cran: HMM | Projects | Ecosyste.ms: Papers

10.1186/s12985-015-0373-6

Glycoside hydrolase family 32 is present in Bacillus subtilis phages
Cited by: 10
Author(s): Halim Maaroufi, Roger C. Levesque
Software Mentions: 1
Published: about 9 years ago

AIV polyantigen epitope expressed by recombinant baculovirus induces a systemic immune response in chicken and mouse models
Cited by: 3
Author(s): Long-Chuan Yu, Jun Pan, Guangwen Cao, Mengsheng Jiang, Yunshan Zhang, Min Zhu, Zi Liang, Xing Zhang, Xiaolong Hu, Renyu Xue, Chengliang Gong
Software Mentions: 1
Published: over 4 years ago

10.3390/v11020195

Classifying the Unclassified: A Phage Classification Method
Cited by: 38
Author(s): Cynthia Maria Chibani, Anton Farr, Sandra Klama, Sascha Dietrich, Heiko Liesegang
Software Mentions: 1
Published: over 5 years ago

10.3390/v11121134

A Novel Genus of Actinobacterial Tectiviridae
Cited by: 15
Author(s): Steven M. Caruso, Tagide N. deCarvalho, Anthony Huynh, George Morcos, Nansen Kuo, Shabnam Parsa, Ivan Erill
Software Mentions: 1
Published: almost 5 years ago

10.3390/v12070721

Pseudomonas Phage PaBG—A Jumbo Member of an Old Parasite Family
Cited by: 8
Author(s): Peter Evseev, Н. Н. Сыкилинда, Anna Gorshkova, Lidia P. Kurochkina, Rustam H. Ziganshin, Valentin Drucker, Konstantin A. Miroshnikov
Software Mentions: 1
Published: over 4 years ago

10.3390/v13091688

Novel Acinetobacter baumannii Bacteriophage Aristophanes Encoding Structural Polysaccharide Deacetylase
Cited by: 9
Author(s): Olga Y. Timoshina, Mikhail M. Shneider, Peter Evseev, Anastasia S Shchurova, Andrey Shelenkov, Yulia Mikhaylova, Olga Sokolova, Аnastasia A. Kasimova, Nikolay P. Arbatsky, Andrey S. Dmitrenok, Yuriy A. Knirel, Konstantin A. Miroshnikov, Anastasiya V. Popova
Software Mentions: 1
Published: about 3 years ago

10.3897/zookeys.788.25323

Description of three new species of Apatelodidae from the southern neotropical region (Lepidoptera, Bombycoidea)
Cited by: 3
Author(s): Daniel Herbin, Hernán Mario Beccacece
Software Mentions: 1
Published: about 6 years ago

10.1186/s13071-016-1837-2

GPCR and IR genes in Schistosoma mansoni miracidia
Cited by: 15
Author(s): Di Liang, Min Zhao, Tianfang Wang, Donald P. McManus, Scott F. Cummins
Software Mentions: 1
Published: about 8 years ago

10.1016/j.patter.2021.100256

AutoStepfinder: A fast and automated step detection method for single-molecule analysis
Cited by: 24
Author(s): Luuk Loeff, Jacob Kerssemakers, Chirlmin Joo, Cees Dekker
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.7215

An ambiguous N-terminus drives the dual targeting of an antioxidant protein Thioredoxin peroxidase (TgTPx1/2) to endosymbiotic organelles inToxoplasma gondii
Cited by: 4
Author(s): Pragati Mastud, Swati Patankar
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.3232

Genome-wide analysis of WRKY transcription factors in wheat (Triticum aestivum L.) and differential expression under water deficit condition
Cited by: 65
Author(s): Pan Ning, C.C. Liu, Jae-Heon Kang, Jinyin Lv
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.7817

Genome-wide identification and expression analysis of the WRKY genes in sugar beet (Beta vulgaris L.) under alkaline stress
Cited by: 23
Author(s): Guo-Qiang Wu, Zhiqiang Li, Han Cao, Jinlong Wang
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.5770

