cran: HMM | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0256196

Finding differentially expressed sRNA-Seq regions with srnadiff
Cited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: over 3 years ago

Selfing is the safest sex for Caenorhabditis tropicalis
Cited by: 30
Author(s): Luke M. Noble, John G Yuen, Lewis Stevens, Nicolas Moya, Riaad Persaud, Marc Moscatelli, Jacqueline L. Jackson, Gaotian Zhang, Rojin Chitrakar, L. Ryan Baugh, Christian Braendle, Erik C. Andersen, Hannah S. Seidel, Matthew V. Rockman
Software Mentions: 13
Published: almost 4 years ago

10.1038/s41408-019-0199-3

Deciphering the chronology of copy number alterations in Multiple Myeloma
Cited by: 35
Author(s): Anıl Aktaş Samur, Stéphane Minvielle, Masood A. Shammas, Mariateresa Fulciniti, Florence Magrangeas, Paul G. Richardson, Philippe Moreau, Michel Attal, Kenneth C. Anderson, Giovanni Parmigiani, Hervé Avet‐Loiseau, Nikhil C. Munshi, Mehmet K. Samur
Software Mentions: 11
Published: over 5 years ago

10.3389/fmed.2020.00247

Growth Rate and Acceleration Analysis of the COVID-19 Pandemic Reveals the Effect of Public Health Measures in Real Time
Cited by: 34
Author(s): Yuri Tani Utsunomiya, Adam Taiti Harth Utsunomiya, Rafaela Beatriz Pintor Torrecilha, Silvana de Cássia Paulan, Marco Milanesi, José Fernando Garcia
Software Mentions: 10
Published: over 4 years ago

10.1186/s40168-021-01054-5

A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere
Cited by: 39
Author(s): Robyn J. Wright, Rafael Bosch, Morgan G. I. Langille, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-021-88943-9

Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages
Cited by: 17
Author(s): Ankit T. Hinsu, Nilam J. Tulsani, Ketankumar Panchal, Ramesh Pandit, Basanti Jyotsana, Nishant A. Dafale, N. B. Patil, Hemant J. Purohit, Chaitanya Joshi, Subhash J. Jakhesara
Software Mentions: 9
Published: over 3 years ago

10.16910/jemr.10.6.1

Abstracts of the 19th European Conference on Eye Movements 2017
Cited by: 3
Author(s): Ralph Radach, Heiner Deubel, Christian Vorstius, Markus Hofmann
Software Mentions: 9
Published: almost 7 years ago

10.3390/ijms22105354

Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley
Cited by: 7
Author(s): Jinhong Kan, Guang Gao, Qiang He, Qian Gao, Congcong Jiang, Sunny Ahmar, Jun Liu, Jing Zhang, Ping Yang
Software Mentions: 8
Published: over 3 years ago

10.3390/biom10010026

Graph Theory-Based Sequence Descriptors as Remote Homology Predictors
Cited by: 12
Author(s): Guillermı́n Agüero-Chapin, Deborah Galpert Cañizares, Reinaldo Molina Ruiz, Evys Ancede-Gallardo, Gisselle Pérez-Machado, G Riva, Agostinho Antunes
Software Mentions: 8
Published: almost 5 years ago

10.1128/mSystems.01356-20

Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities
Cited by: 26
Author(s): Jingjie Du, Ahmed A. Zayed, Kristina A. Kigerl, Kylie Zane, Matthew B. Sullivan, Phillip G. Popovich
Software Mentions: 8
Published: over 3 years ago

10.3390/v11121085

Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages
Cited by: 19
Author(s): Patrick A. de Jonge, F. A. Bastiaan von Meijenfeldt, Laura E van Rooijen, Stan J. J. Brouns, Bas E. Dutilh
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0083984

Characterizing the Infection-Induced Transcriptome of Nasonia vitripennis Reveals a Preponderance of Taxonomically-Restricted Immune Genes
Cited by: 34
Author(s): Timothy B. Sackton, John H. Werren, Andrew G. Clark
Software Mentions: 7
Published: almost 11 years ago

