| 1063 | -- | 1070 | Michael Y. Galperin, David M. Kristensen, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin. Microbial genome analysis: the COG approach |
| 1071 | -- | 1084 | Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Guillaume Gautreau, Adrien Josso, Aurélie Lajus, Jordan Langlois, Hugo Pereira, Rémi Planel, David Roche, Johan Rollin, Zoé Rouy, David Vallenet. MicroScope - an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data |
| 1085 | -- | 1093 | Peter D. Karp, Richard Billington, Ron Caspi, Carol A. Fulcher, Mario Latendresse, Anamika Kothari, Ingrid M. Keseler, Markus Krummenacker, Peter E. Midford, Quang Ong, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti. The BioCyc collection of microbial genomes and metabolic pathways |
| 1094 | -- | 1102 | Dionysios A. Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas S. Brettin, Christopher Bun, Neal Conrad, James J. Davis, Emily M. Dietrich, Terry Disz, Svetlana Gerdes, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, John Santerre, Maulik Shukla, Rick L. Stevens, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo. PATRIC as a unique resource for studying antimicrobial resistance |
| 1103 | -- | 1113 | Kai Blin, Hyun Uk Kim, Marnix H. Medema, Tilmann Weber. Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters |
| 1114 | -- | 1124 | Hao Luo 0002, Chun-Lan Quan, Chong Peng, Feng Gao 0001. Recent development of Ori-Finder system and DoriC database for microbial replication origins |
| 1125 | -- | 1136 | Florian P. Breitwieser, Jennifer Lu, Steven L. Salzberg. A review of methods and databases for metagenomic classification and assembly |
| 1140 | -- | 1150 | Nathan D. Olson, Todd J. Treangen, Christopher Michael Hill, Victoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Mihai Pop. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes |
| 1151 | -- | 1159 | Folker Meyer, Saurabh Bagchi, Somali Chaterji, Wolfgang Gerlach, Ananth Grama, Travis Harrison, Tobias Paczian, William L. Trimble, Andreas Wilke. MG-RAST version 4 - lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis |
| 1160 | -- | 1166 | Kazutaka Katoh, John Rozewicki, Kazunori D. Yamada. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization |
| 1167 | -- | 1180 | David R. Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr. Towards dynamic genome-scale models |
| 1181 | -- | 1192 | Lionel Morgado, Frank Johannes. Computational tools for plant small RNA detection and categorization |
| 1193 | -- | 1204 | Yongsheng Li, Xiyun Jin, Zishan Wang, Lili Li, Hong Chen, Xiaoyu Lin, Song Yi, Yunpeng Zhang, Juan Xu. Systematic review of computational methods for identifying miRNA-mediated RNA-RNA crosstalk |
| 1205 | -- | 1214 | Jincheol Park, Shili Lin. Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures |
| 1215 | -- | 1221 | Gerhard Mayer, Christian Quast, Janine Felden, Matthias Lange 0001, Manuel Prinz, Alfred Pühler, Chris Lawerenz, Uwe Scholz, Frank Oliver Glöckner, Wolfgang Müller 0001, Katrin Marcus, Martin Eisenacher. A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects |
| 1222 | -- | 1237 | Brian B. Luczak, Benjamin T. James, Hani Z. Girgis. A survey and evaluations of histogram-based statistics in alignment-free sequence comparison |
| 1238 | -- | 1249 | Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Zinovyev, Laurence Calzone. Conceptual and computational framework for logical modelling of biological networks deregulated in diseases |
| 1250 | -- | 1268 | Jian Zhang 0020, Zhiqiang Ma, Lukasz A. Kurgan. Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains |
| 1269 | -- | 1279 | Giulia Tini, Luca Marchetti, Corrado Priami, Marie-Pier Scott-Boyer. Multi-omics integration - a comparison of unsupervised clustering methodologies |
| 1280 | -- | 1294 | Bin Liu 0014. BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches |
