cran: HMM | Projects | Ecosyste.ms: Papers

10.7717/peerj.11076

Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow (Salix matsudana)
Cited by: 12
Author(s): Jian Zhang, Shi zheng Shi, Yuna Jiang, Fei Zhong, Guoyuan Liu, Chunmei Yu, Bolin Lian, Yanhong Chen
Software Mentions: 2
Published: over 3 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/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

10.3389/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

10.3389/fpls.2015.01142

Foxtail Millet NF-Y Families: Genome-Wide Survey and Evolution Analyses Identified Two Functional Genes Important in Abiotic Stresses
Cited by: 64
Author(s): Feng Zheng, Guanhua He, Wenbin Zheng, Panpan Lu, Ming Chen, Yaming Gong, Yupo Ma, Zhao‐Shi Xu
Software Mentions: 2
Published: almost 9 years ago

10.1111/tpj.12734

Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage
Cited by: 144
Author(s): Ansgar Gruber, Gabrielle Rocap, Peter G. Kroth, E. Virginia Armbrust, Thomas Möck
Software Mentions: 2
Published: almost 10 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

10.3389/fpsyg.2020.513740

Modeling Human Morphological Competence
Cited by: 4
Author(s): Yohei Oseki, Alec Marantz
Software Mentions: 2
Published: about 4 years ago

10.3390/genes9040221

Genome-Wide Analyses of Calcium Sensors Reveal Their Involvement in Drought Stress Response and Storage Roots Deterioration after Harvest in Cassava
Cited by: 8
Author(s): Wei Hu, Yan Yan, Weiwei Tie, Zehong Ding, Chunlai Wu, Xuezhi Ding, Wenquan Wang, Zhiqiang Xia, Jiao Guo, Ming Peng
Software Mentions: 2
Published: over 6 years ago

10.3390/genes10020131

Evolution and Identification of the WRKY Gene Family in Quinoa (Chenopodium quinoa)
Cited by: 20
Author(s): Hong Yue, Xi Chang, Yongqiang Zhi, Lan Wang, Guangwei Xing, Weining Song, Xiaojun Nie
Software Mentions: 2
Published: almost 6 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

10.1093/gbe/evu130

Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods
Cited by: 40
Author(s): Francisca Cunha Almeida, Alejandro Sánchez-Gracia, José Luis Campos, Julio Rozas
Software Mentions: 2
Published: over 10 years ago

10.1093/gbe/evv126

A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed inEchinococcus multilocularisStem Cells
Cited by: 18
Author(s): Uriel Koziol, Santiago Radío, Pablo Smircich, Magdalena Zarowiecki, Cecilia Fernández, Klaus Brehm
Software Mentions: 2
Published: over 9 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

10.1093/gbe/evaa011

Origin Recognition Complex (ORC) Evolution Is Influenced by Global Gene Duplication/Loss Patterns in Eukaryotic Genomes
Cited by: 9
Author(s): Eduard Ocaña‐Pallarès, Zaida Vergara, Bénédicte Desvoyes, Manuel Tejada‐Jiménez, Ainoa Romero-Jurado, Aurora Galván, Emilio Fernández, Iñaki Ruiz‐Trillo, Crisanto Gutiérrez
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.0020131

Sampling Realistic Protein Conformations Using Local Structural Bias
Cited by: 100
Author(s): Thomas Hamelryck, John T. Kent, Anders Krogh
Software Mentions: 2
Published: about 18 years ago

10.1186/1745-7580-2-2

Cited by: 1,003
Author(s): Jacob Larsen, Ole Lund, Morten Nielsen
Software Mentions: 2
Published: almost 19 years ago

10.1371/journal.pcbi.1004991

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles
Cited by: 18
Author(s): Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph
Software Mentions: 2
Published: over 8 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

10.1186/1471-2105-12-345

BLProt: prediction of bioluminescent proteins based on support vector machine and relieff feature selection
Cited by: 33
Author(s): Krishna Kumar Kandaswamy, Ganesan Pugalenthi, Mehrnaz Khodam Hazrati, Kai‐Uwe Kalies, Thomas Martinetz
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pcbi.1006425

Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence
Cited by: 16
Author(s): Mạnh Cường Ngô, Mads Peter Heide‐Jørgensen, Susanne Ditlevsen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1003847

KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features
Cited by: 266
Author(s): Carolina Arias, Ben Weisburd, Noam Stern-Ginossar, Alexandre Mercier, Alexis S. Madrid, Priya Bellare, Meghan Holdorf, Jonathan S. Weissman, Don Ganem
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12870-020-02345-z

Identification of NHXs in Gossypium species and the positive role of GhNHX1 in salt tolerance
Cited by: 27
Author(s): Lu Long, Jing-Ruo Zhao, Dandan Guo, Xiaonan Ma, Fuchun Xu, Wenwen Yang, Wei Gao
Software Mentions: 2
Published: over 4 years ago

10.1038/srep12525

Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei
Cited by: 60
Author(s): Fernando E. Vega, Stuart M. Brown, Hao Chen, Eric Shen, Mridul Nair, Javier A. Ceja-Navarro, Eoin L. Brodie, Francisco Infante, Patrick F. Dowd, Arnab Pain
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1003272

Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica
Cited by: 161
Author(s): Rays H. Y. Jiang, Irene de Bruijn, Brian J. Haas, Rodrigo Belmonte, Lars Löbach, James Christie, Guido Van den Ackerveken, Arnaud Bottin, Vincent Bulone, Sara M. Díaz-Moreno, Bernard Dumas, Fan Lin, Elodie Gaulin, F. Govers, Laura J. Grenville‐Briggs, Neil R. Horner, Joshua Z. Levin, Marco Mammella, H.J.G. Meijer, Paul F. Morris, Chad Nusbaum, Stan Oome, Andrew J. Phillips, David van Rooyen, Elzbieta Rzeszutek, Márcia Saraiva, Chris J. Secombes, Michael Seidl, Berend Snel, Joost H. M. Stassen, Sean M. Sykes, Sucheta Tripathy, Herbert van den Berg, Julio Vega-Arreguín, Stephan Wawra, Sarah Young, Qiandong Zeng, Javier Diéguez‐Uribeondo, Carsten Russ, Brett M. Tyler, Pieter van West
Software Mentions: 2
Published: over 11 years ago

10.1186/s12870-014-0329-9

Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case
Cited by: 19
Author(s): David Amar, Itziar Frades, Agnieszka Danek, Tatyana Goldberg, Sanjeev Sharma, Pete E. Hedley, Estelle Proux‐Wéra, Erik Andréasson, Ron Shamir, Oren Tzfadia, Erik Alexandersson
Software Mentions: 2
Published: almost 10 years ago

10.1186/1756-0500-7-483

HMM-ModE: implementation, benchmarking and validation with HMMER3
Cited by: 11
Author(s): Swati Sinha, Andrew M. Lynn
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep38433

EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm
Cited by: 39
Author(s): Seong‐Gon Kim, Mrudul Harwani, Ananth Grama, Somali Chaterji
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep41923

A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis
Cited by: 8
Author(s): Zheng Yang, Helen L. Bullifent, Karen Moore, Konrad Paszkiewicz, Richard J. Saint, Stephanie J. Southern, Olivia L. Champion, Nicola J. Senior, Mitali Sarkar‐Tyson, Petra C. F. Oyston, Timothy P. Atkins, Richard W. Titball
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-05656-8

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-elicited effects on bile acid homeostasis: Alterations in biosynthesis, enterohepatic circulation, and microbial metabolism
Cited by: 60
Author(s): Kelly A. Fader, Rance Nault, Chen Zhang, Kazuyoshi Kumagai, Jack R. Harkema, Timothy R. Zacharewski
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-12961-9

Forecasting the onset and course of mental illness with Twitter data
Cited by: 240
Author(s): Andrew Reece, Andrew J. Reagan, Katharina Lix, Peter Sheridan Dodds, Christopher M. Danforth, Ellen J. Langer
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-13513-x

