Dissecting complex transcriptional responses using pathway-level scores based on prior information

Authors: Ward Lucas D, Bussemaker Harmen J, Boorsma Andre

Source: BMC Bioinformatics, Vol 8, Iss Suppl 6, p S6 (2007)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2105/8/S6/S6; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/051e18bc5c8242f182baea86c5ded205

AAV-mediated hepatic expression of SLC30A10 and the Thr95Ile variant attenuates manganese excess and other phenotypes in Slc30a10-deficient mice

Authors: Prajapati, Milankumar, Quenneville, Chelsea B., Zhang, Jared Z., Chong, Grace S., Chiu, Lauren, Ma, Bangyi, Ward, Lucas D., Tu, Ho-Chou, Bartnikas, Thomas B.

Source: In Journal of Biological Chemistry March 2024 300(3)

Advancing diagnosis and management of liver disease in adults through exome sequencing

Authors: Zheng, Melanie, Hakim, Aaron, Konkwo, Chigoziri, Deaton, Aimee M., Ward, Lucas D., Silveira, Marina G., Assis, David N., Liapakis, AnnMarie, Jaffe, Ariel, Jiang, Z. Gordon, Curry, Michael P., Lai, Michelle, Cho, Michael H., Dykas, Daniel, Bale, Allen, Mistry, Pramod K., Vilarinho, Silvia

Source: In eBioMedicine September 2023 95

Rare coding variants in DNA damage repair genes associated with timing of natural menopause

Authors: Ward, Lucas D., Parker, Margaret M., Deaton, Aimee M., Tu, Ho-Chou, Flynn-Carroll, Alexander O., Hinkle, Gregory, Nioi, Paul

Source: In Human Genetics and Genomics Advances 14 April 2022 3(2)

Nonclinical cardiovascular safety evaluation of romosozumab, an inhibitor of sclerostin for the treatment of osteoporosis in postmenopausal women at high risk of fracture

Authors: Turk, James R., Deaton, Aimee M., Yin, Jun, Stolina, Marina, Felx, Melanie, Boyd, Gabrielle, Bienvenu, Jean-Guy, Varela, Aurore, Guillot, Martin, Holdsworth, Gill, Wolfreys, Alison, Dwyer, Denise, Kumar, Sheetal V., de Koning, Emily M., Qu, Yusheng, Engwall, Michael, Locher, Kathrin, Ward, Lucas D., Glaus, Charles, He, Yudong D., Boyce, Rogely Waite

Source: In Regulatory Toxicology and Pharmacology August 2020 115

Classification of Saccharomyces cerevisiae promoter regions into distinct chromatin classes reveals the existence of nucleosome-depleted hotspots of transcription factor occupancy

Authors: Wang, Junbai, Ward, Lucas D., Bussemaker, Harmen J.

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1010.0713

Modernizing Human Cancer Risk Assessment of Therapeutics

Authors: Fielden, Mark R., Ward, Lucas D., Minocherhomji, Sheroy, Nioi, Paul, Lebrec, Herve, Jacobson-Kram, David

Source: In Trends in Pharmacological Sciences March 2018 39(3):232-247

Rationalizing Secondary Pharmacology Screening Using Human Genetic and Pharmacological Evidence

Authors: Deaton, Aimee M, Fan, Fan, Zhang, Wei, Nguyen, Phuong A, Ward, Lucas D, Nioi, Paul

Source: Toxicological sciences. 167(2):593-603

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100078442473.0x000001&indx=1&recIds=ETOCvdc_100078442473.0x000001

Defining functional DNA elements in the human genome

Authors: Kellis, Manolis, Wold, Barbara, Snyderd, Michael P., Bernstein, Bradley E., Kundaje, Anshul, Marinov, Georgi K., Ward, Lucas D., Birney, Ewan, Crawford, Gregory E., Dekker, Job, Dunham, Ian, Elnitski, Laura L., Farnham, Peggy J., Feingold, Elise A., Gerstein, Mark, Giddings, Morgan C., Gilbert, David M., Gingeras, Thomas R., Green, Eric D., Guigo, Roderic, Hubbard, Tim, Kent, Jim, Lieb, Jason D., Myerst, Richard M., Pazin, Michael J., Ren, Bing, Stamatoyannopoulos, John A., Weng, Zhiping, White, Kevin P., Hardison, Ross C.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2014 Apr . 111(17), 6131-6138.