| 1295 | -- | 1307 | Ruiping Wang 0002, Yue Han, Zhangxiang Zhao, Fan Yang, Tingting Chen, Wenbin Zhou, Xianlong Wang, Lishuang Qi, Wenyuan Zhao, Zheng Guo 0002, Yunyan Gu. Link synthetic lethality to drug sensitivity of cancer cells |
| 1308 | -- | 1321 | Yongjun Zhu, Olivier Elemento, Jyotishman Pathak, Fei Wang 0001. Drug knowledge bases and their applications in biomedical informatics research |
| 1322 | -- | 1328 | Qin Tang, Qiong Zhang, Yao Lv, Ya-Ru Miao, An-Yuan Guo. SEGreg: a database for human specifically expressed genes and their regulations in cancer and normal tissue |
| 1329 | -- | 1336 | Florencio Pazos, Monica Chagoyen. Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology |
| 1337 | -- | 1357 | Ali Ezzat, Min Wu 0008, Xiao-Li Li, Chee Keong Kwoh. Computational prediction of drug-target interactions using chemogenomic approaches: an empirical survey |
| 1358 | -- | 1375 | Fernando Carazo, Juan P. Romero, Angel Rubio. Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors |
| 1376 | -- | 1383 | Paul Medvedev. Modeling biological problems in computer science: a case study in genome assembly |
| 1384 | -- | 1394 | Alessandra Dal Molin, Barbara Di Camillo. How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives |
| 1395 | -- | 1402 | Andrés Zalguizuri, Gustavo Caetano-Anollés, Viviana Claudia Lepek. Phylogenetic profiling, an untapped resource for the prediction of secreted proteins and its complementation with sequence-based classifiers in bacterial type III, IV and VI secretion systems |
| 1403 | -- | 1419 | Junpeng Zhang, Thuc Duy Le, Lin Liu 0003, Jiuyong Li. Inferring and analyzing module-specific lncRNA-mRNA causal regulatory networks in human cancer |
| 1420 | -- | 1433 | Shasha Li, Shuaishuai Teng, Junquan Xu, Guannan Su, Yu Zhang, Jianqing Zhao, Suwei Zhang, Haiyan Wang, Wenyan Qin, Zhi John Lu, Yong Guo, Qianyong Zhu, Dong Wang. Microarray is an efficient tool for circRNA profiling |
| 1434 | -- | 1448 | Igor F. Tsigelny. Artificial intelligence in drug combination therapy |
| 1449 | -- | 1464 | Juan Xie, Anjun Ma, Anne Fennell, Qin Ma 0003, Jing Zhao. It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data |
| 1465 | -- | 1474 | Ming Hao, Stephen H. Bryant, Yanli Wang. Open-source chemogenomic data-driven algorithms for predicting drug-target interactions |
| 1477 | -- | 1491 | Daniela Oliveira, Anila Sahar Butt, Armin Haller, Dietrich Rebholz-Schuhmann, Ratnesh Sahay. Where to search top-K biomedical ontologies? |
| 1492 | -- | 1501 | Jue Yang, Hui Song, Kun Cao, Jialei Song, Jianjiang Zhou. Comprehensive analysis of Helicobacter pylori infection-associated diseases based on miRNA-mRNA interaction network |
| 1502 | -- | 1512 | Hua Sun, Pora Kim, Peilin Jia, Aekyung Park, Han Liang, Zhongming Zhao. Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor |
| 1513 | -- | 1523 | António Cruz, Joel P. Arrais, Penousal Machado. Interactive and coordinated visualization approaches for biological data analysis |
| 1524 | -- | 1541 | Zhuo Zhang, Hao Li, Shuai Jiang, Ruijiang Li, Wanying Li, Hebing Chen, Xiaochen Bo. A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data |
| 1542 | -- | 1559 | Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions |
| 1560 | -- | 1567 | David Arndt, Ana Marcu, Yongjie Liang, David S. Wishart. PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes |
| 1568 | -- | 1577 | Huansheng Cao, Qin Ma 0003, Xin Chen, Ying Xu 0001. DOOR: a prokaryotic operon database for genome analyses and functional inference |
| 1576 | -- | 1582 | Paul Stothard, Jason R. Grant, Gary H. Van Domselaar. Visualizing and comparing circular genomes using the CGView family of tools |
| 1583 | -- | 1589 | Shun H. Yip, Pak Chung Sham, Junwen Wang. Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data |
| 1590 | -- | 1603 | Gaoyang Li, Huansheng Cao, Ying Xu 0001. Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes |