CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods

Authors: Piovesan, Damiano, Zago, Davide, Joshi, Parnal, Kaluza, M. Clara De Paolis, Mehdiabadi, Mahta, Ramola, Rashika, Monzon, Alexander Miguel, Reade, Walter, Friedberg, Iddo, Radivojac, Predrag, Tosatto, Silvio C. E.

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Performance

Access URL: http://arxiv.org/abs/2310.06881

Reliable uncertainty estimate for antibiotic resistance classification with Stochastic Gradient Langevin Dynamics

Authors: Hamid, Md-Nafiz, Friedberg, Iddo

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning, Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1811.11145

Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia

Authors: Kilpatrick, Alastair M, Rahman, Farzana, Anjum, Audra, Shome, Sayane, Andalib, K M Salim, Banik, Shrabonti, Chowdhury, Sanjana F, Coombe, Peter, Astroz, Yesid Cuesta, Douglas, J Maxwell, Eranti, Pradeep, Kiran, Aleyna D, Kumar, Sachendra, Lim, Hyeri, Lorenzi, Valentina, Lubiana, Tiago, Mahmud, Sakib, Puche, Rafael, Rybarczyk, Agnieszka, Al Sium, Syed Muktadir, Twesigomwe, David, Zok, Tomasz, Orengo, Christine A, Friedberg, Iddo, Kelso, Janet F, Welch, Lonnie

Source: Bioinformatics. 38(Supplement 1):i19-i27

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100159730243.0x000001&indx=1&recIds=ETOCvdc_100159730243.0x000001

Community-Wide Evaluation of Computational Function Prediction

Authors: Friedberg, Iddo, Radivojac, Predrag

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1601.01048

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Authors: Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, C., Dukka B K., Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Piovesan, Damiano, Tosatto, Silvio, del Pozo, Angela, Fernández, José M, Maietta, Paolo, Valencia, Alfonso, Tress, Michael L, Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W, van Dijk, Aalt DJ, Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C, Vencio, Ricardo ZN, Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael JE, Wass, Mark N, Huntley, Rachael P, Martin, Maria J, O'Donovan, Claire, Robinson, Peter N, Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C, Brenner, Steven E, Linial, Michal, Orengo, Christine A, Rost, Burkhard, Greene, Casey S, Mooney, Sean D, Friedberg, Iddo, Radivojac, Predrag

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1601.00891

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

Authors: Morton, James T, Freed, Stefan D, Lee, Shaun W, Friedberg, Iddo

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1510.06008

An Event-Driven Approach for Studying Gene Block Evolution in Bacteria

Authors: Ream, David C, Bankapur, Asma R, Friedberg, Iddo

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1501.00302

Sequence-Structure Relationship in Proteins: a Computational Analysis of Proteins that Differ in Sequence but Share the Same Fold

Authors: Friedberg, Iddo

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/1310.1403

Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space

Authors: Schnoes, Alexandra M., Ream, David C., Thorman, Alexander W., Babbitt, Patricia C., Friedberg, Iddo

Subject Terms: Quantitative Biology - Genomics, Computer Science - Digital Libraries, Computer Science - Information Theory

Access URL: http://arxiv.org/abs/1301.1740

Biological Database of Images and Genomes: tools for community annotations linking image and genomic information

Authors: Oberlin, Andrew T., Jurkovic, Dominika A., Balish, Mitchell F., Friedberg, Iddo

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1212.0447

Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains

Authors: Fields, Francisco R., Freed, Stefan D., Carothers, Katelyn E., Hamid, Md Nafiz, Hammers, Daniel E., Ross, Jessica N., Kalwajtys, Veronica R., Gonzalez, Alejandro J., Hildreth, Andrew D., Friedberg, Iddo, Lee, Shaun W.

Source: Drug development research. 81(1):43-51

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100102909933.0x000001&indx=1&recIds=ETOCvdc_100102909933.0x000001

Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it

Authors: Nguyen, Huy N, Markin, Alexey, Friedberg, Iddo, Eulenstein, Oliver

Source: Bioinformatics. 36(2):i668-i674

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100115650374.0x000001&indx=1&recIds=ETOCvdc_100115650374.0x000001

Assembling bacterial puzzles: piecing together functions into microbial pathways.