Access URL: https://www.jstor.org/stable/23772466

Comment on 'Using Human 'Experiments of Nature' to Predict Drug Safety Issues: An Example with PCSK9 Inhibitors'

Authors: Ward, Lucas D., Moffat, Graeme J., Yuan, Jing, Nioi, Paul

Source: Drug safety. 41(11):1097-1099

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100130226545.0x000001&indx=1&recIds=ETOCvdc_100130226545.0x000001

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

Authors: Lee, Mark N., Ye, Chun, Villani, Alexandra-Chloé, Raj, Towfique, Li, Weibo, Eisenhaure, Thomas M., Imboywa, Selina H., Chipendo, Portia I., Ran, F. Ann, Slowikowski, Kamil, Ward, Lucas D., Raddassi, Khadir, McCabe, Cristin, Lee, Michelle H., Frohlich, Irene Y., Hafler, David A., Kellis, Manolis, Raychaudhuri, Soumya, Zhang, Feng, Stranger, Barbara E., Benoist, Christophe O., De Jager, Philip L., Regev, Aviv, Hacohen, Nir

Source: Science, 2014 Mar 01. 343(6175), 1119-1119.

Access URL: http://www.jstor.org/stable/24743322

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

Authors: Ward, Lucas D., Kellis, Manolis

Source: Science, 2012 Sep . 337(6102), 1675-1678.

Access URL: http://dx.doi.org/10.1126/science.1225057

Plasma proteomic associations with genetics and health in the UK Biobank

Authors: Sun, Benjamin B., Chiou, Joshua, Traylor, Matthew, Benner, Christian, Hsu, Yi-Hsiang, Richardson, Tom G., Surendran, Praveen, Mahajan, Anubha, Robins, Chloe, Vasquez-Grinnell, Steven G., Hou, Liping, Kvikstad, Erika M., Burren, Oliver S., Davitte, Jonathan, Ferber, Kyle L., Gillies, Christopher E., Hedman, Åsa K., Hu, Sile, Lin, Tinchi, Mikkilineni, Rajesh, Pendergrass, Rion K., Pickering, Corran, Prins, Bram, Baird, Denis, Chen, Chia-Yen, Ward, Lucas D., Deaton, Aimee M., Welsh, Samantha, Willis, Carissa M., Lehner, Nick, Arnold, Matthias, Wörheide, Maria A., Suhre, Karsten, Kastenmüller, Gabi, Sethi, Anurag, Cule, Madeleine, Raj, Anil, Burkitt-Gray, Lucy, Melamud, Eugene, Black, Mary Helen, Fauman, Eric B., Howson, Joanna M. M., Kang, Hyun Min, McCarthy, Mark I., Nioi, Paul, Petrovski, Slavé, Scott, Robert A., Smith, Erin N., Szalma, Sándor, Waterworth, Dawn M., Mitnaul, Lyndon J., Szustakowski, Joseph D., Gibson, Bradford W., Miller, Melissa R., Whelan, Christopher D.

Source: Nature; October 2023, Vol. 622 Issue: 7982 p329-338, 10p

Hotspots of Transcription Factor Colocalization in the Genome of Drosophila melanogaster

Authors: Moorman, Celine, Sun, Ling V., Wang, Junbai, de Wit, Elzo, Talhout, Wendy, Ward, Lucas D., Greil, Frauke, Lu, Xiang-Jun, White, Kevin P., Bussemaker, Harmen J., van Steensel, Bas

Source: Proceedings of the National Academy of Sciences of the United States of America, 2006 Aug 01. 103(32), 12027-12032.

