Publications from Our Senior Scientists:

Kenneth D Clevenger†, Jin Woo Bok†, Rosa Ye†, Galen P Miley, Maria H Verdan , Thomas Velk, Cynthia Chen, KaHoua Yang, Matthew T Robey, Peng Gao, Matthew Lamprecht, Paul M Thomas, Md Nurul Islam, Jonathan M Palmer , Chengcang C Wu*, Nancy P Keller*
& Neil L Kelleher* (2017)
A scalable platform to identify fungal secondary metabolites and their gene clusters. Nature chemical biology published online June 12, 2017

Jin Woo Bok†, Rosa Ye†, Kenneth D Clevenger†, David Mead, Megan Wagner, Amanda Krerowicz,Jessica C Albright, Anthony W Goering, Paul M Thomas, Neil L Kelleher*, Nancy P Keller*and Chengcang C Wu*(2015)  Fungal artificial chromosomes for mining of the fungal secondary metabolome BMC Genomics, 16:343

Andrey Alexeyenko, Björn Nystedt, Francesco Vezzi, Ellen Sherwood, Rosa Ye, Bjarne Knudsen, Martin Simonsen, Benjamin Turner, Pieter de Jong, Cheng-Cang Wu and Joakim Lundeberg1 (2014) Efficient de novo assembly of large and complex genomes by massively parallel sequencing of fosmid pools . BMC Genomics, 15:439.

Hosono, Y., Abe, T., Ishiai, M.,Islam, M. N.,  Arakawa, H., Wang, W., Takeda, S., Ishii, Y., Takata, M., Seki, M. and Enomoto, T. (2014) Tumor suppressor RECQL5 controls recombination induced by DNA cross-linking agentsBiochim Biophys Acta, 1843, 1002-12

Wu CC, Ye R, Jasinovica S, Wagner M, Godiska R, Tong AHY, Lok S, Krerowicz A, Knox C, Mead D, and Lodes M. (2012) Long-span, mate-pair scaffolding and other methods for faster next-generation sequencing library creation. Nature methods. September. Application Notes i-ii.

Zhang H-B, Scheuring CF, Zhang M, Zhang Y, Wu CC, Dong JJ, and Li Y. (2012) Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research. Nature Protocols, 7:479-499.

Zhang M, Zhang Y, Scheuring CF, Wu CC, Dong JJ, and Zhang H-B (2012) Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research. Nature Protocols, 7:467-478.

M.,Islam, M. N., Paquet, N., Fox, D. 3rd., Dray, E., Zheng, X. F., Klein, H., Sung, P. and Wang,  W.(2012) A variant of the BRC repeat is essential for the RECQL5 helicase to interact with RAD51 recombinase for genome stabilization, J Biol Chem. 287, 23808-18

Parsley LC, Wu CC, Mead DA, Gooman RM, and Liles MR (2011) Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications in Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. Pp109-116. Edited by Frans J. de Bruijn, Wiley-Blackwell, NJ, USA.

Schulte D, Ariyadasa R, Shi B, Fleury D, Saski C, Atkins M, Dejong P, Wu CC, Graner A, Langridge P, Stein N. (2011) BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). BMC Genomics. 12:247.

Zhang, M, Wu, YH, Lee, MK, Liu, YH, Rong, Y, Santos TS, Wu, CC, Xie F, Nelson RL, Zhang H-B (2010) Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors. Nucleic Acids Res. 2010 : gkq524v1-gkq524.

Godiska, R, Mead, D, Dhodda V, Wu, CC, Hochstein, R, Karsi, A, Usdin, K, Entezam, A, Ravin, N. (2010) Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli. Nucleic Acids Res. 38:e88.

M.,Islam, M. N., Fox, D. 3rd., Guo, R., Enomoto, T. and Wang, W. (2010) RecQL5 promotesgenome stabilization through two parallel mechanisms-interacting with RNA polymerase II and acting as a helicase, Mol Cell Biol, 30, 2460-72

Wu, CC., Proestou, D., Carter, D., Nicholson, E., Santo,s F., Zhao, S., Zhang, HB., Goldsmith, MR. (2009) Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepodopteran species.  BMC Genomics  10:283 doi:10.1186/1471-2164-10-283.