Authors: Chung, Henri C, Friedberg, Iddo, Bromberg, Yana

Source: NAR Genomics & Bioinformatics; Sep2024, Vol. 6 Issue 3, p1-13, 13p

Assessing computational predictions of the phenotypic effect of cystathionine‐beta‐synthase variants

Authors: Kasak, Laura, Bakolitsa, Constantina, Hu, Zhiqiang, Yu, Changhua, Rine, Jasper, Dimster‐Denk, Dago F., Pandey, Gaurav, Baets, Greet, Bromberg, Yana, Cao, Chen, Capriotti, Emidio, Casadio, Rita, Durme, Joost, Giollo, Manuel, Karchin, Rachel, Katsonis, Panagiotis, Leonardi, Emanuela, Lichtarge, Olivier, Martelli, Pier Luigi, Masica, David, Mooney, Sean D., Olatubosun, Ayodeji, Radivojac, Predrag, Rousseau, Frederic, Pal, Lipika R., Savojardo, Castrense, Schymkowitz, Joost, Thusberg, Janita, Tosatto, Silvio C.E., Vihinen, Mauno, Väliaho, Jouni, Repo, Susanna, Moult, John, Brenner, Steven E., Friedberg, Iddo

Source: Human mutation. 40(9):1530-1545

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100088915277.0x000001&indx=1&recIds=ETOCvdc_100088915277.0x000001

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

Authors: Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy, Lee, Alexandra, Kacsoh, Balint, Crocker, Alex, Lewis, Kimberley, Georghiou, George, Nguyen, Huy, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca, Freddolino, Peter, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José, Gemovic, Branislava, Perovic, Vladimir, Davidović, Radoslav, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex, Antczak, Magdalena, Fabris, Fabio, Wass, Mark, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel, Reeb, Jonas, Ritchie, David, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio, Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage, Jo, Dane, Suh, Erica, Dayton, Jonathan, Larsen, Dallas, Omdahl, Ashton, McGuffin, Liam, Brackenridge, Danielle, Babbitt, Patricia, Yunes, Jeffrey, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti, Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven, Orengo, Christine, Jeffery, Constance, Bosco, Giovanni, Hogan, Deborah, Martin, Maria, O'Donovan, Claire, Mooney, Sean, Greene, Casey, Radivojac, Predrag, Friedberg, Iddo

Source: Genome biology. 20(1):1-23

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190701351.0x000001&indx=1&recIds=ETOCvdc_100190701351.0x000001

Highly Bi-Connected Subgraphs for Computational Protein Function Annotation
International computing and combinatorics conference

Authors: Moon, Jucheol, Friedberg, Iddo, Eulenstein, Oliver

Source: Lecture notes in computer science. 9797:573-586

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCCN601545699&indx=1&recIds=ETOCCN601545699

Discovering genomic islands in unannotated bacterial genomes using sequence embedding.

Authors: Banerjee, Priyanka, Eulenstein, Oliver, Friedberg, Iddo

Source: Bioinformatics Advances; 2024, Vol. 4 Issue 1, p1-10, 10p

Subject Terms: GENETIC variation, ENVIRONMENTAL research, BACTERIAL genes, BACTERIAL evolution, DNA sequencing

Community-Wide Evaluation of Computational Function Prediction

Authors: Friedberg, Iddo, Radivojac, Predrag

Source: Methods in molecular biology. 1446:133-148

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN609112201&indx=1&recIds=ETOCRN609112201

Learning from the unknown: exploring the range of bacterial functionality.

Authors: Mahlich, Yannick, Zhu, Chengsheng, Chung, Henri, Velaga, Pavan K, De Paolis Kaluza, M Clara, Radivojac, Predrag, Friedberg, Iddo, Bromberg, Yana

Source: Nucleic Acids Research; 10/27/2023, Vol. 51 Issue 19, p10162-10175, 14p

Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes

Authors: Ream, David C., Murakami, Samuel T., Schmidt, Emily E., Huang, Guo-Hua, Liang, Chun, Friedberg, Iddo, Cheng, Xiao-Wen

Source: In Virus Research 26 December 2013 178(2):217-225