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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 Mapping of pigmentation QTL on an anchored genome assembly of the cichlid fish, Metriaclima zebra Claire T O¿Quin, Alexi C Drilea, Matthew A Conte, Thomas D Kocher BMC Genomics 2013, 14:287 (27 April 2013) Abstract \| Provisional PDF \| PubMed
	2.	Research article MMP-2 mediates local degradation and remodeling of collagen by annulus fibrosus cells of the intervertebral disc Anshu Rastogi, Hyunchul Kim, Julianne D Twomey, Adam H Hsieh Arthritis Research & Therapy 2013, 15:R57 (27 April 2013) Abstract \| Provisional PDF \| PubMed
	3.	Method TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg Genome Biology 2013, 14:R36 (25 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A major update to TopHat, the popular Bowtie-based spliced aligner
	4.	Case report Aphonia induced by simultaneous bilateral ischemic infarctions of the putamen nuclei: a case report and review of the literature Vladimir V Senatorov, Shirish Satpute, Katherine Perry, David M Kaylie, John W Cole Journal of Medical Case Reports 2013, 7:83 (19 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Rare presentation of isolated acute onset aphonia secondary to simultaneous acute ischemic infarctions of the bilateral basal ganglia related to underlying drug toxicity.
	5.	Research An attenuated Lassa vaccine in SIV-infected rhesus macaques does not persist or cause arenavirus disease but does elicit Lassa virus-specific immunity Juan C Zapata, Bhawna Poonia, Joseph Bryant, Harry Davis, Eugene Ateh, Lanea George, Oswald Crasta, Yan Zhang, Tom Slezak, Crystal Jaing, C Pauza, Marco Goicochea, Dmitry Moshkoff, Igor S Lukashevich, Maria S Salvato Virology Journal 2013, 10:52 (12 February 2013) Abstract \| Full text \| PDF \| PubMed
	6.	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
	7.	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
	8.	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
	9.	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
	10.	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
	11.	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
	12.	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
	13.	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
	14.	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
	15.	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
	16.	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
	17.	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.
	18.	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 \| F1000 Biology
	19.	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
	20.	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
	21.	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.
	22.	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
	23.	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
	24.	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
	25.	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