNA, is particularly well-suited to detecting lineage-specific selection in large genomes as demonstrated using primate species
	20.	Methodology article Improving pan-genome annotation using whole genome multiple alignment Samuel V Angiuoli, Julie C Dunning Hotopp, Steven L Salzberg, Hervé Tettelin BMC Bioinformatics 2011, 12:272 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
	21.	Methodology article DNACLUST: accurate and efficient clustering of phylogenetic marker genes Mohammadreza Ghodsi, Bo Liu, Mihai Pop BMC Bioinformatics 2011, 12:271 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
	22.	Research article *Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii* isolated from diverse human body sites reveals genomic plasticity** Jason W Sahl, J Kristie Johnson, Anthony D Harris, Adam M Phillippy, William W Hsiao, Kerri A Thom, David A Rasko BMC Genomics 2011, 12:291 (4 June 2011) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology
	23.	Research article Apple skin patterning is associated with differential expression of MYB10 Adriana Telias, Kui Lin-Wang, David E Stevenson, Janine M Cooney, Roger P Hellens, Andrew C Allan, Emily E Hoover, James M Bradeen BMC Plant Biology 2011, 11:93 (20 May 2011) Abstract \| Full text \| PDF \| PubMed
	24.	Short report Sequence analysis of fusion protein gene of Newcastle disease virus isolated from outbreaks in Egypt during 2006 Mahmoud HA Mohamed, Sachin Kumar, Anandan Paldurai, Siba K Samal Virology Journal 2011, 8:237 (18 May 2011) Abstract \| Full text \| PDF \| PubMed
	25.	Research article *Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes* Kelly E O'Quin, Daniel Smith, Zan Naseer, Jane Schulte, Samuel D Engel, Yong-Hwee E Loh, J Todd Streelman, Jeffrey L Boore, Karen L Carleton BMC Evolutionary Biology 2011, 11:120 (9 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central