Involvement of Ubiquitin-Conjugating Enzyme (E2 Gene Family) in Ripening Process and Response to Cold and Heat Stress of Vitis vinifera
Cited by: 16
Author(s): Yingying Gao, Yi Wang, H. P. Xin, Shaohua Li, Zhenchang Liang
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-23307-4

Haplotype Heritability Mapping Method Uncovers Missing Heritability of Complex Traits
Cited by: 12
Author(s): Masoud Shirali, Sara Knott, Ricardo Pong‐Wong, Pau Navarro, C.S. Haley
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0118479

Flower Bud Transcriptome Analysis of Sapium sebiferum (Linn.) Roxb. and Primary Investigation of Drought Induced Flowering: Pathway Construction and G-Quadruplex Prediction Based on Transcriptome
Cited by: 21
Author(s): Minglei Yang, Ying Wu, Shiwei Jin, Jinyan Hou, Yingji Mao, Wenbo Liu, Yangcheng Shen, Lifang Wu
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-018-27789-0

Comprehensive in-silico prediction of damage associated SNPs in Human Prolidase gene
Cited by: 21
Author(s): Richa Bhatnager, Amita Suneja Dang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0181551

Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain
Cited by: 8
Author(s): Amélie Wallenhammar, Madhanagopal Anandapadamanaban, Alexander Lemak, Claudio Mirabello, Patrik Lundström, Björn Wallner, Maria Sunnerhagen
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-35590-2

Reconstructing the evolutionary history of F420-dependent dehydrogenases
Cited by: 17
Author(s): María Laura Mascotti, Hemant Kumar, Quốc Thái Nguyễn, Maximiliano Juri Ayub, Marco W. Fraaije
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0160336

Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation
Cited by: 100
Author(s): Lianfu Chen, Yuhua Gong, Yingli Cai, Wei Liu, Yan Zhou, Yang Xiao, Zhangyi Xu, Liang Yin, Xiaoyu Lei, Jinjie Wang, Mengpei Guo, Xiaolong Ma
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-14-807

A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi
Cited by: 27
Author(s): Jana Sperschneider, Donald M. Gardiner, Jennifer Taylor, James K. Hane, Karam B. Singh, John M. Manners
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12859-016-1430-x

GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants
Cited by: 6
Author(s): Katrin Tebel, Vivien Boldt, Anne Steininger, Matthias Port, Grit Ebert, Reinhard Ullmann
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0093907

MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data
Cited by: 92
Author(s): Ankit Gupta, Rohan Kapil, Darshan B. Dhakan, Vineet K. Sharma
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-10-641

Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
Cited by: 157
Author(s): Haley F. Oliver, Renato H. Orsi, Lalit Ponnala, Uri Keich, Wei Wang, Qi Sun, Samuel Cartinhour, Melanie J. Filiatrault, Martin Wiedmann, Kathryn J. Boor
Software Mentions: 2
Published: almost 15 years ago

10.1038/s41598-021-81969-z

Genomic analysis of WD40 protein family in the mango reveals a TTG1 protein enhances root growth and abiotic tolerance in Arabidopsis
Cited by: 17
Author(s): Lin Tan, Haron Salih, Nwe Ni Win Htet, Farrukh Azeem, Rulin Zhan
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-92992-5

The measurement, evolution, and neural representation of action grammars of human behavior
Cited by: 16
Author(s): Dietrich Stout, Thierry Chaminade, Jan Apel, Ali Shafti, A. Aldo Faisal
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0081207

Analysis and Phylogeny of Small Heat Shock Proteins from Marine Viruses and Their Cyanobacteria Host
Cited by: 50
Author(s): Halim Maaroufi, Robert M. Tanguay
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0232756

Genome-wide identification of mitogen-activated protein kinase (MAPK) cascade and expression profiling of CmMAPKs in melon (Cucumis melo L.)
Cited by: 8
Author(s): Xiaolan Zhang, Yuepeng Li, Qiaojuan Xing, Lingqi Yue, Hongyan Qi
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-020-6699-5