Yasukochi, Y, Tanaka-Okuyama, M, Shibata, F, Yoshido, A, Marec, F, Wu, CC., Zhang, H, Goldsmith, MR, Sahara, K. (2009) Extensive conserved synteny of genes between the karyotypes of Manduca sexta and Bombyx mori revealed by BAC-FISH mapping.PLoS One. 4:e7465.

Nishiyama, A., Xin, L., Sharov, A. A., Thomas, M. P., Mowre, G., Meyers, E., Piao, Y., Mehta, S., Yee, S., Stagg, C., Correa-Cerro, L., Bassey, U., Nakatake, Y., Hoang, H., Kim, E., Tapnio,  R., Qian, Y., Dudekula, D., Sharova, L., Zalzman, M., Li, M., Falco, G., Yang, H. T., Lee, S. L., Monti, M., M.,Islam, M. N., et al., (2009) Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factorsCell Stem Cell5, 420-433

Ananiev, EV., Wu, CC., (co-senior authors) Chamberlin, MA., Svitashev, S., Schwartz, C., Gordon-Kamm, W., Tingey S. (2008) Artificial chromosome formation in maize (Zea mays L.). Chromosoma. 118, 157-177.

Saha, S. K., Darmstadt, G. L., Baqui, A. H., M.,Islam, M. N., Qazi, S., Islam, M., Arifeen, S. E., Santosham, M., Black, R. E., and Crook, D. W. (2008) Direct detection of the multidrug resistance genome of Haemophilus influenzae in cerebrospinal fluid of children: Implications for treatment of MeningitisThe Pediatrics Infectious Disease Journal27, 49-53

Godiska R, Mead DA, Dhodda V, Hochstein R, Karsi A, Ravin N, Wu CC. (2008) “Bias-Free Cloning of ‘Unclonable’ DNA for Simplified Genomic Finishing.” In DNA Sequencing III: Dealing with Difficult Templates. (J. Kieleczawa, ed.), Jones and Bartlett Publishers, Sudbury, MA.

Li, Y., Uhm, T., Ren, C., Wu, CC., Santos, T., Lee, M.-K., Yan, B., Santos, F., Zhang, A., Scheuring, C., Sanchez, A., Millena, AC., Nguyen, HT., Kou, H.,  Liu, D., and Zhang, H.-B.  (2007) A plant-transformation – competent BIBAC/BAC -based map of rice for functional analysis and genetic engineering of its genomic sequence. Genome 50: 1-11.

Sahara, K. Yoshido, A., Mareec, F., Fukova, I., Zhang,  HB., Wu, CC., Goldsmith, MR., and Yasukochi, Y. (2007) Conserved synteny of genes between chromosome 15 of Bombyx mori and a chromosome of Manduca sexta shown by five-color BAC-FISH. Genome 50, 1061-1065.

G.A.L. Broggini, B. Le Cam, L. Parisi, Wu, CC., H.-B. Zhang, C. Gessler and A. Patocchi (2007) Construction of a contig of BAC clones spanning the region of the apple scab avirulence gene AvrVg. Fungal Genetics and Biology. 44, 44-51.

Nakajima, Y., Kondo, S., Sugio, S., Sueda, S., M.,Islam, M. N., and Kondo, H. (2007) Structure of the biotin carboxylase domain of pyruvate carboxylase from Bacillus thermodenitrificans, Acta Crystallogr. D 63, 885-890

Wu, CC., S.J. Wang and H.-B.Zhang. (2006) Interactions among genomic structure, function and evolution revealed by comprehensive statistic analysis of the Arabidopsis thaliana genome. Genomics 88, 394-406.

Shultz, J.L., Kurunam, Shopinski, K., Iqbal, M.J., Kazi, S., Zobrist, K., Bashir, R., Yaegashi, S., Lavu, N., Afzal, A.J., Yesudas, C.R., Kassem, M.A., Wu, CC., Zhang, H.-B., Town, C.D., Meksem, K., and Lightfoot, D.A. (2006)The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res., 34: D758 – D765.