Access URL: https://www.jstor.org/stable/30051659

Phenotypes associated with genes encoding drug targets are predictive of clinical trial side effects

Authors: Nguyen, Phuong A., Born, David A., Deaton, Aimee M., Nioi, Paul, Ward, Lucas D.

Source: Nature communications. 10(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131066064.0x000001&indx=1&recIds=ETOCvdc_100131066064.0x000001

Author Correction: Phenotypes associated with genes encoding drug targets are predictive of clinical trial side effects

Authors: Nguyen, Phuong A., Born, David A., Deaton, Aimee M., Nioi, Paul, Ward, Lucas D.

Source: Nature communications. 10(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100130640122.0x000001&indx=1&recIds=ETOCvdc_100130640122.0x000001

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

Authors: Filion, Guillaume J., van Bemmel, Joke G., Braunschweig, Ulrich, Talhout, Wendy, Kind, Jop, Ward, Lucas D., Brugman, Wim, de Castro, Inês J., Kerkhoven, Ron M., Bussemaker, Harmen J., van Steensel, Bas

Source: In Cell 15 October 2010 143(2):212-224

A rare missense variant in NR1H4 associates with lower cholesterol levels

Authors: Deaton, Aimee M., Sulem, Patrick, Nioi, Paul, Benonisdottir, Stefania, Ward, Lucas D., Davidsson, Olafur B., Lao, Socheata, Helgadottir, Anna, Fan, Fan, Jensson, Brynjar O., Norddahl, Gudmundur L., Jonasdottir, Aslaug, Jonasdottir, Adalbjorg, Sigurdsson, Asgeir, Kristjansson, Ragnar P., Oddsson, Asmundur, Arnadottir, Gudny A., Jonsson, Hakon, Olafsson, Isleifur, Eyjolfsson, Gudmundur I., Sigurdardottir, Olof, Bjornsson, Einar S., Olafsson, Sigurdur, Steingrimsdottir, Thora, Rafnar, Thorunn, Thorgeirsson, Gudmundur, Masson, Gisli, Thorleifsson, Gudmar, Gudbjartsson, Daniel F., Holm, Hilma, Thorsteinsdottir, Unnur, Stefansson, Kari

Source: Communications biology. 1(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100130045163.0x000001&indx=1&recIds=ETOCvdc_100130045163.0x000001

Using human genetics to improve safety assessment of therapeutics

Authors: Carss, Keren J., Deaton, Aimee M., Del Rio-Espinola, Alberto, Diogo, Dorothée, Fielden, Mark, Kulkarni, Diptee A., Moggs, Jonathan, Newham, Peter, Nelson, Matthew R., Sistare, Frank D., Ward, Lucas D., Yuan, Jing

Source: Nature Reviews Drug Discovery; February 2023, Vol. 22 Issue: 2 p145-162, 18p

Rare loss of function variants in the hepatokine gene INHBE protect from abdominal obesity.

Authors: Deaton, Aimee M., Dubey, Aditi, Ward, Lucas D., Dornbos, Peter, Flannick, Jason, AMP-T2D-GENES Consortium, Yee, Elaine, Ticau, Simina, Noetzli, Leila, Parker, Margaret M., Hoffing, Rachel A., Willis, Carissa, Plekan, Mollie E., Holleman, Aaron M., Hinkle, Gregory, Fitzgerald, Kevin, Vaishnaw, Akshay K., Nioi, Paul

Source: Nature Communications; 7/27/2022, Vol. 13 Issue 1, p1-12, 12p

Subject Terms: GENETIC variation, ABDOMINAL adipose tissue, ACTIVIN receptors, CORONARY disease, HEART metabolism disorders, WAIST circumference, WAIST-hip ratio