The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins von Kozakov, Dima, Grove, Laurie E, Hall, David R, Bohnuud, Tanggis, Mottarella, Scott E, Luo, Lingqi, Xia, Bing, Beglov, Dmitri, Vajda, Sandor

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Exploring the structural origins of cryptic sites on proteins von Beglov, Dmitri, Hall, David R., Wakefield, Amanda E., Luo, Lingqi, Allen, Karen N., Kozakov, Dima, Whitty, Adrian, Vajda, Sandor

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Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA von Wan, Jonathan C. M., Stephens, Dennis, Luo, Lingqi, White, James R., Stewart, Caitlin M., Rousseau, Benoît, Tsui, Dana W. Y., Diaz, Luis A.

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Ligand deconstruction: Why some fragment binding positions are conserved and others are not von Kozakov, Dima, Hall, David R., Jehle, Stefan, Luo, Lingqi, Ochiana, Stefan O., Jones, Elizabeth V., Pollastri, Michael, Allen, Karen N., Whitty, Adrian, Vajda, Sandor

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Interaction Energetics and Druggability of the Protein–Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2) von Zhong, Mengqi, Lynch, Andrew, Muellers, Samantha N, Jehle, Stefan, Luo, Lingqi, Hall, David R, Iwase, Reina, Carolan, James P, Egbert, Megan, Wakefield, Amanda, Streu, Kristina, Harvey, Christine M, Ortet, Paula C, Kozakov, Dima, Vajda, Sandor, Allen, Karen N, Whitty, Adrian

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The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes von Hogan, John D., Keenan, Jessica L., Luo, Lingqi, Ibn-Salem, Jonas, Lamba, Arjun, Schatzberg, Daphne, Piacentino, Michael L., Zuch, Daniel T., Core, Amanda B., Blumberg, Carolyn, Timmermann, Bernd, Grau, José Horacio, Speranza, Emily, Andrade-Navarro, Miguel A., Irie, Naoki, Poustka, Albert J., Bradham, Cynthia A.

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Integrative genetic and genomic networks identify microRNA associated with COPD and ILD von Pavel, Ana B., Garrison, Carly, Luo, Lingqi, Liu, Gang, Taub, Daniel, Xiao, Ji, Juan-Guardela, Brenda, Tedrow, John, Alekseyev, Yuriy O., Yang, Ivana V., Geraci, Mark W., Sciurba, Frank, Schwartz, David A., Kaminski, Naftali, Beane, Jennifer, Spira, Avrum, Lenburg, Marc E., Campbell, Joshua D.

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Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq von Beane, Jennifer, Vick, Jessica, Schembri, Frank, Anderlind, Christina, Gower, Adam, Campbell, Joshua, Luo, Lingqi, Zhang, Xiao Hui, Xiao, Ji, Alekseyev, Yuriy O, Wang, Shenglong, Levy, Shawn, Massion, Pierre P, Lenburg, Marc, Spira, Avrum

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RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins von Piacentino, Michael L, Zuch, Daniel T, Fishman, Julie, Rose, Sviatlana, Speranza, Emily E, Li, Christy, Yu, Jia, Chung, Oliver, Ramachandran, Janani, Ferrell, Patrick, Patel, Vijeta, Reyna, Arlene, Hameeduddin, Hajerah, Chaves, James, Hewitt, Finnegan B, Bardot, Evan, Lee, David, Core, Amanda B, Hogan, John D, Keenan, Jessica L, Luo, Lingqi, Coulombe-Huntington, Jasmin, Blute, Todd A, Oleinik, Ekaterina, Ibn-Salem, Jonas, Poustka, Albert J, Bradham, Cynthia A

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Distinct effects of knocking down MEK1 and MEK2 on replication of herpes simplex virus type 2 von Zhang, Hao, Feng, Hai, Luo, Lingqi, Zhou, Qi, Luo, Zhijun, Peng, Yihong

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Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core von Lukose, Vinita, Luo, Lingqi, Kozakov, Dima, Vajda, Sandor, Allen, Karen N, Imperiali, Barbara

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Characterization of Ser338 Phosphorylation for Raf-1 Activation von Zang, Mengwei, Gong, Jun, Luo, Lingqi, Zhou, Jing, Xiang, Xiaoqin, Huang, Wei, Huang, Qiren, Luo, Xixi, Olbrot, Martin, Peng, Yihong, Chen, Changyan, Luo, Zhijun

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A benchmark testing ground for integrating homology modeling and protein docking von Bohnuud, Tanggis, Luo, Lingqi, Wodak, Shoshana J., Bonvin, Alexandre M. J. J., Weng, Zhiping, Vajda, Sandor, Schueler‐Furman, Ora, Kozakov, Dima

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Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identifies the Functional Catalytic Core von Lukose, Vinita, Luo, Lingqi, Kozakov, Dima, Vajda, Sandor, Allen, Karen N., Imperiali, Barbara

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Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing von Brothers, John, Kusko, Rebecca, Liu, Gang, Luo, Lingqi, Guardela, Brenda Juan, Tedrow, John, Alekesyev, Yuriy, Yang, Ivana V, Correll, Mick, Geraci, Mark, Quackenbush, John, Sciurba, Frank, Sebastiani, Paola, Lenburg, Marc, Kaminski, Naftali, Schwartz, David A, Spira, Avrum, Beane, Jennifer

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A benchmark testing ground for integrating homology modeling and protein docking von Bohnuud, Tanggis, Luo, Lingqi, Wodak, Shoshana J, Bonvin, Alexandre M J J, Weng, Zhiping, Vajda, Sandor, Schueler-Furman, Ora, Kozakov, Dima

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Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data von Campbell, Joshua D, Liu, Gang, Luo, Lingqi, Xiao, Ji, Gerrein, Joseph, Juan-Guardela, Brenda, Tedrow, John, Alekseyev, Yuriy O, Yang, Ivana V, Correll, Mick, Geraci, Mark, Quackenbush, John, Sciurba, Frank, Schwartz, David A, Kaminski, Naftali, Johnson, W Evan, Monti, Stefano, Spira, Avrum, Beane, Jennifer, Lenburg, Marc E

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Correction: Ligand deconstruction: Why some fragment binding positions are conserved and others are not

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Abstract 3554: Gene and miRNA expression networks specific to never smoker lung adenocarcinoma von Kusko, Rebecca, Garrison, Carly, Wang, Teresa, Campbell, Josh, Perez-Rogers, Joseph, Luo, Lingqi, Beane, Jennifer, Liu, Gang, Kadara, Humam, Belinsky, Steven, Lenburg, Marc E., Spira, Avrum

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Abstract 3077: Dysregulation of microRNA-mRNA regulatory networks in the bronchial airway epithelium of smokers with lung cancer von Pavel, Ana Brandusa, Campbell, Joshua D., Liu, Gang, Zhang, Sherry, Liu, Hanqiao, Luo, Lingqi, Xiao, Ji, Porta, Kate, Whitney, Duncan, Dubinett, Steven, Elashoff, David, Lenburg, Marc E., Spira, Avrum

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