Stupar, R.M., Beaubien, K.A., Jin, W., Song, J., Lee, M-K., Wu, CC., Zhang, H-B., Han, B., Jiang, J. (2006) Structural diversity and differential transcription of the patatin multicopy gene family during potato tuber development. Genetics. 172:1263-75.

Zhang, X., Scheuring, C., Tripathy, S., Wu, CC., Lee, M-K., Ko, A., Tian, K., Arredondo, F., Zhang, H-B., Tyler, B. (2006) An Integrated BAC and Genome Sequence Physical Map of Phytophthora sojae. Molecular Plant-Microbe Interactions, 19:1302-1310.

Xu, Z., van den Berg, MA., Scheuring, C., Covaleda, L., Lu, H., Santos, FA., Uhm, T., Lee, M.-K., Wu, CC., Liu, S. and Zhang, H-B. (2005)Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: A robust physical map of Penicillium chrysogenum. Nucleic.Acid Res. 33: e50.

Wu, CC., Sun, S., Lee, M-K., Xu, Z., Ren, C. and Zhang, H-B. (2005) Chapter 6. Whole genome physical mapping: An overview on methods for DNA fingerprinting. In Handbook of Plant Genome Mapping. pp257-284. Edited by Meksem K. and Gresshoff P., Wiley-VCH Verlag GmbH: Weinheim, Germany

Ren, C., Sun, S., Lee, M-K., Xu, Z., Wu, CC. and Zhang, H-B. (2005) Chapter 4. Genomic libraries and physical mapping (YACs and BACs). In Handbook of Plant Genome Mapping. pp173-214. Edited by Meksem K. and Gresshoff P., Wiley-VCH Verlag GmbH: Weinheim, Germany

M.,Islam, M. N., Sueda, S., and Kondo, H. (2005) Construction of new forms of pyruvate carboxylase to assess the allosteric regulation by acetyl-CoAProtein Engineering, Design & Selection18, 71-78

Wu, CC., Xu, Z. and Zhang, H.-B. (2004) DNA libraries. In Encyclopedia of Molecular Cell Biology and Molecular Medicine Volume 3 (2nd Edition), pp385-425. Edited by Meyers R.A., Wiley-VCH Verlag GmbH: Weinheim, Germany.

Wu, CC., Sun, SK., Nimmakayala, P., Santos, FA., Springman, R., Ding, KJ., Meksem, K., Lightfoot, D., and Zhang, H-B. (2004) A BAC and BIBAC-based physical map of the soybean genome. Genome Res. 14, 319-326.

Wu, CC., Santos, FA., Nimmakayala, P., Springman, R., Meksem, K., Lightfoot, D., and Zhang, H-B. (2004) Construction of a complementary BAC library for soybean genome-wide physical mapping and whole genome sequencing. Theor. Appl. Genet. 109, 1041-1050.

Yasukochi, Y., Ashakumary, LA., Wu, CC., Yoshido, A., Nohata, J., Mita, K. and Sahara, K. (2004) Organization of the Hox Gene Cluster of the silkworm, Bombyx mori: Bombyx ortholog of labial is separated from the Hox cluster but located on the same chromosome. Dev. Genes and Evolution 214, 606-614.

Xu, Z., Sun, S., Covaleda, L., Ding, K., Zhang, A., Wu, CC., Scheuring, C., and Zhang, H-B. (2004) Genome Physical Mapping with Large-insert Bacterial Clones by Fingerprint Analysis: Methodologies, Source Clone Genome Coverage and Contig Map Quality. Genomics 84, 941-951.

Yong-Biao, J., M.,Islam, M. N., Sueda, S., and Kondo, H. (2004) Identification of the catalytic residues involved in the carboxyl transfer of pyruvate carboxylaseBiochemistry43, 5912-5920

Sueda, S., M.,Islam, M. N., and Kondo, H. (2004) Protein engineering of pyruvate carboxylase. Investigation on the function of acetyl-CoA and the quaternary structureEuropean Journal of Biochemistry271, 1391-1400

Zhang, H-B. and Wu, CC. (2001) BAC as tools for genome sequencing. Plant Physiol. Biochem. 39, 1-15