The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora
Cited by: 17
Author(s): Ho Wen Yang, Menghao Yu, Jae Hoon Lee, Tiyakhon Chatnaparat, Youfu Zhao
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/bts403

Decoding properties of tRNA leave a detectable signal in codon usage bias
Cited by: 8
Author(s): Alexander Röth
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0101605

The Metagenomic Telescope
Cited by: 7
Author(s): Balázs Szalkai, Ildikó Scheer, Krisztina Nagy, Beáta G. Vértessy, Vince Grolmusz
Software Mentions: 2
Published: over 10 years ago

10.3390/s20020527

Applying Movement Constraints to BLE RSSI-Based Indoor Positioning for Extracting Valid Semantic Trajectories
Cited by: 15
Author(s): Hani Ramadhan, Yoga Yustiawan, Joonho Kwon
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0240511

Reading Akkadian cuneiform using natural language processing
Cited by: 7
Author(s): Shai Gordin, Gai Gutherz, Ariel Elazary, Avital Romach, Enrique Jiménez, Jonathan Berant, Yoram Cohen
Software Mentions: 2
Published: about 4 years ago

10.1128/mBio.01339-17

Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum
Cited by: 99
Author(s): Victoria E. Sepúlveda, Roberto Márquez, David A. Turissini, William E. Goldman, Daniel R. Matute
Software Mentions: 2
Published: almost 7 years ago

10.1128/mBio.02119-17

The Ancient Link between G-Protein-Coupled Receptors and C-Terminal Phospholipid Kinase Domains
Cited by: 13
Author(s): Johan van den Hoogen, H.J.G. Meijer, Michael Seidl, F. Govers
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-018-4832-5

Grafting or pruning in the animal tree: lateral gene transfer and gene loss?
Cited by: 20
Author(s): Julie C. Dunning Hotopp
Software Mentions: 2
Published: over 6 years ago

10.1128/mSphere.00140-18

The Lactobacillus Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation
Cited by: 67
Author(s): Sarah O’Flaherty, Alexandra B. Crawley, Casey M. Theriot, Rodolphe Barrangou
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.00065-18

Genomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains
Cited by: 29
Author(s): Angela Peña-Gonzalez, Luis M. Rodriguez-R, Chung K. Marston, Jay E. Gee, Christopher A. Gulvik, Cari B. Kolton, Elke Saile, Michael Frace, Alex R. Hoffmaster, Konstantinos T. Konstantinidis
Software Mentions: 2
Published: about 6 years ago

10.1038/s41396-020-0650-2

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant
Cited by: 77
Author(s): Emilie Spasov, Jackson M. Tsuji, Laura Hug, Andrew C. Doxey, Laura A. Sauder, Wayne Parker, Josh D. Neufeld
Software Mentions: 2
Published: over 4 years ago

10.1038/ismej.2013.59

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
Cited by: 177
Author(s): Pascal Hingamp, Nigel Grimsley, Silvia G. Acinas, Camille Clérissi, Lucie Subirana, Julie Poulain, Isabel Ferrera, Hugo Sarmento, Emilie Villar, Gipsi Lima‐Mendez, Karoline Faust, Shinichi Sunagawa, Jean‐Michel Claverie, Hervé Moreau, Yves Desdevises, Peer Bork, Jeroen Raes, Colomban de Vargas, Eric Karsenti, Stefanie Kandels‐Lewis, Olivier Jaillon, Fabrice Not, Stéphane Pesant, Patrick Wincker, Hiroyuki Ogata
Software Mentions: 2
Published: over 11 years ago

10.3390/jof7080600

Transcription Factors in the Fungus Aspergillus nidulans: Markers of Genetic Innovation, Network Rewiring and Conflict between Genomics and Transcriptomics
Cited by: 6
Author(s): Oier Etxebeste
Software Mentions: 2
Published: over 3 years ago

10.3390/jof7080679

Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition
Cited by: 1
Author(s): Pan-Meng Wang, Jianping Xu, Gang Wu, Liu TieZhi, Zhu L. Yang
Software Mentions: 2
Published: about 3 years ago

