cran: HMM | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0155338

Composing a Tumor Specific Bacterial Promoter
Cited by: 7
Author(s): Igor V. Deyneko, Nadine Kasnitz, Sara Leschner, Siegfried Weiß
Software Mentions: 3
Published: over 8 years ago

Toward an interactive article: integrating journals and biological databases
Cited by: 11
Author(s): Arun Rangarajan, Tim Schedl, Karen Yook, Juancarlos Chan, Stephen Haenel, Lolly Otis, Sharon Faelten, Tracey DePellegrin-Connelly, Ruth Isaacson, Marek S. Skrzypek, Steven J Marygold, Raymund Stefancsik, J. Michael Cherry, Paul W. Sternberg, Hans‐Michael Müller
Software Mentions: 3
Published: over 13 years ago

10.1155/2019/7241096

Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles
Cited by: 18
Author(s): Luzhao Pan, Jian Zheng, Jia Liu, Guo Jun, Liu FaWan, Lecheng Liu, Hongjian Wan
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-11-200

Conditional random pattern model for copy number aberration detection
Cited by: 2
Author(s): Fuhai Li, Xiaobo Zhou, Wan‐Ting Huang, Chung Che Chang, Stephen T.C. Wong
Software Mentions: 3
Published: over 14 years ago

10.1186/s12859-016-0899-7

Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans
Cited by: 19
Author(s): Alencar Xavier, William M. Muir, Katy Martin Rainey
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-017-4296-z

Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews
Cited by: 19
Author(s): Michie Kobayashi, Yukie Hiraka, Akira Abe, Hiroki Yaegashi, Satoshi Natsume, Hideko Kikuchi, Hiroki Takagi, Hiromasa Saitoh, Joe Win, Sophien Kamoun, Ryohei Terauchi
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0242683

Characterizing infectious disease progression through discrete states using hidden Markov models
Cited by: 2
Author(s): Kristina Ceres, Y.H. Schukken, Yrjo T. Gröhn
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-37792-0

Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates
Cited by: 20
Author(s): Girish Beedessee, Kanako Hisata, Michael C. Roy, Frances M. Van Dolah, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 3
Published: almost 6 years ago

10.3390/s21072447

A BCI Based Alerting System for Attention Recovery of UAV Operators
Cited by: 8
Author(s): Jong-Hyuk Park, Jonghun Park, Dongmin Shin, Yerim Choi
Software Mentions: 3
Published: over 3 years ago

10.1038/srep40301

Evolution of protein N-glycosylation process in Golgi apparatus which shapes diversity of protein N-glycan structures in plants, animals and fungi
Cited by: 25
Author(s): Peng Wang, Hong Wang, Jiangtao Gai, Xiaoli Tian, Xiaoxiao Zhang, Yongzhi Lv, Yi Jiang
Software Mentions: 3
Published: almost 8 years ago

10.1155/2018/5206758

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses inBrassica rapa
Cited by: 8
Author(s): Nadeem Khan, Chunmei Hu, Waleed Amjad Khan, Emal Naseri, Koeun Han, Hansong Dong, Xilin Hou
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0018880

Arabidopsis Plasmodesmal Proteome
Cited by: 222
Author(s): Lourdes Fernández‐Calvino, Christine Faulkner, John Walshaw, Gerhard Saalbach, Emmanuelle Bayer, Yoselin Benitez‐Alfonso, Andrew J. Maule
Software Mentions: 3
Published: over 13 years ago

10.4056/sigs.651139

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data
Cited by: 60
Author(s): David M. Tanenbaum, Johannes Goll, Sean D. Murphy, P. Naresh Kumar, Nikhat Zafar, Mathangi Thiagarajan, Ramana Madupu, Tanja M. Davidsen, Leonid Kagan, Saul Kravitz, Douglas B. Rusch, Shibu Yooseph
Software Mentions: 3
Published: over 14 years ago

10.1038/srep25107

Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns
Cited by: 27
Author(s): Weike Duan, Zhinan Huang, Xiaoming Song, Tongkun Liu, Hailong Liu, Xilin Hou, Ying Liu
Software Mentions: 3
Published: over 8 years ago

