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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at University of California, Berkeley

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1.

Research article   Open Access

Redeeming qualities: exploring factors that affect women's use of reproductive health vouchers in Cambodia

Carinne D Brody, Julie Freccero, Claire D Brindis, Ben Bellows BMC International Health and Human Rights 2013, 13:13 (26 February 2013)

Abstract | Provisional PDF | PubMed

2.

Research   Open Access

Comparative proteomic analysis of the effect of temperature and fertilizer on gliadin and glutenin accumulation in the developing endosperm and flour from Triticum aestivum L. cv. Butte 86

William J Hurkman, Charlene K Tanaka, William H Vensel, Roger Thilmony, Susan B Altenbach Proteome Science 2013, 11:8 (22 February 2013)

Abstract | Provisional PDF | PubMed

3.

Research   Open Access

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

Stephen R Fairclough, Zehua Chen, Eric Kramer, Qiandong Zeng, Sarah Young, Hugh M Robertson, Emina Begovic, Daniel J Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B Franz Lang, Brian Haas, Chad Nusbaum, Nicole King Genome Biology 2013, 14:R15 (18 February 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Genome sequencing of Salpingoeca rosetta reveals insights into the genome composition of the metazoan ancestor and the evolution of multicellularity

4.

Research article   Open Access Highly Accessed

Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence

Chris M Rands, Aaron Darling, Matthew Fujita, Lesheng Kong, Matthew T Webster, Céline Clabaut, Richard D Emes, Andreas Heger, Stephen Meader, Michael Brent Hawkins, Michael B Eisen, Clotilde Teiling, Jason Affourtit, Benjamin Boese, Peter R Grant, Barbara Rosemary Grant, Jonathan A Eisen, Arhat Abzhanov, Chris P Ponting BMC Genomics 2013, 14:95 (12 February 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

204 years after Charles Darwin’s birth, sequencing of the genome of the Darwin’s Finch Geospiza magnirostris reveals over 13,000 predicted genes, of which two under positive selection may have contributed to beak morphology evolution, which so interested Darwin.

5.

Research   Open Access Highly Accessed

Cyclist route choice, traffic-related air pollution, and lung function: a scripted exposure study

Sarah Jarjour, Michael Jerrett, Dane Westerdahl, Audrey Nazelle, Cooper Hanning, Laura Daly, Jonah Lipsitt, John Balmes Environmental Health 2013, 12:14 (7 February 2013)

Abstract | Provisional PDF | PubMed

6.

Research   Open Access

Expression of the Lhx genes apterous and lim1 in an errant polychaete: implications for bilaterian appendage evolution, neural development, and muscle diversification

Christopher J Winchell, David K Jacobs EvoDevo 2013, 4:4 (1 February 2013)

Abstract | Full text | PDF | PubMed

7.

Method   Open Access Highly Accessed

CGAL: computing genome assembly likelihoods

Atif Rahman, Lior Pachter Genome Biology 2013, 14:R8 (29 January 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A likelihood based approach for better estimation of genome assembly quality

8.

Research   Open Access

Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment

Patanjali Varanasi, Priyanka Singh, Manfred Auer, Paul D Adams, Blake A Simmons, Seema Singh Biotechnology for Biofuels 2013, 6:14 (28 January 2013)

Abstract | Full text | PDF | PubMed

9.

Research article   Open Access Highly Accessed

Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes

Gilda Rauscher, Ivan Simko BMC Plant Biology 2013, 13:11 (22 January 2013)

Abstract | Full text | PDF | PubMed

10.

Review   Open Access

Using a model filamentous fungus to unravel mechanisms of lignocellulose deconstruction

Elizabeth A Znameroski, N Louise Glass Biotechnology for Biofuels 2013, 6:6 (22 January 2013)

Abstract | Provisional PDF | PubMed

11.

Methodology   Open Access

Parental feeding practices in Mexican American families: initial test of an expanded measure

Jeanne M Tschann, Steven E Gregorich, Carlos Penilla, Lauri A Pasch, Cynthia L de Groat, Elena Flores, Julianna Deardorff, Louise C Greenspan, Nancy F Butte International Journal of Behavioral Nutrition and Physical Activity 2013, 10:6 (17 January 2013)

Abstract | Full text | PDF | PubMed

12.

Methodology   Open Access Highly Accessed

2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts

Mariana Leguia, Jennifer AN Brophy, Douglas Densmore, Angel Asante, J Christopher Anderson Journal of Biological Engineering 2013, 7:2 (10 January 2013)

Abstract | Full text | PDF | PubMed

13.

Research article   Open Access

Deep divergences and extensive phylogeographic structure in a clade of lowland tropical salamanders

Sean M Rovito, Gabriela Parra-Olea, Carlos R Vásquez-Almazán, Roberto Luna-Reyes, David B Wake BMC Evolutionary Biology 2012, 12:255 (29 December 2012)

Abstract | Full text | PDF | PubMed

14.

