Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

by Asgari, Ehsaneddin, Mofrad, Mohammad R K
Published in PloS one

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

by Asgari, Ehsaneddin, McHardy, Alice C, Mofrad, Mohammad R K
Published in Scientific reports

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples

by Asgari, Ehsaneddin, Garakani, Kiavash, McHardy, Alice C, Mofrad, Mohammad R K
Published in Bioinformatics

Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning‐enabled molecular diagnostics

by Khaledi, Ariane, Weimann, Aaron, Schniederjans, Monika, Asgari, Ehsaneddin, Kuo, Tzu‐Hao, Oliver, Antonio, Cabot, Gabriel, Kola, Axel, Gastmeier, Petra, Hogardt, Michael, Jonas, Daniel, Mofrad, Mohammad RK, Bremges, Andreas, McHardy, Alice C, Häussler, Susanne
Published in EMBO molecular medicine

Peptide microarrays coupled to machine learning reveal individual epitopes from human antibody responses with neutralizing capabilities against SARS-CoV-2

by Hotop, Sven-Kevin, Reimering, Susanne, Shekhar, Aditya, Asgari, Ehsaneddin, Beutling, Ulrike, Dahlke, Christine, Fathi, Anahita, Khan, Fawad, Lütgehetmann, Marc, Ballmann, Rico, Gerstner, Andreas, Tegge, Werner, Cicin-Sain, Luka, Bilitewski, Ursula, McHardy, Alice C., Brönstrup, Mark
Published in Emerging microbes & infections

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

by Zhou, Naihui, Jiang, Yuxiang, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Supek, Fran, Fernández, José M, Gemovic, Branislava, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad R K, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Wan, Cen, Fa, Rui, Notaro, Marco, Grossi, Giuliano, Valentini, Giorgio, Mesiti, Marco, Ritchie, David W, Aridhi, Sabeur, Bonneau, Richard, Gligorijević, Vladimir, Fang, Hai, Toppo, Stefano, Falda, Marco, Berselli, Michele, Mao, Qizhong, Black, Gage S, Suh, Erica, Dayton, Jonathan B, Larsen, Dallas J, Omdahl, Ashton R, McGuffin, Liam J, Brackenridge, Danielle A, Babbitt, Patricia C, Yunes, Jeffrey M, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, Dai, Suyang, Yao, Shuwei, Cao, Renzhi, Amezola, Miguel, Johnson, Devon, Liu, Yi-Wei, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Björne, Jari, Tolvanen, Martti E E, Salakoski, Tapio, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Orengo, Christine A, Bosco, Giovanni, Martin, Maria J, Mooney, Sean D, Greene, Casey S, Radivojac, Predrag
Published in Genome Biology

EpitopeVec: linear epitope prediction using deep protein sequence embeddings

by Bahai, Akash, Asgari, Ehsaneddin, Mofrad, Mohammad R K, Kloetgen, Andreas, McHardy, Alice C
Published in Bioinformatics

GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations

by Dickson, Andrew, Asgari, Ehsaneddin, McHardy, Alice C, Mofrad, Mohammad R K
Published in Bioinformatics (Oxford, England)

Molecular Insights into the Mechanisms of SUN1 Oligomerization in the Nuclear Envelope

by Jahed, Zeinab, Fadavi, Darya, Vu, Uyen T., Asgari, Ehsaneddin, Luxton, G. W. Gant, Mofrad, Mohammad R.K.
Published in Biophysical journal

TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks

by Nourani, Esmaeil, Asgari, Ehsaneddin, McHardy, Alice C., Mofrad, Mohammad R.K.
Published in IEEE/ACM transactions on computational biology and bioinformatics

DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection

by Asgari, Ehsaneddin, Münch, Philipp C, Lesker, Till R, McHardy, Alice C, Mofrad, Mohammad R K
Published in Bioinformatics

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples

by Asgari, Ehsaneddin, Garakani, Kiavash, McHardy, Alice C, Mofrad, Mohammad R K
Published in Bioinformatics

Molecular Insights into the Mechanisms of SUN1 Oligomerization in the Nuclear Envelope

by Jahed, Zeinab, Fadavi, Darya, Vu, Uyen T., Asgari, Ehsaneddin, Luxton, G. W. Gant, Mofrad, Mohammad R. K.
Published in Biophysical journal