10.1093/jxb/eraa086

Novel routes towards bioplastics from plants: elucidation of the methylperillate biosynthesis pathway from Salvia dorisiana trichomes
Cited by: 12
Author(s): E. Jongedijk, Sebastian Müller, Aalt D. J. van Dijk, Elio Schijlen, Antoine Champagne, Marc Boutry, Mark Levisson, Sander van der Krol, Harro J. Bouwmeester, Jules Beekwilder
Software Mentions: 3
Published: over 4 years ago

10.1038/srep26090

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs
Cited by: 31
Author(s): José Héctor Gálvez, Helen H. Tai, M. Lagüe, Bernie J. Zebarth, Martina V. Strömvik
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1004409

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
Cited by: 116
Author(s): D. Ralph, F. A. Matsen
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pcbi.1007894

Predicting host taxonomic information from viral genomes: A comparison of feature representations
Cited by: 29
Author(s): Francesca Young, Simon Rogers, David L. Robertson
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0228253

Diel patterns in swimming behavior of a vertically migrating deepwater shark, the bluntnose sixgill (Hexanchus griseus)
Cited by: 17
Author(s): Daniel M. Coffey, Mark A. Royer, Carl G. Meyer, Kim N. Holland
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-15-19

Automated alignment-based curation of gene models in filamentous fungi
Cited by: 8
Author(s): Ate van der Burgt, Edouard Severing, Jérôme Collemare, P.J.G.M. de Wit
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2180-6-1

Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus
Cited by: 53
Author(s): Gaudermann Peter, Ina Vogl, Evelyn Zientz, Francisco J. Silva, Andrés Moya, Roy Gross, Thomas Dandekar
Software Mentions: 3
Published: almost 19 years ago

10.3389/fpls.2014.00789

Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes
Cited by: 38
Author(s): Vikash Singh, Mukesh Jain, Rohini Garg
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep39281

Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster
Cited by: 18
Author(s): Mark Phillips, Anthony D. Long, Zachary S. Greenspan, Lee F. Greer, Molly K. Burke, Bryant Villeponteau, Kennedy Matsagas, Cristina L. Rizza, Laurence D. Mueller, Michael R. Rose
Software Mentions: 3
Published: almost 8 years ago

10.3389/fpls.2018.01332

Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family
Cited by: 28
Author(s): Yueying Li, Liangliang He, Jing Li, Jianghua Chen, Changning Liu
Software Mentions: 3
Published: about 6 years ago

10.1093/gigascience/gix017

PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity
Cited by: 49
Author(s): Geng Li, Dongli Li, Zhang Li, Si Qiu, Wenhui Li, Cheng‐Chi Chao, Naibo Yang, Handong Li, Zhen Cheng, Xin Song, Lei Cheng, Xiuqing Zhang, Jian Wang, Huanming Yang, Kun Ma, Yong Hou, Bo Li
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-019-2624-9

Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions
Cited by: 4
Author(s): Norbert Bokros, S. Popescu, George V. Popescu
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giz036

The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition
Cited by: 78
Author(s): Yajiang Huang, Li Xiao, Zhongren Zhang, Rui Zhang, Zhengjia Wang, Chun-Ying Huang, Ren Huang, Yumeng Luan, Tongqiang Fan, Jianhua Wang, Chen Shen, Shenmei Zhang, Xinwang Wang, Jennifer J. Randall, Bingsong Zheng, Jiasheng Wu, Qixiang Zhang, Guohua Xia, Chao Xu, Ming Chen, Liangsheng Zhang, Wenkai Jiang, Li‐Zhi Gao, Zhiduan Chen, Charles A. Leslie, L.J. Grauke, Jianqin Huang
Software Mentions: 3
Published: over 5 years ago

10.1093/gbe/evz023

PDZ Domains Across the Microbial World: Molecular Link to the Proteases, Stress Response, and Protein Synthesis
Cited by: 10
Author(s): Vijaykumar Yogesh Muley, Yusuf Akhter, Sanjeev Galande
Software Mentions: 3
Published: almost 6 years ago

10.1534/genetics.119.301907

Layers of Cryptic Genetic Variation Underlie a Yeast Complex Trait
Cited by: 24
Author(s): Jonathan T. Lee, Alessandro L V Coradini, Amy Shen, Ian M. Ehrenreich
Software Mentions: 3
Published: almost 6 years ago

