TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases

by Alan Medlar, Liisa Holm
Published 2018-07-01

Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.

by Ilya Plyusnin, Liisa Holm, Petri Törönen
Published 2019-11-01

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing

by Panu Somervuo, Patrik Koskinen, Peng Mei, Liisa Holm, Petri Auvinen, Lars Paulin
Published 2018-07-01

Genome Sequence of Dickeya solani, a New soft Rot Pathogen of Potato, Suggests its Emergence May Be Related to a Novel Combination of Non-Ribosomal Peptide/Polyketide Synthetase...

by Linda Garlant, Patrik Koskinen, Leo Rouhiainen, Pia Laine, Lars Paulin, Petri Auvinen, Liisa Holm, Minna Pirhonen
Published 2013-12-01

Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.

by Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas
Published 2014-02-01

Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193.

by Johanna Nykyri, Outi Niemi, Patrik Koskinen, Jussi Nokso-Koivisto, Miia Pasanen, Martin Broberg, Ilja Plyusnin, Petri Törönen, Liisa Holm, Minna Pirhonen, E Tapio Palva
Published 2012-01-01

Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1

by Outi Niemi, Pia Laine, Patrik Koskinen, Miia Pasanen, Ville Pennanen, Heidi Harjunpää, Johanna Nykyri, Liisa Holm, Lars Paulin, Petri Auvinen, E. Tapio Palva, Minna Pirhonen
Published 2017-12-01

Bracketing phenogenotypic limits of mammalian hybridization

by Yoland Savriama, Mia Valtonen, Juhana I. Kammonen, Pasi Rastas, Olli-Pekka Smolander, Annina Lyyski, Teemu J. Häkkinen, Ian J. Corfe, Sylvain Gerber, Isaac Salazar-Ciudad, Lars Paulin, Liisa Holm, Ari Löytynoja, Petri Auvinen, Jukka Jernvall
Published 2018-01-01

Transcriptome analysis reveals signature of adaptation to landscape fragmentation.

by Panu Somervuo, Jouni Kvist, Suvi Ikonen, Petri Auvinen, Lars Paulin, Patrik Koskinen, Liisa Holm, Minna Taipale, Anne Duplouy, Annukka Ruokolainen, Suvi Saarnio, Jukka Sirén, Jukka Kohonen, Jukka Corander, Mikko J Frilander, Virpi Ahola, Ilkka Hanski
Published 2014-01-01

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

by Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg
Published 2019-11-01