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ComBat-seq: batch effect adjustment for RNA-seq count data
Zhang, Yuqing, Parmigiani, Giovanni, Johnson, W Evan
Published in NAR genomics and bioinformatics (01.09.2020)
Published in NAR genomics and bioinformatics (01.09.2020)
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GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins
Brůna, Tomáš, Lomsadze, Alexandre, Borodovsky, Mark
Published in NAR genomics and bioinformatics (01.06.2020)
Published in NAR genomics and bioinformatics (01.06.2020)
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PHROG: families of prokaryotic virus proteins clustered using remote homology
Terzian, Paul, Olo Ndela, Eric, Galiez, Clovis, Lossouarn, Julien, Pérez Bucio, Rubén Enrique, Mom, Robin, Toussaint, Ariane, Petit, Marie-Agnès, Enault, François
Published in NAR genomics and bioinformatics (01.09.2021)
Published in NAR genomics and bioinformatics (01.09.2021)
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Bilingual language model for protein sequence and structure
Heinzinger, Michael, Weissenow, Konstantin, Sanchez, Joaquin Gomez, Henkel, Adrian, Mirdita, Milot, Steinegger, Martin, Rost, Burkhard
Published in NAR genomics and bioinformatics (01.12.2024)
Published in NAR genomics and bioinformatics (01.12.2024)
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Hi-C analyses with GENOVA: a case study with cohesin variants
van der Weide, Robin H, van den Brand, Teun, Haarhuis, Judith H I, Teunissen, Hans, Rowland, Benjamin D, de Wit, Elzo
Published in NAR genomics and bioinformatics (01.06.2021)
Published in NAR genomics and bioinformatics (01.06.2021)
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PBSIM3: a simulator for all types of PacBio and ONT long reads
Ono, Yukiteru, Hamada, Michiaki, Asai, Kiyoshi
Published in NAR genomics and bioinformatics (01.12.2022)
Published in NAR genomics and bioinformatics (01.12.2022)
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Deep soft K-means clustering with self-training for single-cell RNA sequence data
Chen, Liang, Wang, Weinan, Zhai, Yuyao, Deng, Minghua
Published in NAR genomics and bioinformatics (01.06.2020)
Published in NAR genomics and bioinformatics (01.06.2020)
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DeepMicrobes: taxonomic classification for metagenomics with deep learning
Liang, Qiaoxing, Bible, Paul W, Liu, Yu, Zou, Bin, Wei, Lai
Published in NAR genomics and bioinformatics (01.03.2020)
Published in NAR genomics and bioinformatics (01.03.2020)
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Contrastive learning on protein embeddings enlightens midnight zone
Heinzinger, Michael, Littmann, Maria, Sillitoe, Ian, Bordin, Nicola, Orengo, Christine, Rost, Burkhard
Published in NAR genomics and bioinformatics (01.06.2022)
Published in NAR genomics and bioinformatics (01.06.2022)
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Benchmarking of long-read correction methods
Dohm, Juliane C, Peters, Philipp, Stralis-Pavese, Nancy, Himmelbauer, Heinz
Published in NAR genomics and bioinformatics (01.06.2020)
Published in NAR genomics and bioinformatics (01.06.2020)
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A network-based integrated framework for predicting virus–prokaryote interactions
Wang, Weili, Ren, Jie, Tang, Kujin, Dart, Emily, Ignacio-Espinoza, Julio Cesar, Fuhrman, Jed A, Braun, Jonathan, Sun, Fengzhu, Ahlgren, Nathan A
Published in NAR genomics and bioinformatics (01.06.2020)
Published in NAR genomics and bioinformatics (01.06.2020)
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Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases
Zhao, Mengge, Havrilla, James M, Fang, Li, Chen, Ying, Peng, Jacqueline, Liu, Cong, Wu, Chao, Sarmady, Mahdi, Botas, Pablo, Isla, Julián, Lyon, Gholson J, Weng, Chunhua, Wang, Kai
Published in NAR genomics and bioinformatics (01.06.2020)
Published in NAR genomics and bioinformatics (01.06.2020)
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Variable selection in microbiome compositional data analysis
Susin, Antoni, Wang, Yiwen, Lê Cao, Kim-Anh, Calle, M Luz
Published in NAR genomics and bioinformatics (01.06.2020)
Published in NAR genomics and bioinformatics (01.06.2020)
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BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
Firtina, Can, Park, Jisung, Alser, Mohammed, Kim, Jeremie S, Cali, Damla Senol, Shahroodi, Taha, Ghiasi, Nika Mansouri, Singh, Gagandeep, Kanellopoulos, Konstantinos, Alkan, Can, Mutlu, Onur
Published in NAR genomics and bioinformatics (01.03.2023)
Published in NAR genomics and bioinformatics (01.03.2023)
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