10.1093/gbe/evab125

Homology and Modular Evolution of CATCHR at the Origin of the Eukaryotic Endomembrane System
Cited by: 9
Author(s): Carlos Santana-Molina, Fernando Gutiérrez, Damien P. Devos
Software Mentions: 3
Published: over 3 years ago

10.1093/gigascience/giaa062

CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems
Cited by: 27
Author(s): Victor Alexandre Padilha, Omer S. Alkhnbashi, Shiraz A. Shah, André C. P. L. F. de Carvalho, Rolf Backofen
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.11465

Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage
Cited by: 9
Author(s): Zerui Yang, Chunzhu Xie, Yuying Huang, Wenli An, Shanshan Liu, Song Huang, Xiasheng Zheng
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-020-02576-0

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat
Cited by: 33
Author(s): Ting Zhu, Yue Liu, Liting Ma, Xiaoying Wang, Dazhong Zhang, Yuyan Han, Qin Ding, Lingjian Ma
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0244220

Deterministic modelling of seed dispersal based on observed behaviours of an endemic primate in Brazil
Cited by: 1
Author(s): Nima Raghunathan, Louis François, Eliana Cazetta, Jean-Luc Pitance, Kristel De Vleeschouwer, Alain Hambuckers
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-14-672

The shaping and functional consequences of the dosage effect landscape in multiple myeloma
Cited by: 18
Author(s): Mehmet K. Samur, Parantu K. Shah, Xujun Wang, Stéphane Minvielle, Florence Magrangeas, Hervé Avet-Loiseau, Nikhil C. Munshi, Li Cheng
Software Mentions: 3
Published: about 11 years ago

10.1186/s12859-017-1705-x

An evaluation of copy number variation detection tools for cancer using whole exome sequencing data
Cited by: 121
Author(s): Fatima Zare, Michelle Dow, Nicholas J. Monteleone, Abdelrahman Hosny, Sheida Nabavi
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.3579

Predicting the host of influenza viruses based on the word vector
Cited by: 18
Author(s): Beibei Xu, Zhiying Tan, Kenli Li, Taijiao Jiang, Yousong Peng
Software Mentions: 3
Published: over 7 years ago

10.1186/s13059-021-02379-y

diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data
Cited by: 4
Author(s): Paolo Marangio, Ka Ying Toby Law, Guido Sanguinetti, Sander Granneman
Software Mentions: 3
Published: over 3 years ago

10.3390/insects12090815

Adaptation of Fig Wasps (Agaodinae) to Their Host Revealed by Large-Scale Transcriptomic Data
Cited by: 3
Author(s): Lianfu Chen, Simon T. Segar, Bhanumas Chantarasuwan, Da‐Mien Wong, Rong Wang, Xiaoyong Chen, Hui Yu
Software Mentions: 3
Published: about 3 years ago

10.1186/s12870-018-1583-z

Photoperiod response-related gene SiCOL1 contributes to flowering in sesame
Cited by: 14
Author(s): Rong Zhou, Pan Liu, Donghua Li, Xiurong Zhang, Xin Wei
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2156-9-92

A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan
Cited by: 23
Author(s): Chang‐Yu Lin, Ling-Hui Li, Sheng-Feng Ho, Tzu-Po Chuang, Jer‐Yuarn Wu, Yuan-Tsong Chen, Cathy S.J. Fann
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2229-14-147

A novel motif in the NaTrxh N-terminus promotes its secretion, whereas the C-terminus participates in its interaction with S-RNase in vitro
Cited by: 9
Author(s): Alejandra Ávila-Castañeda, Javier Andrés Juárez‐Díaz, Rogelio Rodríguez-Sotrés, Carlos E. Bravo-Alberto, Claudia Patricia Ibarra-Sánchez, Alejandra Zavala-Castillo, Yuridia Cruz‐Zamora, León P. Martínez-Castilla, Judith Márquez‐Guzmán, Felipe Cruz‐García
Software Mentions: 2
Published: over 10 years ago

10.3389/fpls.2015.00910

Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling
Cited by: 69
Author(s): Mehanathan Muthamilarasan, Venkata Suresh Bonthala, Rohit Khandelwal, Jananee Jaishankar, Shweta Shweta, Kashif Nawaz
Software Mentions: 2
Published: about 9 years ago