What is an archaeon and are the Archaea really unique?
Cited by: 7
Author(s): Ajith Harish
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.3497

BioFuelDB: a database and prediction server of enzymes involved in biofuels production
Cited by: 7
Author(s): Nikhil Chaudhary, Ankit Gupta, Sudheer Gupta, Vineet K. Sharma
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.7153

Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plant Nelumbo nucifera
Cited by: 21
Author(s): Tianyu Mao, Yaoyao Liu, Huanhuan Zhu, Jie Zhang, Jiangke Yang, Qiang Fu, Nian Wang, Ze Wang
Software Mentions: 1
Published: over 5 years ago

10.1098/rsta.2011.0546

Signal processing for molecular and cellular biological physics: an emerging field
Cited by: 9
Author(s): Max A. Little, Nick Jones
Software Mentions: 1
Published: almost 12 years ago

10.1002/pld3.287

Origin and evolution of a gibberellin‐deactivating enzyme GAMT
Cited by: 3
Author(s): Chi Zhang, Minta Chaiprasongsuk, André S. Chanderbali, Xinlu Chen, Jianyu Fu, Douglas E. Soltis, Feng Chen
Software Mentions: 1
Published: almost 4 years ago

10.3390/plants8120536

Comparative Analysis of the YABBY Gene Family of Bienertia sinuspersici, a Single-Cell C4 Plant
Cited by: 11
Author(s): Prabhakaran Soundararajan, So Youn Won, Dong Suk Park, Yeon-Hee Lee, Jung Sun Kim
Software Mentions: 1
Published: almost 5 years ago

10.3390/plants9101301

Genome-Wide Identification of the TCP Gene Family in Broussonetia papyrifera and Functional Analysis of BpTCP8, 14 and 19 in Shoot Branching
Cited by: 5
Author(s): Mingzhu Zhao, Xianjun Peng, Naizhi Chen, Shihua Shen
Software Mentions: 1
Published: about 4 years ago

10.3390/plants9070885

Genome-Wide Identification and Expression Profile Analysis of the Phospholipase C Gene Family in Wheat (Triticum aestivum L.)
Cited by: 13
Author(s): Xianguo Wang, Yang Liu, Li Zheng, Xiang Gao, Jian Dong, Jiacheng Zhang, Longlong Zhang, Linda S. Thomashow, David M. Weller, Mingming Yang
Software Mentions: 1
Published: over 4 years ago

10.3390/plants9040515

Freezing Tolerance and Expression of β-amylase Gene in Two Actinidia arguta Cultivars with Seasonal Changes
Cited by: 9
Author(s): Shi Sun, Jinbao Fang, Miaomiao Lin, Xiujuan Qi, Jinyong Chen, Ran Wang, Zhi Li, Yukuo Li, Muhammad Abid
Software Mentions: 1
Published: over 4 years ago

10.3390/plants8070203

Genome-Wide Identification and Characterization of JAZ Protein Family in Two Petunia Progenitors
Cited by: 8
Author(s): Shaoze Tian, Siyu Liu, Yu Wang, Kun Wang, Chaoqun Yin, Yuanzheng Yue, Huirong Hu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.0040188

Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters
Cited by: 377
Author(s): Dongying Wu, Sean C. Daugherty, Susan E. Van Aken, Grace Pai, Kisha Watkins, Hoda Khouri, Luke J. Tallon, Jennifer Zaborsky, Helen E. Dunbar, Phat L. Tran, Nancy A. Moran, Jonathan A. Eisen
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pcbi.1004509

Beyond the E-Value: Stratified Statistics for Protein Domain Prediction
Cited by: 19
Author(s): Alejandro Ochoa, John D. Storey, Manuel Llinás, Mona Singh
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pcbi.0020041

Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays
Cited by: 146
Author(s): Rameen Beroukhim, Ming Gang Lin, Yuhyun Park, Ke Hao, Xiaojun Zhao, Levi A. Garraway, Edward A. Fox, Ephraim P. Hochberg, Ingo K. Mellinghoff, Matthias Hofer, A. Descazeaud, Mark A. Rubin, Matthew Meyerson, Wing Hung Wong, William R. Sellers, Cheng Li
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pcbi.1002163

Podbat: A Novel Genomic Tool Reveals Swr1-Independent H2A.Z Incorporation at Gene Coding Sequences through Epigenetic Meta-Analysis
Cited by: 31
Author(s): Laia Sadeghi, Carolina Bonilla, Annelie Strålfors, Karl Ekwall, J. Peter Svensson
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pcbi.1003337

Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein
Cited by: 14
Author(s): Davi R. Ortega, Guoya Mo, Kwang-Woon Lee, Hongjun Zhou, Jérôme Baudry, Frederick W. Dahlquist, Igor B. Zhulin
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pcbi.0010027

Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes
Cited by: 140
Author(s): Qinghu Ren, Ian T. Paulsen
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pcbi.1008030

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis
Cited by: 18
Author(s): Amrit Dhar, D. Ralph, Vladimir N. Minin, F. A. Matsen
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1003684

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes
Cited by: 71
Author(s): John A. Capra, Melissa J. Hubisz, Dennis Kostka, Katherine S. Pollard, Adam Siepel
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1002626

Cell Contact–Dependent Outer Membrane Exchange in Myxobacteria: Genetic Determinants and Mechanism
Cited by: 98
Author(s): Darshankumar T. Pathak, Xueming Wei, Alex Bucuvalas, Daniel H. Haft, Dietlind L. Gerloff, Daniel Wall
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1006795

Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba
Cited by: 52
Author(s): Rebekah L. Rogers, Ling Shao, Kevin R. Thornton
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1004324

Genetic Interactions Involving Five or More Genes Contribute to a Complex Trait in Yeast
Cited by: 79
Author(s): Matthew Taylor, Ian M. Ehrenreich
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1006158

Gene-Environment Interactions in Stress Response Contribute Additively to a Genotype-Environment Interaction
Cited by: 18
Author(s): Takeshi Matsui, Ian M. Ehrenreich
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1003088

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry
Cited by: 230
Author(s): P.J.G.M. de Wit, Ate van der Burgt, Bilal Ӧkmen, Ioannis Stergiopoulos, Kamel A. Abd-Elsalam, Andrea Aerts, Ali H. Bahkali, Henriek G. Beenen, Pranav Chettri, Murray P. Cox, Erwin Datema, Ronald P. de Vries, Braham Dhillon, Austen R. D. Ganley, S.A. Griffiths, Yanan Guo, Richard Hamelin, Bernard Henrissat, M. Shahjahan Kabir, M. Karimi Jashni, G.H.J. Kema, Sylvia Klaubauf, Alla Lapidus, Anthony Levasseur, Erika Lindquist, Rahim Mehrabi, Robin A. Ohm, Timothy J. Owen, Asaf Salamov, Arne Schwelm, Elio Schijlen, Hui Sun, H.A. van den Burg, Roeland C. H. J. van Ham, Shuguang Zhang, Stephen B. Goodwin, Igor V. Grigoriev, Jérôme Collemare, Rosie E. Bradshaw
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1002090

Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells
Cited by: 120
Author(s): Florian Lienert, Fabio Mohn, Vijay Tiwari, Tuncay Baubec, Tim Roloff, Dimos Gaidatzis, Michael Stadler, Dirk Schübeler
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.1004696

Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus aculeatus
Cited by: 120
Author(s): Nadezhda V. Terekhanova, Maria D. Logacheva, Aleksey A. Penin, Tatyana V. Neretina, A. E. Barmintseva, Georgii A. Bazykin, Alexey S. Kondrashov, N. S. Mugue
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0171758

A comprehensive software suite for protein family construction and functional site prediction
Cited by: 8
Author(s): David R. Haft, Daniel H. Haft
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0030287