10.1155/2019/1429316

Transcriptomic Evidence of Adaptive Evolution of the Epiphytic Fern Asplenium nidus
Cited by: 6
Author(s): Jiao Zhang, Li Liu, Jiang-Ping Shu, Dongmei Jin, Hui Shen, Hongfeng Chen, Rui Zhang, Yue‐Hong Yan
Software Mentions: 2
Published: almost 5 years ago

10.1155/2017/1707231

Evolution of the Apicomplexan Sugar Transporter Gene Family Repertoire
Cited by: 3
Author(s): Ousman Mahmud, Jessica C. Kissinger
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0167216

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures
Cited by: 10
Author(s): Senta Heiss-Blanquet, Françoise Fayolle-Guichard, Vincent Lombard, Agnès Hébert, Pedro M. Coutinho, Alexis Groppi, Annick Barre, Bernard Henrissat
Software Mentions: 2
Published: almost 8 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

10.7554/eLife.45530

The genetic factors of bilaterian evolution
Cited by: 38
Author(s): Peter Heger, Wen Zheng, Anna Rottmann, Kristen A. Panfilio, Thomas Wiehe
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms140815423

Detecting and Comparing Non-Coding RNAs in the High-Throughput Era
Cited by: 21
Author(s): Giovanni Bussotti, Cédric Notredame, Anton J. Enright
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms19082191

Mesotheliomas in Genetically Engineered Mice Unravel Mechanism of Mesothelial Carcinogenesis
Cited by: 10
Author(s): Didier Jean, Marie‐Claude Jaurand
Software Mentions: 2
Published: over 6 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

10.3390/ijms20235948

Genome-Wide Analysis of the FABP Gene Family in Liver of Chicken (Gallus gallus): Identification,Dynamic Expression Profile, and RegulatoryMechanism
Cited by: 18
Author(s): Zhang Wang, Yaxin Yue, Zi-Ming Liu, Liyu Yang, Hong Li, Zhuanjian Li, Guoxi Li, Yanbin Wang, Yadong Tian, Xin Kang, Xiaojun Liu
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms21144905

Genome-Wide Identification and Expression Profile Analysis of the PHT1 Gene Family in Gossypium hirsutum and Its Two Close Relatives of Subgenome Donor Species
Cited by: 4
Author(s): Sheng Cai, Fujie Liu, Baoliang Zhou
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21175987

Molecular Evolutionary and Expression Pattern Analysis of AKR Genes Shed New Light on GalUR Functional Characteristics in Brassica rapa
Cited by: 3
Author(s): Weike Duan, Zhinan Huang, Ying Liu, Xiaoming Song, Xiaochuan Sun, Can Jin, Yunpeng Wang, Jizhong Wang
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22083914

Fish-Ing for Enhancers in the Heart
Cited by: 2
Author(s): Costantino Parisi, Shikha Vashisht, Cecilia Lanny Winata
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-9-S1-S8

HMMEditor: a visual editing tool for profile hidden Markov model
Cited by: 14
Author(s): Jianyong Dai, Jianlin Cheng
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2164-14-700

Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods
Cited by: 17
Author(s): Choumouss Kamoun, Thibaut Payen, Aurélie Hua-Van, Jonathan Filée
Software Mentions: 2
Published: about 11 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

10.1515/biol-2021-0063

In silico analysis of glycosyltransferase 2 family genes in duckweed (Spirodela polyrhiza) and its role in salt stress tolerance
Cited by: 0
Author(s): Meiqin Jiang, Peng Wang, Ligang Xu, Xiuxu Ye, Hongxiang Fan, Junxiang Cheng, Jinting Chen
Software Mentions: 2
Published: almost 4 years ago

10.3390/s19143216

Detecting Anomalies of Satellite Power Subsystem via Stage-Training Denoising Autoencoders
Cited by: 10
Author(s): Weihua Jin, Bo Sun, Zhidong Liu, Shijie Zhang, Zhonggui Chen
Software Mentions: 1
Published: over 5 years ago