10.3389/fpls.2016.01374

Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs)
Cited by: 56
Author(s): . Shumayla, Shailesh Sharma, Rohit Kumar, Venugopal Mendu, Kashmir Singh, Santosh Kumar Upadhyay
Software Mentions: 2
Published: about 8 years ago

10.3389/fphys.2021.637306

Identification of Copy Number Variation Among Nonsyndromic Cleft Lip and or Without Cleft Palate With Hypodontia: A Genome-Wide Association Study
Cited by: 3
Author(s): Norliana Ghazali, Normastura Abd Rahman, Ahmad Azlina, Sarina Sulong, Thirumulu Ponnuraj Kannan
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2016.00025

Genome-Wide Identification and Expression Analysis of the WRKY Gene Family in Cassava
Cited by: 85
Author(s): Yunxie Wei, Shi Hong, Zhiqiang Xia, Weiwei Tie, Zehong Ding, Yan Yan, Wenquan Wang, Wei Hu, Kaimian Li
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12865-017-0197-9

Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India
Cited by: 8
Author(s): Sumanta Banerjee, Parth Sarthi Sen Gupta, Amal Kumar Bandyopadhyay
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2148-10-233

Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily
Cited by: 115
Author(s): Johannes Engelken, Henner Brinkmann, Iwona Adamska
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2105-11-275

HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data
Cited by: 7
Author(s): Erdogan Taskesen, Renée Beekman, Jeroen de Ridder, Bas J. Wouters, Justine K. Peeters, Ivo P. Touw, Marcel J. T. Reinders, Ruud Delwel
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2148-9-85

Origin and evolution of the RIG-I like RNA helicase gene family
Cited by: 224
Author(s): Jun Zou, Ming Chang, Pin Nie, Chris J. Secombes
Software Mentions: 2
Published: almost 16 years ago

10.3389/fneur.2021.720650

Automated Movement Assessment in Stroke Rehabilitation
Cited by: 3
Author(s): Tamim Ahmed, Kowshik Thopalli, Thanassis Rikakis, Pavan Turaga, Aisling Kelliher, Jia-Bin Huang, Steven L. Wolf
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2017.02504

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment
Cited by: 15
Author(s): Mabel Ting Wong, Weijun Wang, Marie Couturier, Fakhria M. Razeq, Vincent Lombard, Pascal Lapébie, Elizabeth A. Edwards, Nicolas Terrapon, Bernard Henrissat, Emma R. Master
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2164-11-435

Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development
Cited by: 153
Author(s): Amarjeet Singh, Jitender Giri, Sanjay Kapoor, Akhilesh K. Tyagi, Girdhar K. Pandey
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2105-8-104

HMM-ModE – Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences
Cited by: 34
Author(s): Prashant K. Srivastava, Dhwani Desai, Soumyadeep Nandi, Andrew M. Lynn
Software Mentions: 2
Published: over 17 years ago

10.3389/fnins.2018.00603

Task-Evoked Dynamic Network Analysis Through Hidden Markov Modeling
Cited by: 117
Author(s): Andrew Quinn, Diego Vidaurre, Romesh Abeysuriya, Robert Becker, Anna C. Nobre, Mark W. Woolrich
Software Mentions: 2
Published: about 6 years ago

10.3389/fpls.2021.707496

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress
Cited by: 5
Author(s): Jirui Gong, Tianlong Shi, Yuke Li, Han-Cheng Wang, Fēi Li
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-021-07475-8

Extensive structural variation in the Bowman-Birk inhibitor family in common wheat (Triticum aestivum L.)
Cited by: 11
Author(s): Yucong Xie, Karl Ravet, Stephen Pearce
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2016.02171

Bacillus thuringiensis and Bacillus weihenstephanensis Inhibit the Growth of Phytopathogenic Verticillium Species
Cited by: 49
Author(s): Jacqueline Hollensteiner, Franziska Wemheuer, Rebekka Harting, Anna M. Kolarzyk, Stefani Maria Díaz Valerio, Anja Poehlein, Elżbieta Brzuszkiewicz, Kai Nesemann, Susanna A. Braus‐Stromeyer, Gerhard H. Braus, Rolf Daniel, Heiko Liesegang
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2012.00362