A Novel Extracellular Metallopeptidase Domain Shared by Animal Host-Associated Mutualistic and Pathogenic Microbes
Cited by: 90
Author(s): Sirintra Nakjang, Didier Ndeh, Anil Wipat, David N. Bolam, Robert P. Hirt
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0034046

Molecular Evolution of the Neuropeptide S Receptor
Cited by: 21
Author(s): Thejkiran Pitti, Narayanan Manoj
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0009424

Geographic Structuring of the Plasmodium falciparum Sarco(endo)plasmic Reticulum Ca2+ ATPase (PfSERCA) Gene Diversity
Cited by: 41
Author(s): Ronan Jambou, Axel Martinelli, João Pinto, Simonetta Gribaldo, Eric Legrand, Makhtar Niang, Nimol Kim, Pharath Lim, Volnay Béatrice, Marie-Thérèse Ekala, Christiane Bouchier, Thierry Fandeur, Pedro Berzosa, Agustín Benito, Isabel Dinis Ferreira, Cynthia de Oliveira Ferreira, Pedro Paulo Vieira, Maria das Graças Costa Alecrim, Odile Mercereau–Puijalon, Pedro Vitor Lemos Cravo
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0087609

The B-Subdomain of the Xenopus laevis XFIN KRAB-AB Domain Is Responsible for Its Weaker Transcriptional Repressor Activity Compared to Human ZNF10/Kox1
Cited by: 10
Author(s): Nadine Born, Hans‐Jürgen Thiesen, Peter Lorenz
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0104150

Transcriptome Analysis of the Oil-Rich Tea Plant, Camellia oleifera, Reveals Candidate Genes Related to Lipid Metabolism
Cited by: 58
Author(s): Enhua Xia, Jianjun Jiang, Hui Huang, Liping Zhang, Haibin Zhang, Li‐Zhi Gao
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0005179

Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data
Cited by: 32
Author(s): Farid Benachenhou, Patric Jern, Merja Oja, Göran Sperber, Vidar Blikstad, Panu Somervuo, Samuel Kaski, Jonas Blomberg
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0047456

Hyperdiversity of Genes Encoding Integral Light-Harvesting Proteins in the Dinoflagellate Symbiodinium sp
Cited by: 28
Author(s): Lynda Evon Boldt, David Yellowlees, William Leggat
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0198854

SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information
Cited by: 0
Author(s): Ikram Allam, Delphine Flatters, Géraldine Caumes, Leslie Regad, Vincent Delos, Grégory Nuel, Anne-Claude Camproux
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0057535

Proteomic Analysis of Bifidobacterium longum subsp. infantis Reveals the Metabolic Insight on Consumption of Prebiotics and Host Glycans
Cited by: 68
Author(s): Jae-Han Kim, Hyun Joo An, Daniel Garrido, J. Bruce German, Carlito B. Lebrilla, David A. Mills
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0111858

Antennal-Expressed Ammonium Transporters in the Malaria Vector Mosquito Anopheles gambiae
Cited by: 37
Author(s): R. Jason Pitts, Stephen Derryberry, Fadi E. Pulous, Laurence J. Zwiebel
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0112921

Analysis of Non-Typeable Haemophilous influenzae VapC1 Mutations Reveals Structural Features Required for Toxicity and Flexibility in the Active Site
Cited by: 9
Author(s): Brooke Hamilton, Alexander Manzella, Karyn Schmidt, Victoria DiMarco, J. Scott Butler
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0100278

Prediction of Membrane Transport Proteins and Their Substrate Specificities Using Primary Sequence Information
Cited by: 91
Author(s): Nitish K. Mishra, Junil Chang, Patrick Xuechun Zhao
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0225339

Quantum dots reveal heterogeneous membrane diffusivity and dynamic surface density polarization of dopamine transporter
Cited by: 11
Author(s): Oleg Kovtun, Ian Tomlinson, Riley S. Ferguson, Sandra J. Rosenthal
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0173043