10.3390/toxins9040135

Protein Discovery: Combined Transcriptomic and Proteomic Analyses of Venom from the Endoparasitoid Cotesia chilonis (Hymenoptera: Braconidae)
Cited by: 34
Author(s): Ziwen Teng, Shijiao Xiong, Gang Xu, Shi-Yu Gan, Xuan Chen, David Stanley, Zhichao Yan, Gōngyín Yè, Qi Fang
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.00166-16

Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis
Cited by: 81
Author(s): Lee Bergstrand, Erick Cardenas, Johannes Holert, Jonathan D. Van Hamme, William W. Mohn
Software Mentions: 1
Published: over 8 years ago

10.1128/mBio.01498-15

Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela , an Endosymbiotic Kinetoplastid
Cited by: 29
Author(s): Vojtěch David, Pavel Flegontov, Evgeny S. Gerasimov, Goro Tanifuji, Hassan Hashimi, Maria D. Logacheva, Shinichiro Maruyama, Naoko T. Onodera, Michael W. Gray, John M. Archibald, Julius Lukeš
Software Mentions: 1
Published: almost 9 years ago

10.1128/mSphere.00408-17

Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal
Cited by: 63
Author(s): Jamie McGowan, David A. Fitzpatrick
Software Mentions: 1
Published: almost 7 years ago

10.1128/mSystems.00070-19

Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways
Cited by: 48
Author(s): Yusuke Minato, Daryl M. Gohl, Joshua M. Thiede, Jeremy M. Chacón, William R. Harcombe, Fumito Maruyama, Anthony D. Baughn
Software Mentions: 1
Published: about 5 years ago

10.1107/S2052252519016634

Evidence for binary Smc complexes lacking kite subunits in archaea
Cited by: 1
Author(s): Jae Heung Jeon, Han Sol Lee, Hang‐Sik Shin, Mi Jeong Kwak, Yeon-Gil Kim, Stephan Gruber, Byung‐Ha Oh
Software Mentions: 1
Published: almost 5 years ago

10.3390/jof6030131

Exploring the Extracellular Macromolecular Composition of Crude Extracts of Penicillium rubens Strain 212 for Elucidation Its Mode of Action as a Biocontrol Agent
Cited by: 0
Author(s): María Alejandra Carreras, Eduardo A. Espeso, Alba Gutiérrez-Docio, Silvia Moreno-Fernández, Marín Pródanov, María Dolores Hernando, P. Melgarejo, Inmaculada Larena
Software Mentions: 1
Published: over 4 years ago

10.1155/2021/8899263

Software Defect Prediction for Healthcare Big Data: An Empirical Evaluation of Machine Learning Techniques
Cited by: 24
Author(s): Bilal Khan, Rashid Naseem, Muhammad Arif Shah, Karzan Wakil, Atif Khan, M. Irfan Uddin, Marwan Mahmoud
Software Mentions: 1
Published: over 3 years ago

10.1007/s00232-021-00176-z

Unveiling the Dynamics of KRAS4b on Lipid Model Membranes
Cited by: 3
Author(s): César A. López, Animesh Agarwal, Que N. Van, Andrew Stephen, S. Gnanakaran
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.66057

Differential dopaminergic modulation of spontaneous cortico–subthalamic activity in Parkinson’s disease
Cited by: 9
Author(s): Abhinav Sharma, Diego Vidaurre, Jan Vesper, Alfons Schnitzler, Esther Florin
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms15045472

Effect of Wnt3a on Keratinocytes Utilizing in Vitro and Bioinformatics Analysis
Cited by: 2
Author(s): Ju Suk Nam, Chiranjib Chakraborty, Ashish Ranjan Sharma, Young Her, Kee Jeong Bae, Garima Sharma, George Priya Doss, Sang Soo Lee, Misun Hong, Dong Keun Song
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms17040556

Prediction of Toxin Genes from Chinese Yellow Catfish Based on Transcriptomic and Proteomic Sequencing
Cited by: 13
Author(s): Bing Xie, Xiaofeng Li, Zhilong Lin, Zhiqiang Ruan, Min Wang, Jie Liu, Ting Tong, Jia Li, Yu Huang, Bo Wen, Yu Sun, Qiong Shi
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms19061598