10.1186/s12859-017-1942-z

A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa
Cited by: 17
Author(s): Megan J. Bowman, Jane A. Pulman, Tiffany L. Liu, Kevin L. Childs
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12859-021-04264-8

mLoc-mRNA: predicting multiple sub-cellular localization of mRNAs using random forest algorithm coupled with feature selection via elastic net
Cited by: 6
Author(s): Prabina Kumar Meher, Anil Rai, Atmakuri Ramakrishna Rao
Software Mentions: 6
Published: over 3 years ago

10.1186/s13100-019-0156-5

Subtype classification and functional annotation of L1Md retrotransposon promoters
Cited by: 15
Author(s): Meng Zhou, Andrew D. Smith
Software Mentions: 6
Published: over 5 years ago

10.1093/g3journal/jkab074

MultiPhATE2: code for functional annotation and comparison of phage genomes
Cited by: 11
Author(s): Carol L. Ecale Zhou, Jeffrey A. Kimbrel, Robert A. Edwards, Katelyn McNair, Brian Souza, Stephanie Malfatti
Software Mentions: 5
Published: over 3 years ago

10.1083/jcb.201711097

Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1
Cited by: 3
Author(s): Christoph Schiklenk, Boryana Petrova, Marc Kschonsak, Markus Hassler, Carlo Klein, Toby J. Gibson, Christian H. Haering
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.70394

Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans
Cited by: 14
Author(s): Gurmeet Kaur, Lakshminarayan M. Iyer, A. Maxwell Burroughs, L. Aravind
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-15-459

Structured RNAs and synteny regions in the pig genome
Cited by: 19
Author(s): Christian Anthon, Hakim Tafer, Jakob Hull Havgaard, Bo Thomsen, Jakob Hedegaard, Stefan E. Seemann, Sachin Pundhir, Stephanie Kehr, Sebastian Bartschat, Marie Konge Nielsen, Rasmus Oestergaard Nielsen, Merete Fredholm, Peter F. Stadler, Jan Gorodkin
Software Mentions: 5
Published: over 10 years ago

10.1186/s12870-020-02814-5

Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple
Cited by: 8
Author(s): Yan Shi, Xingtan Zhang, Xiaojun Chang, Mei Yan, Hui Zhao, Yuan Qin, Haifeng Wang
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0119198

Genome-Wide Analysis of Homeobox Gene Family in Legumes: Identification, Gene Duplication and Expression Profiling
Cited by: 47
Author(s): Annapurna Bhattacharjee, Rajesh Ghangal, Rohini Garg, Mukesh Jain
Software Mentions: 5
Published: over 9 years ago

10.1186/s12915-021-01139-5

The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching
Cited by: 21
Author(s): Tobias Mourier, Denise Anete Madureira de Alvarenga, Abhinav Kaushik, Anielle de Pina-Costa, Olga Douvropoulou, Qingtian Guan, Francisco J. Guzmán‐Vega, Sarah Forrester, Filipe Vieira Santos de Abreu, Cesare Bianco Júnior, Júlio César de Souza, Sílvia Bahadian Moreira, Zelinda Maria Braga Hirano, Alcides Pissinatti, Maria de Fátima Ferreira-da-Cruz, Ricardo Lourenço de Oliveira, Stefan T. Arold, Daniel C. Jeffares, Patrícia Brasil, Cristiana Ferreira Alves de Brito, Richard Culleton, Cláudio Tadeu Daniel-Ribeiro, Arnab Pain
Software Mentions: 5
Published: about 3 years ago

10.1186/1471-2164-15-946

Conservation analysis of the CydX protein yields insights into small protein identification and evolution
Cited by: 35
Author(s): Rondine J. Allen, Evan P. Brenner, Caitlin E. VanOrsdel, Jessica J. Hobson, David J. Hearn, Matthew R. Hemm
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0085568