Genome-wide characterization and expression profiling of HD-Zip gene family related to abiotic stress in cassava
Cited by: 34
Author(s): Zehong Ding, Lili Fu, Yan Yan, Weiwei Tie, Zhiqiang Xia, Wenquan Wang, Ming Peng, Wei Hu, Jiaming Zhang
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0012439

An Economic Evaluation of Home Management of Malaria in Uganda: An Interactive Markov Model
Cited by: 16
Author(s): Yoel Lubell, Anne Mills, Christopher J M Whitty, Sarah G. Staedke
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0055417

The Mitochondrion-Like Organelle of Trimastix pyriformis Contains the Complete Glycine Cleavage System
Cited by: 30
Author(s): Zuzana Zubáčová, Lukáš Novák, Jitka Bublíková, Vojtěch Vacek, J. Fousek, Jakub Rídl, Jan Tachezy, Pavel Doležal, Čestmı́r Vlček, Vladimı́r Hampl
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0155435

The Kinome of Pacific Oyster Crassostrea gigas, Its Expression during Development and in Response to Environmental Factors
Cited by: 16
Author(s): Yanouk Epelboin, Laure Quintric, Éric Guévélou, Pierre Boudry, Vianney Pichereau, Charlotte Corporeau
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0136993

Genome-Wide Identification and Expression Analysis of the NAC Transcription Factor Family in Cassava
Cited by: 59
Author(s): Wei Hu, Yunxie Wei, Zhiqiang Xia, Yan Yan, Xin Hou, Meiling Zou, Cheng Lü, Wenquan Wang, Ming Peng
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0002386

Deciphering the Ubiquitin-Mediated Pathway in Apicomplexan Parasites: A Potential Strategy to Interfere with Parasite Virulence
Cited by: 80
Author(s): Nadia Ponts, Jingjing Yang, Duk-Won D. Chung, Jacques Prudhomme, Thomas Girke, Paul Horrocks, Karine G. Le Roch
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0034775

Genome-Wide Identification and Mapping of NBS-Encoding Resistance Genes in Solanum tuberosum Group Phureja
Cited by: 99
Author(s): Roberto Lozano, Olga Ponce, Manuel Ramírez, Nelly Mostajo, Gisella Orjeda
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0012052

Transcription Profiling of Epstein-Barr Virus Nuclear Antigen (EBNA)-1 Expressing Cells Suggests Targeting of Chromatin Remodeling Complexes
Cited by: 23
Author(s): Ramakrishna Sompallae, Simone Callegari, Siamak A. Kamranvar, Maria G. Masucci
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0132863

"PP2C7s", Genes Most Highly Elaborated in Photosynthetic Organisms, Reveal the Bacterial Origin and Stepwise Evolution of PPM/PP2C Protein Phosphatases
Cited by: 12
Author(s): David Kerk, Dylan M. Silver, R. Glen Uhrig, Greg B. G. Moorhead
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0028012

Comparative Genomic and Transcriptomic Characterization of the Toxigenic Marine Dinoflagellate Alexandrium ostenfeldii
Cited by: 86
Author(s): Nina Jaeckisch, Ines Yang, Sylke Wohlrab, Gernot Glöckner, Juergen Kroymann, Heiko Vogel, Allan Cembella, Uwe John
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0081518

Caste-Specific Expression Patterns of Immune Response and Chemosensory Related Genes in the Leaf-Cutting Ant, Atta vollenweideri
Cited by: 30
Author(s): Sarah I. Koch, Katrin Groh, Heiko Vogel, Bill S. Hannson, Christoph Johannes Kleineidam, Ewald Große-Wilde
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0228233

In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)
Cited by: 9
Author(s): Md. Parvez Mosharaf, Hafizur Rahman, Md. Asif Ahsan, Zobaer Akond, Fee Faysal Ahmed, Md. Mazharul Islam, Mohammad Ali Moni, Md. Nurul Haque Mollah
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0102825

