Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: hmm
https://packages.ecosyste.ms/registries/pypi.org/packages/hmm
Functions for inference on HMMs
1 version
Latest release: over 7 years ago
2,622 downloads last month
Papers Mentioning hmm 55
10.1371/journal.pone.0257047
Off-chip prefetching based on Hidden Markov Model for non-volatile memory architecturesCited by: 0
Author(s): Adrián Lamela, Óscar G. Ossorio, Guillermo Vinuesa, Benjamín Sahelices
Software Mentions: 10
Published: about 3 years ago
10.1038/srep30794
Genome-wide Identification and Structural, Functional and Evolutionary Analysis of WRKY Components of MulberryCited by: 33
Author(s): Vinay Kumar Baranwal, Nisha Negi, Paramjit Khurana
Software Mentions: 7
Published: over 8 years ago
10.1186/s13100-019-0156-5
Subtype classification and functional annotation of L1Md retrotransposon promotersCited by: 15
Author(s): Meng Zhou, Andrew D. Smith
Software Mentions: 6
Published: over 5 years ago
10.1186/s13068-018-1036-9
Genome-resolved metagenomics of sugarcane vinasse bacteriaCited by: 16
Author(s): Noriko A. Cassman, Késia Silva Lourenço, Janaína Braga do Carmo, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 6
Published: almost 7 years ago
10.1371/journal.pgen.1009038
Selection and hybridization shaped the rapid spread of African honey bee ancestry in the AmericasCited by: 40
Author(s): Erin Calfee, Marcelo Nicolás Agra, María Alejandra Palacio, Santiago R. Ramírez, Graham Coop
Software Mentions: 6
Published: about 4 years ago
10.1128/mSystems.00385-21
Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid SoilCited by: 22
Author(s): Yunha Hwang, Janina Rahlff, Dirk Schulze‐Makuch, Michael Schloter, Alexander J. Probst
Software Mentions: 6
Published: over 3 years ago
10.3389/fpls.2018.00018
Genome-Wide Identification of Cyclic Nucleotide-Gated Ion Channel Gene Family in Wheat and Functional Analyses of TaCNGC14 and TaCNGC16Cited by: 37
Author(s): Jia Guo, Md. Ashraful Islam, Haocheng Lin, Changan Ji, Yinghui Duan, Peng Liu, Qingdong Zeng, Brad Day, Zhensheng Kang, Jun Guo
Software Mentions: 5
Published: almost 7 years ago
10.1093/g3journal/jkab074
MultiPhATE2: code for functional annotation and comparison of phage genomesCited 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
10.1186/1471-2164-15-946
Conservation analysis of the CydX protein yields insights into small protein identification and evolutionCited 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
10.1534/g3.119.400617
Population Selection and Sequencing of<i>Caenorhabditis elegans</i>Wild Isolates Identifies a Region on Chromosome III Affecting Starvation ResistanceCited by: 21
Author(s): Amy K. Webster, Anthony Hung, Brad T. Moore, Ryan Guzman, James M. Jordan, Rebecca E. W. Kaplan, Jonathan D. Hibshman, Robyn E. Tanny, Daniel E. Cook, Erik C. Andersen, L. Ryan Baugh
Software Mentions: 4
Published: about 5 years ago
10.1016/j.envsoft.2018.02.011
Modelling background air pollution exposure in urban environments: Implications for epidemiological researchCited by: 27
Author(s): Álvaro Gómez-Losada, José C.M. Pires, Rafael Pino‐Mejías
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-020-07100-0
Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificusCited by: 16
Author(s): Marina Athanasouli, Hanh Witte, Christian Weiler, Tobias Loschko, Gabi Eberhardt, Ralf J. Sommer, Christian Rödelsperger
Software Mentions: 4
Published: about 4 years ago
10.1186/gb-2008-9-1-r7
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced AlignmentsCited by: 2,092
Author(s): Brian J. Haas, Steven L. Salzberg, Wei Zhu, Mihaela Pertea, Jonathan Allen, Joshua Orvis, Owen White, C. Robin Buell, Jennifer Wortman
Software Mentions: 4
Published: almost 17 years ago
10.1038/s41598-019-40659-7
Genome-wide Analysis of bZIP Transcription Factors in wheat and Functional Characterization of a TabZIP under Abiotic StressCited by: 70