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines
Cited by: 58
Author(s): Oliver Rupp, J. Ole Becker, Karina Brinkrolf, Christina Timmermann, Nicole Borth, Alfred Pühler, Thomas Noll, Alexander Goesmann
Software Mentions: 5
Published: almost 11 years ago

10.2196/24073

A Natural Language Processing–Based Virtual Patient Simulator and Intelligent Tutoring System for the Clinical Diagnostic Process: Simulator Development and Case Study
Cited by: 14
Author(s): Raffaello Furlan, Mauro Gatti, Roberto Menè, Dana Shiffer, Chiara Marchiori, Alessandro Giaj Levra, Vincenzo Saturnino, Enrico Brunetta, Franca Dipaola
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2172-9-8

Evaluation of MHC class I peptide binding prediction servers: Applications for vaccine research
Cited by: 219
Author(s): Honghuang Lin, Surajit Ray, Songsak Tongchusak, Ellis L. Reinherz, Vladimir Brusic
Software Mentions: 5
Published: over 16 years ago

10.1186/s12864-019-6019-0

Identification of methylation states of DNA regions for Illumina methylation BeadChip
Cited by: 12
Author(s): Ximei Luo, Fang Wang, Guohua Wang, Yuming Zhao
Software Mentions: 5
Published: over 4 years ago

10.1186/s13100-020-00224-w

Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains
Cited by: 14
Author(s): Mahoko Takahashi Ueda, Kirill Kryukov, Satomi Mitsuhashi, Hiroaki Mitsuhashi, Tadashi Imanishi, So Nakagawa
Software Mentions: 5
Published: about 4 years ago

10.3390/genes10060427

Genomic Evidence of Recombination in the Basidiomycete Wallemia mellicola
Cited by: 10
Author(s): Xiaohuan Sun, Cene Gostinčar, Chao Fang, Janja Zajc, Yong Hou, Zewei Song, Nina Gunde‐Cimerman
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0109715

Genome-Wide Identification and Tissue-Specific Expression Analysis of UDP-Glycosyltransferases Genes Confirm Their Abundance in Cicer arietinum (Chickpea) Genome
Cited by: 33
Author(s): Ranu Sharma, Vimal Rawat, C.G. Suresh
Software Mentions: 5
Published: about 10 years ago

10.3390/ijms20205043

Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco (Nicotiana tabacum L.)
Cited by: 18
Author(s): Ge Bai, Da-Hai Yang, Peijian Cao, Huaiying Yao, Yihan Zhang, Xuejun Chen, Bingguang Xiao, Feng Li, Zhenyu Wang, Jun Yang, He Xie
Software Mentions: 5
Published: about 5 years ago

10.15252/msb.20145654

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle
Cited by: 21
Author(s): Benedikt Zacher, Michael Lidschreiber, Patrick Cramer, Julien Gagneur, Achim Tresch
Software Mentions: 5
Published: almost 10 years ago

10.3389/fmicb.2013.00279

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter
Cited by: 59
Author(s): C. Ryan Penton, Timothy A. Johnson, John F. Quensen, Shoko Iwai, James R. Cole, James M. Tiedje
Software Mentions: 4
Published: almost 12 years ago

10.1186/s13059-016-1116-8

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Cited by: 112
Author(s): Shaman Narayanasamy, Yohan Jarosz, Emilie Muller, Anna Heintz‐Buschart, Malte Herold, Anne Kaysen, Cédric Christian Laczny, Nicolás Pinel, Patrick May, Paul Wilmes
Software Mentions: 4
Published: almost 8 years ago

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: almost 9 years ago

10.1186/s40168-017-0340-0

Feed in summer, rest in winter: microbial carbon utilization in forest topsoil
Cited by: 104
Author(s): Lucia Žifčáková, Tomáš Větrovský, Vincent Lombard, Bernard Henrissat, Adina Howe, Petr Baldrián
Software Mentions: 4
Published: about 7 years ago