Genome Duplication and Gene Loss Affect the Evolution of Heat Shock Transcription Factor Genes in Legumes
Cited by: 58
Author(s): Ying-Ren Lin, Ying Cheng, Jing Jin, Xiaolei Jin, Haiyang Jiang, Hanwei Yan, Beijiu Cheng
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0232220

Exploring novel bacterial terpene synthases
Cited by: 27
Author(s): Gajendar Komati Reddy, Nicole G. H. Leferink, Maiko Umemura, Syed Thouheed Ahmed, Rainer Breitling, Nigel S. Scrutton, Eriko Takano
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0176188

The putative drug efflux systems of the Bacillus cereus group
Cited by: 11
Author(s): Karl A. Hassan, Annette Fagerlund, Liam D. H. Elbourne, Aniko Vörös, Jasmin K. Kroeger, Roger Simm, Nicolas J. Tourasse, Sarah Finke, Peter J. F. Henderson, Ole Andreas Økstad, Ian T. Paulsen, Anne‐Brit Kolstø
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0007349

The Repertoire of Heterotrimeric G Proteins and RGS Proteins in Ciona intestinalis
Cited by: 2
Author(s): R. Prasobh, Narayanan Manoj
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0029817

The Origin of GPCRs: Identification of Mammalian like Rhodopsin, Adhesion, Glutamate and Frizzled GPCRs in Fungi
Cited by: 151
Author(s): Arunkumar Krishnan, Markus Sällaman Almén, Robert Fredriksson, Helgi B. Schiöth
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0002834

In Vitro Analysis of Integrated Global High-Resolution DNA Methylation Profiling with Genomic Imbalance and Gene Expression in Osteosarcoma
Cited by: 76
Author(s): Bekim Sadiković, Maisa Yoshimoto, Khaldoun Al-Romaih, Georges Maire, Maria Zieleńska, Jeremy A. Squire
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0096284

Network Identification of Hormonal Regulation
Cited by: 3
Author(s): Daniël J. Vis, Johan A. Westerhuis, Huub C. J. Hoefsloot, Ferdinand Roelfsema, J. van der Greef, Margriet M. W. B. Hendriks, Age K. Smilde
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0081994

X-Ray Solution Scattering of Squid Heavy Meromyosin: Strengthening the Evidence for an Ancient Compact off State
Cited by: 8
Author(s): Richard E. Gillilan, V. S. Senthil Kumar, E. O'Neall-Hennessey, Carolyn Cohen, Jerry H. Brown
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0080833

Characterisation of AmphiAmR11, an Amphioxus (Branchiostoma floridae) D2-Dopamine-Like G Protein-Coupled Receptor
Cited by: 4
Author(s): Asha L. Bayliss, Peter Evans
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0085139

Large Scale Identification and Categorization of Protein Sequences Using Structured Logistic Regression
Cited by: 12
Author(s): Bjørn Panyella Pedersen, Georgiana Ifrim, Poul Liboriussen, Kristian B. Axelsen, Michael G. Palmgren, Poul Nissen, Carsten Wiuf, Christian N. S. Pedersen
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0005519

Genome Degradation in Brucella ovis Corresponds with Narrowing of Its Host Range and Tissue Tropism
Cited by: 107
Author(s): Renée M. Tsolis, Rekha Seshadri, Renato L. Santos, Félix J. Sangari, Juan M. García Lobo, M. de Jong, Qinghu Ren, Garry Myers, Lauren Brinkac, Karen E. Nelson, Robert T. DeBoy, Samuel V. Angiuoli, Hoda Khouri, George Dimitrov, Jeffrey R. Robinson, Stephanie Mulligan, Richard L. Walker, Philip E. Elzer, Karl A. Hassan, Ian T. Paulsen
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0151481

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets
Cited by: 27
Author(s): Oskar E. Karlsson, Jenny Larsson, Juliette Hayer, Mikael Berg, Magdalena Jacobson
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0114089

