The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins
Kozakov, Dima, Grove, Laurie E, Hall, David R, Bohnuud, Tanggis, Mottarella, Scott E, Luo, Lingqi, Xia, Bing, Beglov, Dmitri, Vajda, Sandor
Published in Nature protocols (01.05.2015)
Published in Nature protocols (01.05.2015)
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Journal Article
Exploring the structural origins of cryptic sites on proteins
Beglov, Dmitri, Hall, David R., Wakefield, Amanda E., Luo, Lingqi, Allen, Karen N., Kozakov, Dima, Whitty, Adrian, Vajda, Sandor
Published in Proceedings of the National Academy of Sciences - PNAS (10.04.2018)
Published in Proceedings of the National Academy of Sciences - PNAS (10.04.2018)
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Journal Article
Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA
Wan, Jonathan C. M., Stephens, Dennis, Luo, Lingqi, White, James R., Stewart, Caitlin M., Rousseau, Benoît, Tsui, Dana W. Y., Diaz, Luis A.
Published in Nature communications (23.08.2022)
Published in Nature communications (23.08.2022)
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Journal Article
Ligand deconstruction: Why some fragment binding positions are conserved and others are not
Kozakov, Dima, Hall, David R., Jehle, Stefan, Luo, Lingqi, Ochiana, Stefan O., Jones, Elizabeth V., Pollastri, Michael, Allen, Karen N., Whitty, Adrian, Vajda, Sandor
Published in Proceedings of the National Academy of Sciences - PNAS (19.05.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (19.05.2015)
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Journal Article
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)
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
Published in Biochemistry (Easton) (04.02.2020)
Published in Biochemistry (Easton) (04.02.2020)
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Journal Article
The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes
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.
Published in Developmental biology (15.04.2020)
Published in Developmental biology (15.04.2020)
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Journal Article
Integrative genetic and genomic networks identify microRNA associated with COPD and ILD
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.
Published in Scientific reports (11.08.2023)
Published in Scientific reports (11.08.2023)
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Journal Article
Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq
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
Published in Cancer prevention research (Philadelphia, Pa.) (01.06.2011)
Published in Cancer prevention research (Philadelphia, Pa.) (01.06.2011)
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Journal Article
RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins
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
Published in Development (Cambridge) (15.02.2016)
Published in Development (Cambridge) (15.02.2016)
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Journal Article
Distinct effects of knocking down MEK1 and MEK2 on replication of herpes simplex virus type 2
Zhang, Hao, Feng, Hai, Luo, Lingqi, Zhou, Qi, Luo, Zhijun, Peng, Yihong
Published in Virus research (01.06.2010)
Published in Virus research (01.06.2010)
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Journal Article
Characterization of Ser338 Phosphorylation for Raf-1 Activation
Zang, Mengwei, Gong, Jun, Luo, Lingqi, Zhou, Jing, Xiang, Xiaoqin, Huang, Wei, Huang, Qiren, Luo, Xixi, Olbrot, Martin, Peng, Yihong, Chen, Changyan, Luo, Zhijun
Published in The Journal of biological chemistry (14.11.2008)
Published in The Journal of biological chemistry (14.11.2008)
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Journal Article
Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing
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
Published in BMC proceedings (01.10.2012)
Published in BMC proceedings (01.10.2012)
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Journal Article
A Load Transfer based Energy Saving Scheme for Hybrid Optical Wireless Access Networks
Cong, YU, Lingqi, LUO, Xiaoling, LIU, Jingwen, ZHANG, Jianhua, SHEN
Published in 2019 28th Wireless and Optical Communications Conference (WOCC) (01.05.2019)
Published in 2019 28th Wireless and Optical Communications Conference (WOCC) (01.05.2019)
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Conference Proceeding
A benchmark testing ground for integrating homology modeling and protein docking
Bohnuud, Tanggis, Luo, Lingqi, Wodak, Shoshana J., Bonvin, Alexandre M. J. J., Weng, Zhiping, Vajda, Sandor, Schueler‐Furman, Ora, Kozakov, Dima
Published in Proteins, structure, function, and bioinformatics (01.01.2017)
Published in Proteins, structure, function, and bioinformatics (01.01.2017)
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Journal Article
Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data
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
Published in RNA (Cambridge) (01.02.2015)
Published in RNA (Cambridge) (01.02.2015)
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Journal Article
Correction: Ligand deconstruction: Why some fragment binding positions are conserved and others are not
Published in Proceedings of the National Academy of Sciences - PNAS
(14.07.2015)
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Journal Article
Abstract 3554: Gene and miRNA expression networks specific to never smoker lung adenocarcinoma
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
Published in Cancer research (Chicago, Ill.) (01.10.2014)
Published in Cancer research (Chicago, Ill.) (01.10.2014)
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Journal Article
Abstract 3077: Dysregulation of microRNA-mRNA regulatory networks in the bronchial airway epithelium of smokers with lung cancer
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
Published in Cancer research (Chicago, Ill.) (01.08.2015)
Published in Cancer research (Chicago, Ill.) (01.08.2015)
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Journal Article