10.1186/s13227-019-0135-4

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes
Cited by: 16
Author(s): Graham A. McCulloch, Andrew Oliphant, Peter K. Dearden, Andrew J. Veale, Charles W. Ellen, Jonathan M. Waters
Software Mentions: 4
Published: about 5 years ago

10.1111/1751-7915.13578

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site
Cited by: 75
Author(s): Jesse C. Thomas, Adelumola Oladeinde, Troy J. Kieran, John W. Finger, Natalia J. Bayona‐Vásquez, John C. Cartee, James C. Beasley, John C. Seaman, J Vuan McArthur, Olin E. Rhodes, Travis C. Glenn
Software Mentions: 4
Published: over 4 years ago

10.1111/1462-2920.13706

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir
Cited by: 21
Author(s): A. J. Freedman, BoonFei Tan, Janelle R. Thompson
Software Mentions: 4
Published: over 7 years ago

10.1186/s12862-021-01762-4

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume
Cited by: 10
Author(s): Man Zhang, Ping Li, Xiao-lan Yan, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-019-6121-3

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)
Cited by: 22
Author(s): Mingjia Tang, Liang Xu, Yan Wang, Wanwan Cheng, Xiaobo Luo, Yang Xie, Lu Fan, Liwang Liu
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008580

A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation
Cited by: 23
Author(s): Diego Vidaurre
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0024542

Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing
Cited by: 62
Author(s): Dale N. Richardson, Mark F. Rogers, Adam Labadorf, Asa Ben-Hur, Hui Guo, Andrew H. Paterson, Anireddy S. N. Reddy
Software Mentions: 4
Published: about 13 years ago

10.1186/s12870-020-02334-2

The mechanism of potato resistance to Globodera rostochiensis: comparison of root transcriptomes of resistant and susceptible Solanum phureja genotypes
Cited by: 5
Author(s): А. В. Кочетов, А. А. Егорова, Anastasiya Y. Glagoleva, К. В. Стрыгина, Elena K. Khlestkina, С. В. Герасимова, Natalja V. Shatskaya, Gennady V. Vasilyev, Д. А. Афонников, Nikolay A. Shmakov, Olga Antonova, Natalia V. Alpatyeva, А. В. Хютти, Olga Afanasenko, Т. А. Гавриленко
Software Mentions: 4
Published: about 4 years ago

10.1186/s13578-017-0138-6

Comparative analysis of pre- and post-parasitic transcriptomes and mining pioneer effectors of Heterodera avenae
Cited by: 20
Author(s): Dan Yang, Changlong Chen, Qian Liu, Heng Jian
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2105-10-10

Bayesian DNA copy number analysis
Cited by: 34
Author(s): Paola Mv Rancoita, Marcus Hutter, Francesco Bertoni, Ivo Kwee
Software Mentions: 4
Published: almost 16 years ago

10.1186/1471-2164-13-55

Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics
Cited by: 22
Author(s): Fekadu Yadetie, Stephen Butcher, Hilde Elise Førde, Coen Campsteijn, Jean‐Marie Bouquet, Odd André Karlsen, France Denœud, Raghu Metpally, Eric M. Thompson, J. Robert Manak, Anders Goksøyr, Daniel Chourrout
Software Mentions: 4
Published: almost 13 years ago

10.1038/s41598-017-12401-8

Similarity-Based Segmentation of Multi-Dimensional Signals
Cited by: 14
Author(s): Rainer Machné, Douglas B. Murray, Peter F. Stadler
Software Mentions: 4
Published: about 7 years ago

10.1186/s12859-021-04180-x

Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets
Cited by: 15
Author(s): Teresita M. Porter, Mehrdad Hajibabaei
Software Mentions: 4
Published: over 3 years ago

10.1093/bib/bbaa232

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
Cited by: 99
Author(s): Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Alex Bateman, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F Löchel, Marı́a Jesús Martı́n, Roman Martin, Julian Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine O’Toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Piñeros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pcbi.1003234

ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data
Cited by: 4
Author(s): André Yoshiaki Kashiwabara, Ígor Bonadio, Vitor Onuchic, Felipe Amado, Rafael Mathias, Alan Mitchell Durham
Software Mentions: 4
Published: about 11 years ago

10.1038/s41598-018-37309-9

HRGPred: Prediction of herbicide resistant genes with k-mer nucleotide compositional features and support vector machine
Cited by: 8
Author(s): Prabina Kumar Meher, Tanmaya Kumar Sahu, K. Raghunandan, Shachi Gahoi, Nalini Kanta Choudhury, Atmakuri Ramakrishna Rao
Software Mentions: 4
Published: almost 6 years ago

10.1093/jxb/erx163

The diversity of CO2-concentrating mechanisms in marine diatoms as inferred from their genetic content
Cited by: 26
Author(s): Chen Shen, Christopher L. Dupont, Brian M. Hopkinson
Software Mentions: 4
Published: over 7 years ago

10.3390/plants10061154

Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice
Cited by: 9
Author(s): Hongjia Zhang, Seong-Ho Jang, San Mar Lar, Ah-Rim Lee, Fangyuan Cao, Jeonghwan Seo, Soon-Wook Kwon
Software Mentions: 4
Published: over 3 years ago

10.1038/s41597-019-0263-7

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation
Cited by: 9
Author(s): Jesse C. J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Vítor A. P. Martins dos Santos, Peter J. Schaap, María Suárez-Diez
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-9-S2-S17

Array CGH data modeling and smoothing in Stationary Wavelet Packet Transform domain
Cited by: 15
Author(s): Heng Huang, Nha Nguyen, S. Oraintara, An Vo
Software Mentions: 4
Published: almost 17 years ago

10.3389/fpls.2015.00918

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
Cited by: 61
Author(s): Vikash Singh, Mukesh Jain
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-016-1014-0

The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum
Cited by: 83
Author(s): Evelien M. Bunnik, Gayani Batugedara, Anita Saraf, Jacques Prudhomme, Laurence Florens, Karine G. Le Roch
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-017-11327-5

Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea
Cited by: 26
Author(s): Vikash Singh, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2018.00028

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome
Cited by: 68
Author(s): Sophie S. Abby, Michael Melcher, Melina Kerou, Mart Krupovìč, Michaela Stieglmeier, Claudia Rossel, Kevin Pfeifer, Christa Schleper
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2105-10-381

Prediction of protein binding sites in protein structures using hidden Markov support vector machine
Cited by: 43
Author(s): Bin Liu, Xiaolong Wang, Lei Lin, Buzhou Tang, Qian Dong, Xuan Wang
Software Mentions: 3
Published: about 15 years ago

10.3389/fmicb.2019.02019

Population Genomics of an Obligately Halophilic Basidiomycete Wallemia ichthyophaga
Cited by: 8
Author(s): Cene Gostinčar, Xiaohuan Sun, Janja Zajc, Chao Fang, Yong Hou, Yonglun Luo, Nina Gunde‐Cimerman, Zewei Song
Software Mentions: 3
Published: about 5 years ago

10.1186/1476-4598-12-140

Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations
Cited by: 53
Author(s): Ângela Aguirres Fachel, Ana Carolina Tahira, Santiago A. Vilella-Arias, Vinicius Maracaja‐Coutinho, Etel Rp Gimba, Giselle Maria Vignal, Franz Campos, Eduardo M. Reis, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: about 11 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

10.3389/fmicb.2018.00782

Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence
Cited by: 32
Author(s): Liang Wang, Jiawei Yan, Michael J. Wise, Qinghua Liu, James Asenso, Yue Huang, Shiyun Dai, Zhanzhong Liu, Yan Du, Daoquan Tang
Software Mentions: 3
Published: over 6 years ago