Factors Influencing the Diversity of Iron Uptake Systems in Aquatic Microorganisms
Cited by: 19
Author(s): Dhwani Desai, Falguni Desai, Julie LaRoche
Software Mentions: 2
Published: almost 13 years ago

10.3389/fmicb.2019.00662

Genes Associated With Psychrotolerant Bacillus cereus Group Isolates
Cited by: 5
Author(s): Sarah M. Beno, Renato H. Orsi, Rachel A. Cheng, David J. Kent, Jasna Kovač, Diana R. Duncan, N.H. Martin, Martin Wiedmann
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-3

Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana
Cited by: 138
Author(s): Jingyin Yu, Sadia Tehrim, Fengqi Zhang, Chaobo Tong, Junyan Huang, Xiaohui Cheng, Caihua Dong, Yanqiu Zhou, Rui Qin, Wei Hua, Liu S
Software Mentions: 2
Published: almost 11 years ago

10.3389/fgene.2018.00590

PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins
Cited by: 34
Author(s): Jiaotong Yang, Yue Liu, Hengyu Yan, Tian Tian, Qi You, Liwei Zhang, Wenying Xu, Zhen Su
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2019.02945

The Fungal-Specific Transcription Factor VpFSTF1 Is Required for Virulence in Valsa pyri
Cited by: 11
Author(s): Alex Machio Kange, Ai Xia, Jierui Si, Bingxin Li, Xiong Zhou, Gan Ai, Feng He, Daolong Dou
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2019.02435

Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake
Cited by: 37
Author(s): Jiro F. Mori, Lin-Xing Chen, Gerdhard L Jessen, Sarah B. Rudderham, Joyce McBeth, Matthew B.J. Lindsay, G. F. Slater, Jillian F. Banfield, Lesley A. Warren
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-020-6547-7

From methylglyoxal to pyruvate: a genome-wide study for the identification of glyoxalases and D-lactate dehydrogenases in Sorghum bicolor
Cited by: 19
Author(s): Bidisha Bhowal, Sneh L. Singla‐Pareek, Sudhir K. Sopory, Charanpreet Kaur
Software Mentions: 2
Published: almost 5 years ago

10.1002/evl3.59

Recent admixture between species of the fungal pathogen Histoplasma
Cited by: 27
Author(s): Colin S. Maxwell, Victoria E. Sepúlveda, David A. Turissini, William E. Goldman, Daniel R. Matute
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-017-1777-7

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding
Cited by: 13
Author(s): Joseph Guhlin, Kevin A.T. Silverstein, Peng Zhou, Peter Tiffin, Nevin D. Young
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-015-2196-7

Genome-wide identification and evolutionary analyses of bZIP transcription factors in wheat and its relatives and expression profiles of anther development related TabZIP genes
Cited by: 46
Author(s): Xueyin Li, Shiqing Gao, Yimiao Tang, Lei Li, Fengjie Zhang, Biane Feng, Zhaofeng Fang, Lingjian Ma, Changping Zhao
Software Mentions: 2
Published: about 9 years ago

10.3389/fncom.2013.00103

Compositionality in neural control: an interdisciplinary study of scribbling movements in primates
Cited by: 11
Author(s): Moshe Abeles, Markus Diesmann, Tamar Flash, Theo Geisel, Johannes M. Herrmann, Mina Teicher
Software Mentions: 2
Published: almost 12 years ago

10.1002/ece3.3593

Search and foraging behaviors from movement data: A comparison of methods
Cited by: 53
Author(s): Ashley Bennison, Stuart Bearhop, Thomas W. Bodey, Stephen C. Votier, W. James Grecian, Ewan D. Wakefield, Keith C. Hamer, Mark Jessopp
Software Mentions: 2
Published: almost 7 years ago

10.15252/msb.20209880

Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes
Cited by: 22
Author(s): Georgy Smyshlyaev, Alex Bateman, O. Barábas
Software Mentions: 2
Published: over 3 years ago

10.3390/e21111130

Dynamical Behavior of β-Lactamases and Penicillin- Binding Proteins in Different Functional States and Its Potential Role in Evolution
Cited by: 9
Author(s): Feng Wang, Haoming Zhou, Xinlei Wang, Peng Tao
Software Mentions: 2
Published: about 5 years ago