Using Hidden Markov Models to Improve Quantifying Physical Activity in Accelerometer Data – A Simulation Study
Cited by: 20
Author(s): Vitali Witowski, Ronja Foraita, Yannis Pitsiladis, Iris Pigeot, Norman Wirsik
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0219775

Identification, expression, alternative splicing and functional analysis of pepper WRKY gene family in response to biotic and abiotic stresses
Cited by: 29
Author(s): Jun Zheng, Feng Liu, Zhu C, Xuefeng Li, Xiang Dai, Bo‐Yi Yang, Xuexiao Zou, Yanqing Ma
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0003551

Analyses and Comparison of Accuracy of Different Genotype Imputation Methods
Cited by: 122
Author(s): Yu‐Fang Pei, Jian Jian Li, Lei Zhang, Christopher J. Papasian, Hong‐Wen Deng
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0012483

A Score of the Ability of a Three-Dimensional Protein Model to Retrieve Its Own Sequence as a Quantitative Measure of Its Quality and Appropriateness
Cited by: 14
Author(s): León P. Martínez-Castilla, Rogelio Rodríguez-Sotrés
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0181443

Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.)
Cited by: 60
Author(s): Jian Ma, Yujie Yang, Wei Luo, Congcong Yang, Ping Ding, Yaxi Liu, Liang Qiao, Zhijian Chang, Hao Geng, Penghao Wang, Qiantao Jiang, Jirui Wang, Guoyue Chen, Yuming Wei, Youliang Zheng, Xiujin Lan
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0013472

Genome-Wide Identification of HrpL-Regulated Genes in the Necrotrophic Phytopathogen Dickeya dadantii 3937
Cited by: 26
Author(s): Shihui Yang, Peng Quan, Zhang Qiu, Lifang Zou, Yán Li, Christelle Robert, Leighton Pritchard, Hui Liu, Raymond Hovey, Qi Wang, Paul R. J. Birch, Ian K. Toth, Ching‐Hong Yang
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0013102

Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
Cited by: 767
Author(s): Hui Yao, Jingyuan Song, Chang Liu, Kun Luo, Jianping Han, Ying Liu, Xiaohui Pang, Xu Hong, Yingjie Zhu, Pei‐Gen Xiao, Shilin Chen
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0191308

Identification and expression analyses of WRKY genes reveal their involvement in growth and abiotic stress response in watermelon (Citrullus lanatus)
Cited by: 43
Author(s): Xiaozhen Yang, Hao Li, Yongchao Yang, Yongqi Wang, Yanling Mo, Ruimin Zhang, Yong Zhang, Junsheng Ma, Chunhua Wei, Xian Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0201240

Constructing a DNA barcode reference library for southern herbs in China: A resource for authentication of southern Chinese medicine
Cited by: 27
Author(s): Lu Gong, Xiaodi Qiu, Juan Huang, Wen Xu, Jun Bai, Jing Zhang, He Su, Chu Mei Xu, Zhihai Huang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0257392

Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat
Cited by: 2
Author(s): Muhammad Numan, Shazia Anwer Bukhari, Mujeeb ur Rehman, Ghulam Mustafa, Bushra Sadia
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0069865

Implementation Fidelity of the National Malaria Control Program in Burkina Faso
Cited by: 23
Author(s): Valéry Ridde, Thomas Druetz, Serge Poppy, Séni Kouanda, Slim Haddad
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0074936

Actin Structure-Dependent Stepping of Myosin 5a and 10 during Processive Movement
Cited by: 16
Author(s): Jianjun Bao, Daniel M Huck, Laura K. Gunther, James R. Sellers, Takeshi Sakamoto
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0084157

BOBA FRET: Bootstrap-Based Analysis of Single-Molecule FRET Data
Cited by: 28
Author(s): S. König, Mélodie C. A. S. Hadzic, E Fiorini, Richard Börner, Danny Kowerko, Wolf U. Blanckenhorn, Roland K. O. Sigel
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0234423

