DASHR 2.0: integrated database of human small non-coding RNA genes and mature products
Kuksa, Pavel P, Amlie-Wolf, Alexandre, Katanić, Živadin, Valladares, Otto, Wang, Li-San, Leung, Yuk Yee
Published in Bioinformatics (15.03.2019)
Published in Bioinformatics (15.03.2019)
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Journal Article
DASHR: database of small human noncoding RNAs
Leung, Yuk Yee, Kuksa, Pavel P, Amlie-Wolf, Alexandre, Valladares, Otto, Ungar, Lyle H, Kannan, Sampath, Gregory, Brian D, Wang, Li-San
Published in Nucleic acids research (04.01.2016)
Published in Nucleic acids research (04.01.2016)
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Journal Article
High-order neural networks and kernel methods for peptide-MHC binding prediction
Kuksa, Pavel P, Min, Martin Renqiang, Dugar, Rishabh, Gerstein, Mark
Published in Bioinformatics (Oxford, England) (15.11.2015)
Published in Bioinformatics (Oxford, England) (15.11.2015)
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Journal Article
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements
Hwang, Yih-Chii, Lin, Chiao-Feng, Valladares, Otto, Malamon, John, Kuksa, Pavel P, Zheng, Qi, Gregory, Brian D, Wang, Li-San
Published in Bioinformatics (15.04.2015)
Published in Bioinformatics (15.04.2015)
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Journal Article
HiPR: High-throughput probabilistic RNA structure inference
Kuksa, Pavel P., Li, Fan, Kannan, Sampath, Gregory, Brian D., Leung, Yuk Yee, Wang, Li-San
Published in Computational and structural biotechnology journal (01.01.2020)
Published in Computational and structural biotechnology journal (01.01.2020)
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Journal Article
INFERNO: inferring the molecular mechanisms of noncoding genetic variants
Amlie-Wolf, Alexandre, Tang, Mitchell, Mlynarski, Elisabeth E, Kuksa, Pavel P, Valladares, Otto, Katanic, Zivadin, Tsuang, Debby, Brown, Christopher D, Schellenberg, Gerard D, Wang, Li-San
Published in Nucleic acids research (28.09.2018)
Published in Nucleic acids research (28.09.2018)
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Journal Article
Scalable approaches for functional analyses of whole-genome sequencing non-coding variants
Kuksa, Pavel P, Greenfest-Allen, Emily, Cifello, Jeffrey, Ionita, Matei, Wang, Hui, Nicaretta, Heather, Cheng, Po-Liang, Lee, Wan-Ping, Wang, Li-San, Leung, Yuk Yee
Published in Human molecular genetics (20.10.2022)
Published in Human molecular genetics (20.10.2022)
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Journal Article
SPAR: small RNA-seq portal for analysis of sequencing experiments
Kuksa, Pavel P, Amlie-Wolf, Alexandre, Katanić, Živadin, Valladares, Otto, Wang, Li-San, Leung, Yuk Yee
Published in Nucleic acids research (02.07.2018)
Published in Nucleic acids research (02.07.2018)
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Journal Article
NIAGADS Alzheimer's GenomicsDB: A resource for exploring Alzheimer's disease genetic and genomic knowledge
Greenfest‐Allen, Emily, Valladares, Otto, Kuksa, Pavel P., Gangadharan, Prabhakaran, Lee, Wan‐Ping, Cifello, Jeffrey, Katanic, Zivadin, Kuzma, Amanda B., Wheeler, Nicholas, Bush, William S., Leung, Yuk Yee, Schellenberg, Gerard, Stoeckert, Christian J., Wang, Li‐San
Published in Alzheimer's & dementia (01.02.2024)
Published in Alzheimer's & dementia (01.02.2024)
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Journal Article
Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis
Vandivier, Lee E., Campos, Rafael, Kuksa, Pavel P., Silverman, Ian M., Wang, Li-San, Gregory, Brian D.