10.1038/s42003-021-02533-z

Rates of contributory de novo mutation in high and low-risk autism families
Cited by: 18
Author(s): Seungtai Yoon, Adriana Muñoz, Boris Yamrom, Yoon-ha Lee, Peter Andrews, Steven C. Marks, Zihua Wang, Catherine Reeves, Lara Winterkorn, Abba M. Krieger, Andreas Buja, Kith Pradhan, Michael Ronemus, Kristin K. Baldwin, Dan Levy, Michael Wigler, Ivan Iossifov
Software Mentions: 2
Published: about 3 years ago

10.3389/fgene.2017.00078

Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca
Cited by: 28
Author(s): Yunpeng Cao, Yuepeng Han, Dong Meng, Guohui Li, Dahui Li, Qing Jin, Yi Lin, Yongping Cai
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.00928

Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems
Cited by: 34
Author(s): Lin-Xing Chen, Basem Al-Shayeb, Raphaël Méheust, Wenjun Li, Jennifer A. Doudna, Jillian F. Banfield
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.637595

The RsmA RNA-Binding Proteins in Pseudomonas syringae Exhibit Distinct and Overlapping Roles in Modulating Virulence and Survival Under Different Nutritional Conditions
Cited by: 9
Author(s): Jun Li, Menghao Yu, Yixin Ge, Yuee Tian, Baishi Hu, Youfu Zhao
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-021-07705-z

The dissection of R genes and locus Pc5.1 in Phytophthora capsici infection provides a novel view of disease resistance in peppers
Cited by: 13
Author(s): Jin-Song Du, Hang Liao, Qian Hao, Haitao Yang, S. Ali, Radwa Salah Ezaat Badawy, Xiaoyu Xu, Haidong Tan, Lihong Su, Huanxiu Li, Zou KaiXi, Li Yu, Bo Sun, Lijin Lin, Yunsong Lai
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0190938

Extension of the viral ecology in humans using viral profile hidden Markov models
Cited by: 22
Author(s): Zurab Bzhalava, Emilie Hultin, Joakim Dillner
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-021-07601-6

Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment
Cited by: 9
Author(s): Zhiwei Chen, Longhua Zhou, Panpan Jiang, Ruiju Lu, Nigel G. Halford, Chenghong Liu
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-021-07958-8

Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues
Cited by: 10
Author(s): Jiecuo Duo, Huan Xiong, Xiongxiong Wu, Yuan Li, Jianping Si, Chao Zhang, Ran Duan
Software Mentions: 2
Published: about 3 years ago

10.1186/1741-7007-4-29

Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic
Cited by: 83
Author(s): Daniel H. Haft, Ian T. Paulsen, Naomi Ward, Jeremy D. Selengut
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pone.0253845

The Shortest Duration Constrained Hidden Markov Model: Data denoise and forecast optimization on the country-product matrix for the Fitness-Complexity Algorithm
Cited by: 0
Author(s): Pengcheng Song, Xiangyu Zong, Ximing Chen, Qingwei Zhao, Lubingzhi Guo
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms8050669

A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion
Cited by: 1
Author(s): Daniela Becker, Denny Popp, Hauke Harms, Florian Centler
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-6-177

Comparative analysis of programmed cell death pathways in filamentous fungi
Cited by: 98
Author(s): Natalie D. Fedorova, Jonathan H. Badger, Geoff Robson, Jennifer Wortman, William C. Nierman
Software Mentions: 2
Published: almost 19 years ago

10.1186/s12915-020-0754-1

Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids
Cited by: 40
Author(s): Anzhelika Butenko, Frederik Opperdoes, Olga Flegontova, Aleš Horák, Vladimı́r Hampl, Patrick J. Keeling, Ryan M.R. Gawryluk, Denis V. Tikhonenkov, Pavel Flegontov, Julius Lukeš
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0025189

Identification of Plasmodium vivax Proteins with Potential Role in Invasion Using Sequence Redundancy Reduction and Profile Hidden Markov Models
Cited by: 10
Author(s): Daniel Restrepo-Montoya, David Becerra, Juan G. Carvajal-Patiño, Alvaro Monguí, Luís Fernando Niño, Manuel Elkín Patarroyo, Manuel A. Patarroyo
Software Mentions: 2
Published: about 13 years ago