10.3390/vaccines2030515

Peptide Vaccine: Progress and Challenges
Cited by: 479
Author(s): Weidang Li, Medha Joshi, Smita Singhania, Kyle H. Ramsey, Ashlesh K. Murthy
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2019.02612

Evaluation of Human Milk Microbiota by 16S rRNA Gene Next-Generation Sequencing (NGS) and Cultivation/MALDI-TOF Mass Spectrometry Identification
Cited by: 22
Author(s): Primož Treven, Aleksander Mahnič, Maja Rupnik, Majda Golob, Tina Pirš, Bojana Bogovič Matijašić, Petra Mohar Lorbeg
Software Mentions: 3
Published: about 5 years ago

10.3390/microorganisms8050653

Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae
Cited by: 33
Author(s): Jamie McGowan, Richard O’Hanlon, Rebecca A. Owens, David A. Fitzpatrick
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.01880

Comparative Analysis of Clinical and Environmental Strains of Exophiala spinifera by Long-Reads Sequencing and RNAseq Reveal Adaptive Strategies
Cited by: 4
Author(s): Yinggai Song, Minghao Du, Nickolas Menezes da Silva, Ence Yang, Vânia Aparecida Vicente, G. S. de Hoog, Ruoyu Li
Software Mentions: 3
Published: over 4 years ago

10.3389/fnins.2013.00074

Abrupt changes in the patterns and complexity of anterior cingulate cortex activity when food is introduced into an environment
Cited by: 14
Author(s): Barak F. Caracheo, Eldon Emberly, Shirin Hadizadeh, James M. Hyman, Jeremy K. Seamans
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13072-018-0235-8

The large fraction of heterochromatin in Drosophila neurons is bound by both B-type lamin and HP1a
Cited by: 23
Author(s): Alexey V. Pindyurin, Artem A. Ilyin, Anton V. Ivankin, Mikhail V. Tselebrovsky, Valentina V. Nenasheva, Elena A. Mikhaleva, Ludo Pagie, Bas van Steensel, Yuri Y. Shevelyov
Software Mentions: 3
Published: about 6 years ago

10.1099/mgen.0.000080

Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems
Cited by: 34
Author(s): Eleanor Jameson, Andrew C. Doxey, Ruth L. Airs, Kevin J. Purdy, J. Colin Murrell, Yin Chen
Software Mentions: 3
Published: about 8 years ago

10.1186/s40168-018-0573-6

A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
Cited by: 44
Author(s): Sean Benler, Ana G Cobián-Güemes, Katelyn McNair, Shr-Hau Hung, Kyle Levi, Robert A. Edwards, Forest Rohwer
Software Mentions: 3
Published: about 6 years ago

10.1038/s41422-019-0196-x

A two-step lineage reprogramming strategy to generate functionally competent human hepatocytes from fibroblasts
Cited by: 38
Author(s): Bingqing Xie, Dihua Sun, Yuanyuan Du, Jinping Jia, Shicheng Sun, Jun Xu, Yifang Liu, Chengang Xiang, Sitong Chen, Huangfan Xie, Qiming Wang, Guang‐Ya Li, Xuehui Lyu, Hui Shen, Shiyu Li, Min Wu, Xiaonan Zhang, Ying Pu, Kuanhui Xiang, Weifeng Lai, Peng Du, Zhenghong Yuan, Li Cheng, Yan Shi, Shichun Lu, Hongkui Deng
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-019-6319-4

Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae
Cited by: 14
Author(s): Jing Li, Xiaotong Gao, Shiye Sang, Changning Liu
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0060116

Insight into the Evolution of the Histidine Triad Protein (HTP) Family in Streptococcus
Cited by: 20
Author(s): Zhu‐Qing Shao, Yanmei Zhang, Xiuzhen Pan, Bin Wang, Jian-Qun Chen
Software Mentions: 3
Published: over 11 years ago

10.1186/s13072-017-0141-5

Genome-wide search for Zelda-like chromatin signatures identifies GAF as a pioneer factor in early fly development
Cited by: 23
Author(s): Arbel Moshe, Tommy Kaplan
Software Mentions: 3
Published: over 7 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