Genome-Wide Screening and Characterization of the Dof Gene Family in Physic Nut (Jatropha curcas L.)
Cited by: 13
Author(s): Peipei Wang, Jing Li, Xiaotong Gao, Di Zhang, Anlin Li, Changning Liu
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms19071863

Do Actomyosin Single-Molecule Mechanics Data Predict Mechanics of Contracting Muscle?
Cited by: 27
Author(s): Alf Månsson, Marko Ušaj, Luisa Moretto, Dilson E. Rassier
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms19092510

Genome-Wide Bioinformatics Analysis of MAPK Gene Family in Kiwifruit (Actinidia Chinensis)
Cited by: 20
Author(s): Wang Gang, Tao Wang, Zhemin Jia, Jinsong Xuan, Pan Delin, Xuehua Zhang, Jiyu Zhang
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms20020251

Genome-Wide Characterization and Identification of Trihelix Transcription Factor and Expression Profiling in Response to Abiotic Stresses in Rice (Oryza sativa L.)
Cited by: 32
Author(s): Jiaming Li, Minghui Zhang, Jian Sun, Xinrui Mao, Jing Wang, Jingguo Wang, Hualong Liu, Hongliang Zheng, Zhen Zhen, Hongwei Zhao, Detang Zou
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms20020262

Investigation of the AQP Family in Soybean and the Promoter Activity of TIP2;6 in Heat Stress and Hormone Responses
Cited by: 22
Author(s): Feng Zheng, Na Liu, Gu-Wen Zhang, Fuge Niu, Shengchun Xu, Yaming Gong
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms221810128

Genome-Wide Identification MIKC-Type MADS-Box Gene Family and Their Roles during Development of Floral Buds in Wheel Wingnut (Cyclocarya paliurus)
Cited by: 5
Author(s): Yinquan Qu, Weilong Kong, Qian Wang, Xiangxiang Fu
Software Mentions: 1
Published: about 3 years ago

10.3390/ijms221910350

Pseudomonas Phage MD8: Genetic Mosaicism and Challenges of Taxonomic Classification of Lambdoid Bacteriophages
Cited by: 6
Author(s): Peter Evseev, Anna A. Lukianova, Н. Н. Сыкилинда, Anna Gorshkova, Alexander A. Bondar, Mikhail M. Shneider, Мarsel R. Kabilov, Valentin Drucker, Konstantin A. Miroshnikov
Software Mentions: 1
Published: about 3 years ago

10.1111/jnc.12462

A conserved sequence in calmodulin regulated spectrin‐associated protein 1 links its interaction with spectrin and calmodulin to neurite outgrowth
Cited by: 25
Author(s): Mikayala D.A. King, Gareth W. Phillips, Paola A. Bignone, Nandini V. L. Hayes, Jennifer C. Pinder, Anthony J. Baines
Software Mentions: 1
Published: about 11 years ago

10.1186/1743-0003-8-66

Rehabilitation of gait after stroke: a review towards a top-down approach
Cited by: 411
Author(s): Juan Manuel Belda Lois, Silvia Mena-del Horno, Ignacio Bermejo-Bosch, Juan C. Moreno, José L Pons, Dario Farina, Marco Iosa, Marco Molinari, Federica Tamburella, Ander Ramos, Andrea Caria, Teodoro Solis‐Escalante, Clemens Brunner, Massimiliano Rea
Software Mentions: 1
Published: almost 14 years ago

10.1093/dnares/dst056

Comprehensive Expression Analysis of Rice Armadillo Gene Family During Abiotic Stress and Development
Cited by: 55
Author(s): Manisha Sharma, Amarjeet Singh, Alka Shankar, Amita Pandey, Vinay Kumar Baranwal, Sanjay Kapoor, Akhilesh K. Tyagi, Girdhar K. Pandey
Software Mentions: 1
Published: almost 11 years ago

Projects: cran: HMM

Papers Mentioning HMM 577