Author(s): Pragya Agarwal, Vinay Kumar Baranwal, Paramjit Khurana
Software Mentions: 3
Published: over 5 years ago
10.1155/2015/813047
<i>In Silico</i>Identification of Highly Conserved Epitopes of Influenza A H1N1, H2N2, H3N2, and H5N1 with Diagnostic and Vaccination PotentialCited by: 17
Author(s): José Esteban Muñoz-Medina, Carlos Javier Sánchez-Vallejo, Alfonso Méndez‐Tenorio, Irma Eloísa Monroy-Muñoz, Javier Ángeles-Martínez, Andrea Santos Coy-Arechavaleta, Clara Esperanza Santacruz-Tinoco, Joaquín González-Ibarra, Yu-Mei Anguiano-Hernández, César González-Bonilla, Eva Ramón-Gallegos, José Alberto Díaz-Quiñonez
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12864-021-07828-3
The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stressCited by: 9
Author(s): Weihua Su, Chang Zhang, Dongjiao Wang, Yongjuan Ren, Tingting Sun, Jingfang Feng, Yachun Su, Liping Xu, Mutian Shi, Youxiong Que
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-021-07689-w
Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress responseCited by: 13
Author(s): Yuan Yuan, Xiping Yang, Mengfan Feng, Hongyan Ding, Muhammad Tahir Khan, Jisen Zhang, Muqing Zhang
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-019-6389-3
Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stressesCited by: 13
Author(s): Qi Yang, Xiaocui Niu, Xiao-Li Tian, Xiujuan Zhang, Jingyu Cong, Ruigang Wang, Guosheng Zhang, G. Li
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12864-018-4680-3
Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticityCited by: 48
Author(s): Paula Moolhuijzen, Pao Theen See, James K. Hane, Gongjun Shi, Zhaohui Liu, Richard P. Oliver, Caroline S. Moffat
Software Mentions: 2
Published: over 6 years ago
10.1186/s12864-018-5214-8
Comparative genomics of downy mildews reveals potential adaptations to biotrophyCited by: 42
Author(s): Kyle Fletcher, Steven J. Klosterman, Lida Derevnina, Frank N. Martin, Lien Bertier, S. T. Koike, Sebastian Reyes-Chin-Wo, Beiquan Mou, Richard W. Michelmore
Software Mentions: 2
Published: almost 6 years ago
10.3390/v13050928
Phage Biocontrol of Pseudomonas aeruginosa in WaterCited by: 10
Author(s): Ari Kauppinen, Sallamaari Siponen, Tarja Pitkänen, Karin Holmfeldt, Anna Pursiainen, Eila Torvinen, Ilkka T. Miettinen
Software Mentions: 2
Published: over 3 years ago
10.3390/plants8080275
Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus)Cited by: 7
Author(s): Shijiang Cao, Han Cheng, Jiashuo Zhang, Mohammad Aslam, Mei Yan, Anqi Hu, Lili Lin, Simon Peter Ojolo, Hui Zhao, S. V. G. N. Priyadarshani, Yu Yu, Gaoshao Cao, Yuan Qin
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pgen.1003272
Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasiticaCited 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
10.1371/journal.pone.0194487
The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasitesCited by: 24
Author(s): Goro Tanifuji, Shun Takabayashi, Keitaro Kume, Mizue Takagi, Takuro Nakayama, Ryoma Kamikawa, Yuji Inagaki, Takeji Hashimoto
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0189738
The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebeesCited by: 21
Author(s): Paul Schmid‐Hempel, Markus Aebi, Seth M. Barribeau, Toshihiko Kitajima, Louis du Plessis, Regula Schmid‐Hempel, Stefan Zoller
Software Mentions: 2
Published: almost 7 years ago
10.12688/f1000research.18776.2
RVDB-prot, a reference viral protein database and its HMM profilesCited by: 37
Author(s): Thomas Bigot, Sarah Temmam, Philippe Pérot, Marc Éloit
Software Mentions: 2
Published: about 4 years ago
10.3389/fmicb.2015.00440
The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elementsCited by: 61
Author(s): Raheleh Sheibani-Tezerji, Muhammad Naveed, Marc-André Jehl, Angela Sessitsch, Thomas Rattei, Birgit Mitter
Software Mentions: 2
Published: over 9 years ago
10.3389/fnins.2018.00603
Task-Evoked Dynamic Network Analysis Through Hidden Markov ModelingCited by: 117