Identification, characterization and functional differentiation of the NAC gene family and its roles in response to cold stress in ginseng, Panax ginseng C.A. Meyer
Cited by: 15
Author(s): Lihe Qian, Chengfei Sun, Jiazhuang Han, Li Li, Kangyu Wang, Yanfang Wang, Jing Chen, Mingzhu Zhao, Yi Wang, Meiping Zhang
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0014753

Hidden Markov Model Analysis of Maternal Behavior Patterns in Inbred and Reciprocal Hybrid Mice
Cited by: 14
Author(s): Valeria Carola, Olivier Mirabeau, Cornelius Gross
Software Mentions: 1
Published: over 13 years ago

10.1186/s13578-021-00641-1

Elevated NTCP expression by an iPSC-derived human hepatocyte maintenance medium enhances HBV infection in NTCP-reconstituted HepG2 cells
Cited by: 3
Author(s): Xinlei Li, Zhaohui Xu, Bidisha Mitra, Minghang Wang, Haitao Guo, Zongdi Feng
Software Mentions: 1
Published: over 3 years ago

10.3390/cells10081974

UBE2L3, a Partner of MuRF1/TRIM63, Is Involved in the Degradation of Myofibrillar Actin and Myosin
Cited by: 9
Author(s): Dulce Peris-Moreno, Mélodie Malige, Agnès Claustre, Andrea M. Armani, Cécile Coudy‐Gandilhon, Christiane Deval, Daniel Béchet, Pierre Fafournoux, Marco Sandri, Lydie Combaret, Daniel Taillandier, Cécile Polge
Software Mentions: 1
Published: over 3 years ago

10.3390/cells9071590

Non-Muscle Myosin 2A (NM2A): Structure, Regulation and Function
Cited by: 34
Author(s): Cláudia Brito, Sandra Sousa
Software Mentions: 1
Published: over 4 years ago

10.3390/cells8020086

The Catalase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis
Cited by: 49
Author(s): Wei Wang, Yingying Cheng, Dongdong Chen, Dan Liu, Mengjiao Hu, Jie Dong, Xiaopei Zhang, Lirong Song, Fafu Shen
Software Mentions: 1
Published: almost 6 years ago

10.1155/2015/493769

Estimating Latent Attentional States Based on Simultaneous Binary and Continuous Behavioral Measures
Cited by: 3
Author(s): Zhe Chen
Software Mentions: 1
Published: almost 10 years ago

10.1155/2021/5770981

Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles
Cited by: 2
Author(s): Zhehan Shen, Taigang Liu, Ting Xu
Software Mentions: 1
Published: over 3 years ago

10.1155/2015/635437

Developing of the Computer Method for Annotation of Bacterial Genes
Cited by: 1
Author(s): Mikhail A. Golyshev, Eugene V. Korotkov
Software Mentions: 1
Published: almost 9 years ago

10.4054/DemRes.2019.41.50

Living arrangement dynamics of older adults in Mexico: Latent class analysis in an accelerated longitudinal design
Cited by: 4
Author(s): Curtis Huffman, Ricardo Regules-García, Delfino Vargas-Chanes
Software Mentions: 1
Published: almost 5 years ago

10.1002/ece3.4819

Use of hidden Markov capture–recapture models to estimate abundance in the presence of uncertainty: Application to the estimation of prevalence of hybrids in animal populations
Cited by: 10
Author(s): Nina Luisa Santostasi, Paolo Ciucci, Romolo Caniglia, Elena Fabbri, Luigi Molinari, Willy Reggioni, Olivier Giménez
Software Mentions: 1
Published: almost 6 years ago

10.1002/ece3.5254

Microbial communities across a hillslope‐riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock
Cited by: 19
Author(s): Adi Lavy, David Geller McGrath, Paula B. Matheus Carnevali, Jiamin Wan, Dong Wang, Tetsu K. Tokunaga, Brian C. Thomas, Kenneth H. Williams, Susan S. Hubbard, Jillian F. Banfield
Software Mentions: 1
Published: over 5 years ago

Projects: cran: HMM

Papers Mentioning HMM 577