10.1371/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

10.1371/journal.pone.0004207

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum
Cited by: 97
Author(s): Dongying Wu, Jason Raymond, Martin Wu, Sourav Chatterji, Qinghu Ren, Joel E. Graham, Donald A. Bryant, Frank T. Robb, Albert S. Colman, Luke J. Tallon, Jonathan H. Badger, Ramana Madupu, Naomi Ward, Jonathan A. Eisen
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.pone.0043652

Pitfalls of Establishing DNA Barcoding Systems in Protists: The Cryptophyceae as a Test Case
Cited by: 26
Author(s): Kerstin Hoef‐Emden
Software Mentions: 3
Published: about 12 years ago

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

10.1186/s12915-020-00804-5

The rise of diversity in metabolic platforms across the Candidate Phyla Radiation
Cited by: 37
Author(s): Alexander L. Jaffe, Cindy J. Castelle, Paula B. Matheus Carnevali, Simonetta Gribaldo, Jillian F. Banfield
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0043245

A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters
Cited by: 62
Author(s): Nemin Celik, Chaille T Webb, Denisse L. Leyton, Kathryn E. Holt, Eva Heinz, Rebecca J. Gorrell, Terry Kwok, Thomas Naderer, Richard A. Strugnell, Terence P. Speed, Rohan D. Teasdale, Vladimir A Likić, Trevor Lithgow
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-018-4521-4

Lineage-specific duplications of NBS-LRR genes occurring before the divergence of six Fragaria species
Cited by: 20
Author(s): Yan Zhong, Xiaohui Zhang, Zong‐Ming Cheng
Software Mentions: 3
Published: almost 7 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

10.1186/1471-2105-12-175

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

10.1155/2018/5206758

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses in<i>Brassica rapa</i>
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

10.1186/s12864-015-1494-4

De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response
Cited by: 41
Author(s): Hai-Bin Zhang, Enhua Xia, Hui Huang, Jianjun Jiang, Benying Liu, Li‐Zhi Gao
Software Mentions: 3
Published: over 9 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

10.1186/1471-2105-10-418

TransportTP: A two-phase classification approach for membrane transporter prediction and characterization
Cited by: 57
Author(s): Haiquan Li, Vagner A. Benedito, Michael K. Udvardi, Patrick Xuechun Zhao
Software Mentions: 3
Published: almost 15 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

10.1186/s12915-020-00943-9

The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia
Cited by: 45
Author(s): Hao Song, Ximing Guo, Lina Sun, Qianghui Wang, Fengming Han, Haiyan Wang, Gregory A. Wray, Phillip L. Davidson, Qing Wang, Zhi Hu, Cong Zhou, Zhi Yu, Mei‐Jie Yang, Jie Feng, Shi Pu, Yi Zhou, Libin Zhang, Tao Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-016-2707-1

The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos
Cited by: 32
Author(s): William P. Wysocki, Eduardo Ruiz‐Sánchez, Yanbin Yin, Melvin R. Duvall
Software Mentions: 3
Published: over 8 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

10.1186/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

10.1371/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

10.1371/journal.pone.0209139

Computational framework for targeted high-coverage sequencing based NIPT
Cited by: 7
Author(s): Hindrek Teder, Priit Paluoja, Kadri Rekker, Andres Salumets, Kaarel Krjutškov, Priit Palta
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0053779

Mining of Novel Thermo-Stable Cellulolytic Genes from a Thermophilic Cellulose-Degrading Consortium by Metagenomics
Cited by: 44
Author(s): Yu Xia, Feng Ju, Hhp Fang, Tong Zhang
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12866-021-02184-4

Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses
Cited by: 2
Author(s): Delphine Larivière, Laura M. Wickham, Kenneth C. Keiler, Anton Nekrutenko
Software Mentions: 3
Published: over 3 years ago

Projects: cran: HMM

Papers Mentioning HMM 577