10.1186/s12859-019-2984-1

Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico
Cited by: 6
Author(s): Ngaam J. Cheung, Wookyung Yu
Software Mentions: 2
Published: about 5 years ago

10.1002/mbo3.333

Comparative genome‐wide analysis reveals that Burkholderia contaminans <scp>MS</scp>14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis
Cited by: 35
Author(s): Peng Deng, Xiaoqiang Wang, Sonya M. Baird, Kurt C. Showmaker, Linda L. Smith, Daniel G. Peterson, Shi‐En Lu
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0109920

Identification and Molecular Characterization of MYB Transcription Factor Superfamily in C4 Model Plant Foxtail Millet (Setaria italica L.)
Cited by: 91
Author(s): Mehanathan Muthamilarasan, Rohit Khandelwal, Chandra Bhan Yadav, Venkata Suresh Bonthala, Yusuf Khan, Manoj Prasad
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0058809

Classify Hyperdiploidy Status of Multiple Myeloma Patients Using Gene Expression Profiles
Cited by: 12
Author(s): Yingxiang Li, Xujun Wang, Hongliang Zheng, Chengyang Wang, Stéphane Minvielle, Florence Magrangeas, Hervé Avet-Loiseau, Parantu K. Shah, Yong Zhang, Nikhil C. Munshi, Cheng Li
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0048941

Piecewise Polynomial Representations of Genomic Tracks
Cited by: 2
Author(s): Maxime Tarabichi, Vincent Detours, Tomasz Konopka
Software Mentions: 2
Published: about 12 years ago

10.1111/1751-7915.12556

Comparison of biofilm formation and motility processes in arsenic‐resistant Thiomonas spp. strains revealed divergent response to arsenite
Cited by: 11
Author(s): Julien Farasin, Sandrine Koechler, Hugo Varet, Julien Deschamps, Marie‐Agnès Dillies, Caroline Proux, Mathieu Erhardt, Aline Huber, Bernd Jagla, Romain Briandet, Jean‐Yves Coppée, Florence Arsène-Ploetze
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.ymeth.2018.03.012

Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut
Cited by: 32
Author(s): Eleanor Jameson, Mussa Quareshy, Yin Chen
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0135655

Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales
Cited by: 22
Author(s): Mary Ellen Heavner, Wang Qiu, Hai-Ping Cheng
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0160334

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies
Cited by: 10
Author(s): Martin Norling, Oskar Karlsson Lindsjö, Hadrien Gourlé, Erik Bongcam‐Rudloff, Juliette Hayer
Software Mentions: 2
Published: over 8 years ago

10.1186/s40462-019-0163-7

Acoustic evaluation of behavioral states predicted from GPS tracking: a case study of a marine fishing bat
Cited by: 20
Author(s): Edward Hurme, Eliezer Gurarie, Stefan Greif, L. Gerardo Herrera M., José Juan Flores‐Martínez, Gerald S. Wilkinson, Yossi Yovel
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0231197

Metagenomics analysis reveals features unique to Indian distal gut microbiota
Cited by: 19
Author(s): Kirandeep Kaur, Indu Khatri, Akil Akhtar, S. Subramanian, T.N.C. Ramya
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0101631

Genetic Organization of Interphase Chromosome Bands and Interbands in Drosophila melanogaster
Cited by: 57
Author(s): И. Ф. Жимулев, Tatyana Yu Zykova, Fyodor P. Goncharov, V. A. Khoroshko, Olga V. Demakova, V. F. Semeshin, Galina V. Pokholkova, Lidiya V. Boldyreva, D S Demidova, Vladimir N. Babenko, С. А. Демаков, E. S. Belyaeva
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0018011

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees
Cited by: 96
Author(s): Dongying Wu, Martin Wu, Aaron L. Halpern, Douglas B. Rusch, Shibu Yooseph, M.E. Frazier, J. Craig Venter, Jonathan A. Eisen
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-13-621

Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major
Cited by: 37
Author(s): Vijayendran Gowri, Indira Ghosh, Amit Sharma, Rentala Madhubala
Software Mentions: 2
Published: about 12 years ago

Projects: cran: HMM

Papers Mentioning HMM 577