Author(s): Andrew Quinn, Diego Vidaurre, Romesh Abeysuriya, Robert Becker, Anna C. Nobre, Mark W. Woolrich
Software Mentions: 2
Published: about 6 years ago
10.1093/gbe/evv079
Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless BeesCited by: 48
Author(s): Daniel Tamarit, Kirsten Ellegaard, Johan Wikander, Tobias Olofsson, Alejandra Vásquez, Siv G. E. Andersson
Software Mentions: 2
Published: over 9 years ago
10.1128/JB.00639-19
Nisin J, a Novel Natural Nisin Variant, Is Produced by Staphylococcus capitis Sourced from the Human Skin MicrobiotaCited by: 44
Author(s): Julie N O'Sullivan, Paula M. O’Connor, Mary C. Rea, Órla O’Sullivan, Calum J. Walsh, Brian Healy, Harsh Mathur, Des Field, Colin Hill, R. Paul Ross
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41396-020-00750-8
Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soilsCited by: 18
Author(s): Andrew T. Giguere, Stephanie A. Eichorst, Dimitri V. Meier, Craig W. Herbold, Andreas Richter, Chris Greening, Dagmar Woebken
Software Mentions: 2
Published: about 4 years ago
10.7554/eLife.54532
Deep evolutionary analysis reveals the design principles of fold A glycosyltransferasesCited by: 47
Author(s): Rahil Taujale, Aarya Venkat, Liang-Chin Huang, Zhongliang Zhou, Wayland Yeung, Khaled Rasheed, Sheng Li, Arthur S. Edison, Kelley W. Moremen, Natarajan Kannan
Software Mentions: 2
Published: over 4 years ago
10.3390/microorganisms8040554
Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for BioremediationCited by: 10
Author(s): Luz Breton‐Deval, Ayixón Sánchez-Reyes, Alejandro Sánchez-Flores, Katy Juárez, Ilse Salinas-Peralta, Patricia Mussali-Galante
Software Mentions: 1
Published: over 4 years ago
10.3390/toxins9080234
Venomics of Remipede Crustaceans Reveals Novel Peptide Diversity and Illuminates the Venom’s Biological RoleCited by: 27
Author(s): Björn M. von Reumont, Eivind A.B. Undheim, Robin-Tobias Jauss, Ronald A. Jenner
Software Mentions: 1
Published: over 7 years ago
10.21315/tlsr2018.29.1.3
Genome Organization of Escherichia Phage YD-2008.s: A New Entry to Siphoviridae FamilyCited by: 2
Author(s): Dharmela Sellvam, Nyok-Sean Lau, Yahya Mat Arip
Software Mentions: 1
Published: almost 7 years ago
10.1186/s12864-016-2556-y
Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution systemCited by: 39
Author(s): Lin Kang, Dau Dayal Aggarwal, Eugenia Rashkovetsky, Abraham B. Korol, Pawel Michalak
Software Mentions: 1
Published: over 8 years ago
10.3389/fphys.2020.594845
Genome Mining and Expression Analysis of Carboxylesterase and Glutathione S-Transferase Genes Involved in Insecticide Resistance in Eggplant Shoot and Fruit Borer, Leucinodes orbonalis (Lepidoptera: Crambidae)Cited by: 7
Author(s): B Kariyanna, A. Prabhuraj, R. Asokan, Aditi Agrawal, R. Gandhi Gracy, Poonam Jyoti, T. Venkatesan, M. Bheemanna, Basavaraj Kalmath, J. R. Diwan, Y. Pampanna, M. Mohan
Software Mentions: 1
Published: about 4 years ago
10.3389/fpls.2018.00161
Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri)Cited by: 68
Author(s): Xin Qiao, Hong Yin, Leiting Li, Runze Wang, Juyou Wu, Shaoling Zhang
Software Mentions: 1
Published: almost 7 years ago
10.1128/MRA.00779-20
Complete Genome Sequence of<i>Sulfitobacter</i>Phage ϕGT1, Isolated from a Tidal FlatCited by: 2
Author(s): Chung Yeon Hwang, Yirang Cho, Gwang Il Jang, Byung C. Cho, Stephen C. Hardies
Software Mentions: 1
Published: over 4 years ago
10.1186/1475-2859-10-30
Characterization of a cryptic plasmid pSM429 and its application for heterologous expression in psychrophilic PseudoalteromonasCited by: 16
Author(s): Dian‐Li Zhao, Zichao Yu, Ping‐Yi Li, Zhaoyu Wu, Xiu-Lan Chen, Mei Shi, Yong Yu, Bo Chen, Biao Zhou, Yuzhong Zhang
Software Mentions: 1
Published: over 13 years ago
10.1242/bio.036137
Evolution and multiple origins of zona pellucida genes in vertebratesCited by: 12