Methodology   Open Access

Standardization and validation of a cytometric bead assay to assess antibodies to multiple Plasmodium falciparum recombinant antigens

Bartholomew N Ondigo, Gregory S Park, Severin O Gose, Benjamin M Ho, Lyticia A Ochola, George O Ayodo, Ayub V Ofulla, Chandy C John Malaria Journal 2012, 11:427 (21 December 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

With optimization, the cytometric bead assay may be the preferred method of testing for antibodies to P. falciparum antigens, as the assay can test for antibodies to multiple recombinant antigens from a single plasma sample and produces a greater range of values in positive samples.

15.

Review   Subscription

Biophysical regulation of stem cell behavior within the niche

Anthony Conway, David V Schaffer Stem Cell Research & Therapy 2012, 3:50 (14 December 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Conway and Schaffer review the biophysical aspects of the microenvironment which are involved in the regulation of stem cell development and fate, including mechanoregulation and the spatial organization of cues. 

16.

Research   Open Access

Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants

Pia Damm Petersen, Jane Lau, Berit Ebert, Fan Yang, Yves Verhertbruggen, Jin Sun Kim, Patanjali Varanasi, Anongpat Suttangkakul, Manfred Auer, Dominique Loqué, Henrik Vibe Scheller Biotechnology for Biofuels 2012, 5:84 (26 November 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The irregular xylem (irx) mutation in Arabidopsis collapses the stem, causing dwarfism, and can be rescued by cell-specific control of xylan expression to create viable plants with enhanced traits for biofuel production.

17.

Research article   Open Access

Forward chemical genetic screens in Arabidopsis identify genes that influence sensitivity to the phytotoxic compound sulfamethoxazole

Karl J Schreiber, Ryan S Austin, Yunchen Gong, Jianfeng Zhang, Pauline Fung, Pauline W Wang, David S Guttman, Darrell Desveaux BMC Plant Biology 2012, 12:226 (24 November 2012)

Abstract | Full text | PDF | PubMed

18.

Research article   Open Access

A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome

Daniel Capurso, Hao Xiong, Mark R Segal BMC Genomics 2012, 13:630 (15 November 2012)

Abstract | Full text | PDF | PubMed

19.

Research   Open Access Highly Accessed

Environmental justice implications of arsenic contamination in California’s San Joaquin Valley: a cross-sectional, cluster-design examining exposure and compliance in community drinking water systems

Carolina L Balazs, Rachel Morello-Frosch, Alan E Hubbard, Isha Ray Environmental Health 2012, 11:84 (14 November 2012)

Abstract | Full text | PDF | PubMed

20.

Research article   Open Access Highly Accessed

Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: A comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. kukunoris

Weizhao Yang, Yin Qi, Ke Bi, Jinzhong Fu BMC Genomics 2012, 13:588 (1 November 2012)

Abstract | Full text | PDF | PubMed

21.

Research   Open Access Highly Accessed

Whole genome sequencing of phage resistant Bacillus anthracis mutants reveals an essential role for cell surface anchoring protein CsaB in phage AP50c adsorption

Kimberly A Bishop-Lilly, Roger D Plaut, Peter E Chen, Arya Akmal, Kristin M Willner, Amy Butani, Shakia Dorsey, Vishwesh Mokashi, Alfred J Mateczun, Carol Chapman, Matroner George, Truong Luu, Timothy D Read, Richard Calendar, Scott Stibitz, Shanmuga Sozhamannan Virology Journal 2012, 9:246 (26 October 2012)

Abstract | Full text | PDF | PubMed

22.

Short report   Open Access

A divergent variant of Grapevine leafroll-associated virus 3 is present in California

YeeMey Seah, Abhineet M Sharma, Siming Zhang, Rodrigo PP Almeida, Siobain Duffy Virology Journal 2012, 9:235 (13 October 2012)

Abstract | Full text | PDF | PubMed

23.

Nano Express   Open Access

Resistive switching of Au/ZnO/Au resistive memory: an in situ observation of conductive bridge formation

Chung-Nan Peng, Chun-Wen Wang, Tsung-Cheng Chan, Wen-Yuan Chang, Yi-Chung Wang, Hung-Wei Tsai, Wen-Wei Wu, Lih-Juann Chen, Yu-Lun Chueh Nanoscale Research Letters 2012, 7:559 (8 October 2012)

Abstract | Full text | PDF | PubMed

24.

Research article   Open Access Highly Accessed

Callose plug deposition patterns vary in pollen tubes of Arabidopsis thaliana ecotypes and tomato species

Peng Qin, Dylan Ting, Andrew Shieh, Sheila McCormick BMC Plant Biology 2012, 12:178 (3 October 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The distance from pollen grain pore to the first callose plug varies within Arabidopsis ecotypes and tomato species, with plug deposition patterns being heritable and associated with pollen tube growth rate.

25.

Research   Open Access

Molecular mapping of the Pi2/9 allelic gene Pi2-2 conferring broad-spectrum resistance to Magnaporthe oryzae in the rice cultivar Jefferson

Nan Jiang, Zhiqiang Li, Jun Wu, Yue Wang, Liqun Wu, Suhua Wang, Dan Wang, Ting Wen, Yi Liang, Pingyong Sun, Jinling Liu, Liangying Dai, Zhilong Wang, Chao Wang, Meizhong Luo, Xionglun Liu, Guo-Liang Wang Rice 2012, 5:29 (3 October 2012)

Abstract | Full text | PDF

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