Published in The Plant cell (01.11.2015)
Published in The Plant cell (01.11.2015)
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Journal Article
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants
Kuksa, Pavel P, Lee, Chien-Yueh, Amlie-Wolf, Alexandre, Gangadharan, Prabhakaran, Mlynarski, Elizabeth E, Chou, Yi-Fan, Lin, Han-Jen, Issen, Heather, Greenfest-Allen, Emily, Valladares, Otto, Leung, Yuk Yee, Wang, Li-San
Published in Bioinformatics (01.06.2020)
Published in Bioinformatics (01.06.2020)
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Journal Article
Genetic, transcriptomic, histological, and biochemical analysis of progressive supranuclear palsy implicates glial activation and novel risk genes
Farrell, Kurt, Humphrey, Jack, Chang, Timothy, Zhao, Yi, Leung, Yuk Yee, Kuksa, Pavel P., Patil, Vishakha, Lee, Wan-Ping, Kuzma, Amanda B., Valladares, Otto, Cantwell, Laura B., Wang, Hui, Ravi, Ashvin, De Sanctis, Claudia, Han, Natalia, Christie, Thomas D., Afzal, Robina, Kandoi, Shrishtee, Whitney, Kristen, Krassner, Margaret M., Ressler, Hadley, Kim, SoongHo, Dangoor, Diana, Iida, Megan A., Casella, Alicia, Walker, Ruth H., Nirenberg, Melissa J., Renton, Alan E., Babrowicz, Bergan, Coppola, Giovanni, Raj, Towfique, Höglinger, Günter U., Müller, Ulrich, Golbe, Lawrence I., Morris, Huw R., Hardy, John, Revesz, Tamas, Warner, Tom T., Jaunmuktane, Zane, Mok, Kin Y., Rademakers, Rosa, Dickson, Dennis W., Ross, Owen A., Wang, Li-San, Goate, Alison, Schellenberg, Gerard, Geschwind, Daniel H., Hopfner, Franziska, Roeber, Sigrun, Herms, Jochen, Troakes, Claire, Gelpi, Ellen, Compta, Yaroslau, van Swieten, John C., Rajput, Alex, Hinton, Fairlie, de Yebenes, Justo García, Crary, John F., Naj, Adam
Published in Nature communications (09.09.2024)
Published in Nature communications (09.09.2024)
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Journal Article
Biological Sequence Classification with Multivariate String Kernels
Kuksa, Pavel P.
Published in IEEE/ACM transactions on computational biology and bioinformatics (01.09.2013)
Published in IEEE/ACM transactions on computational biology and bioinformatics (01.09.2013)
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Journal Article
Transcriptome-wide measurement of plant RNA secondary structure
Foley, Shawn W, Vandivier, Lee E, Kuksa, Pavel P, Gregory, Brian D
Published in Current opinion in plant biology (01.10.2015)
Published in Current opinion in plant biology (01.10.2015)
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Journal Article
Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease
Kuksa, Pavel P, Liu, Chia-Lun, Fu, Wei, Qu, Liming, Zhao, Yi, Katanic, Zivadin, Clark, Kaylyn, Kuzma, Amanda B, Ho, Pei-Chuan, Tzeng, Kai-Teh, Valladares, Otto, Chou, Shin-Yi, Naj, Adam C, Schellenberg, Gerard D, Wang, Li-San, Leung, Yuk Yee
Published in Journal of Alzheimer's disease (01.01.2022)
Published in Journal of Alzheimer's disease (01.01.2022)
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Introducing the NIAGADS Alzheimer’s GenomicsDB API: A toolkit for remote exploration of Alzheimer’s disease genetics
Greenfest‐Allen, Emily, Klamann, Conor, Mlynarski, Elizabeth E., Kuksa, Pavel P., Gangadharan, Prabhakaran, Kuzma, Amanda B, Valladares, Otto, Leung, Yuk Yee, Stoeckert, Christian J, Wang, Li‐San
Published in Alzheimer's & dementia (01.12.2021)
Published in Alzheimer's & dementia (01.12.2021)
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