Author(s): Jia‐Xun Feng, Huanfang Tian, Qiaomu Hu, Yan Meng, Hang Xiao
Software Mentions: 1
Published: about 6 years ago
10.1186/1756-0500-7-388
ClonorESTdb: a comprehensive database for Clonorchis sinensis EST sequencesCited by: 13
Author(s): Dae‐Won Kim, Won Gi Yoo, Sang‐Hyun Lee, Myoung-Ro Lee, Yu-Jung Kim, Shin‐Hyeong Cho, Won-Ja Lee, Jung‐Won Ju
Software Mentions: 1
Published: over 10 years ago
10.1186/s12951-015-0137-x
A nanomolecular approach to decrease adhesion of biofouling-producing bacteria to graphene-coated materialCited by: 48
Author(s): Carolina Parra, Fernando Dorta, Edra Jiménez, Ricardo Henríquez, Cristián Ramírez, Rodrigo Rojas, Patricio Villalobos
Software Mentions: 1
Published: about 9 years ago
10.3390/ijerph18147385
Can Administrative Health Data Improve the Gold Standard? Evidence from a Model of the Progression of Myocardial InfarctionCited by: 0
Author(s): Son Nghiem, Jonathan Williams, Clifford Afoakwah, Quan Huynh, Shu‐Kay Ng, Joshua Byrnes
Software Mentions: 1
Published: over 3 years ago
10.1186/s12866-019-1400-3
Ruminal metagenomic analyses of goat data reveals potential functional microbiota by supplementation with essential oil-cobalt complexesCited by: 20
Author(s): Zhaomin Lei, Ke Zhang, Chao Li, Ting Jiao, Jianping Wu, Yubing Wei, Kechuan Tian, Chong Li, Defu Tang, Delmer Davis, D. P. Casper, Hui Jiang, Xiaolong Wang, Jianfu Wang
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pgen.1004109
DAF-16/FoxO Directly Regulates an Atypical AMP-Activated Protein Kinase Gamma Isoform to Mediate the Effects of Insulin/IGF-1 Signaling on Aging in Caenorhabditis elegansCited by: 51
Author(s): Jennifer M. A. Tullet, Caroline Araiz, Matthew J. Sanders, Catherine Au, Alexandre Benedetto, Irene Papatheodorou, Emily Clark, Kathrin Schmeißer, Daniel C. Jones, Eugene F. Schuster, Janet M. Thornton, David Gems
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0088947
Genomic Survey, Gene Expression Analysis and Structural Modeling Suggest Diverse Roles of DNA Methyltransferases in LegumesCited by: 42
Author(s): Rohini Garg, Romika Kumari, Sneha Tiwari, Shweta Goyal
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0194335
Molecular evolution and functional divergence of eukaryotic translation initiation factor 2-alpha kinasesCited by: 11
Author(s): K. Hari Krishna, Mithilesh Kumar
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0010909
MixHMM: Inferring Copy Number Variation and Allelic Imbalance Using SNP Arrays and Tumor Samples Mixed with Stromal CellsCited by: 31
Author(s): Zongzhi Liu, Ao Li, Vincent P. Schulz, Min Chen, David Tuck
Software Mentions: 1
Published: over 14 years ago
10.1186/s12864-019-5679-0
Genomic analyses of aminoacyl tRNA synthetases from human-infecting helminthsCited by: 1
Author(s): Preeti Goel, Suhel Parvez, Amit Sharma
Software Mentions: 1
Published: over 5 years ago
10.3390/v10100577
Biodiversity of Streptococcus thermophilus Phages in Global Dairy FermentationsCited by: 27
Author(s): Katherine Lavelle, Inés Martínez, Horst Neve, Gabriele Andrea Lugli, Charles M. A. P. Franz, Marco Ventura, Fabio Dal Bello, Douwe van Sinderen, Jennifer Mahony
Software Mentions: 1
Published: about 6 years ago
10.1038/s41598-021-96711-y
HES and Mox genes are expressed during early mesoderm formation in a mollusk with putative ancestral featuresCited by: 0
Author(s): Attila Placido Sachslehner, Elisabeth Zieger, Andrew Calcino, Andreas Wanninger
Software Mentions: 1
Published: about 3 years ago
10.1371/journal.pone.0018509
An Integrated Approach for Finding Overlooked Genes in ShigellaCited by: 8
Author(s): Junping Peng, Jian Yang, Qi Jin
Software Mentions: 1
Published: over 13 years ago
10.1093/database/baz094
ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factorsCited by: 2
Author(s): Rahila Sardar, Abhinav Kaushik, Rajan Kumar Pandey, Asif Mohmmed, Shakir Ali, Dinesh Gupta
Software Mentions: 1
Published: almost 6 years ago