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: finder

https://packages.ecosyste.ms/registries/pypi.org/packages/finder

Command line interface for searching a given pattern in the given directory/file paths
3 versions
Latest release: over 7 years ago
48 downloads last month

Papers Mentioning finder 236

10.1093/molbev/msab091
Piggybacking on Niche Adaptation Improves the Maintenance of Multidrug-Resistance Plasmids
Cited by: 20
Author(s): Julia Maria Kloos, João Alves Gama, Joachim Hegstad, Ørjan Samuelsen, Pål Jarle Johnsen
Software Mentions: 11
Published: over 3 years ago
10.1038/s41598-019-46168-x
Cytotoxic unsaturated electrophilic compounds commonly target the ubiquitin proteasome system
Cited by: 16
Author(s): Karthik Selvaraju, Arjan Mofers, Paola Pellegrini, Johannes Salomonsson, Alexandra Ahlner, Vivian Morad, Ellin-Kristina Hillert, Belén Espinosa, Elias S.J. Arnér, Lasse Jensen, Jonas Malmström, Maria V. Turkina, Pádraig D’Arcy, Michael A. Walters, Maria Sunnerhagen, Stig Linder
Software Mentions: 10
Published: over 5 years ago
10.1111/1755-0998.13266
Chromosome‐level genome assembly of <i>Paralithodes platypus</i> provides insights into evolution and adaptation of king crabs
Cited by: 11
Author(s): Boping Tang, Zhongkai Wang, Qiu-Ning Liu, Zhengfei Wang, Yandong Ren, Huayun Guo, Tingting Qi, Yue‐Tian Li, Huabin Zhang, Senhao Jiang, Baoming Ge, Fujun Xuan, Yue Sun, Shusheng She, Tin Yam Chan, Zhongli Sha, Hui Jiang, Haorong Li, Wei Jiang, Yanli Qin, Kun Wang, Qiang Qiu, Wen Wang, Xinzheng Li, Ngan Kee Ng, Dai-Zhen Zhang, Yongxin Li
Software Mentions: 9
Published: about 4 years ago
10.1111/mec.14054
The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB
Cited by: 60
Author(s): Rodrigo Pracana, Anurag Priyam, Levantis Ilya, Richard A. Nichols, Yannick Wurm
Software Mentions: 8
Published: over 7 years ago
10.1186/s13062-016-0110-0
Altools: a user friendly NGS data analyser
Cited by: 5
Author(s): Salvatore Camiolo, Gaurav Sablok, Andrea Porceddu
Software Mentions: 7
Published: almost 9 years ago
10.1186/1471-2105-10-325
Riboswitch Detection Using Profile Hidden Markov Models
Cited by: 33
Author(s): Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, Annangarachari Krishnamachari, Supratim Sengupta
Software Mentions: 7
Published: about 15 years ago
10.3389/fpls.2021.683681
Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant (Solanum melongena)
Cited by: 9
Author(s): Saad Serfraz, Vikas Sharma, Florian Maumus, Xavier Aubriot, Andrew D. W. Geering, Pierre‐Yves Teycheney
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-015-2324-4
Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout
Cited by: 10
Author(s): Henrique César Pereira Figueiredo, Siomar C. Soares, Felipe Luiz Pereira, Fernanda Alves Dorella, Alex F. Carvalho, Júnia Pacheco Teixeira, Vasco Azevedo, Carlos Augusto Gomes Leal
Software Mentions: 6
Published: almost 9 years ago
10.1186/s12859-018-2252-9
npInv: accurate detection and genotyping of inversions using long read sub-alignment
Cited by: 26
Author(s): Haojing Shao, Devika Ganesamoorthy, Tânia Duarte, Minh Duc Cao, Clive Hoggart, Lachlan Coin
Software Mentions: 5
Published: over 6 years ago
10.1101/2020.12.05.409821
Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures
Cited by: 6
Author(s): Martina Zafferani, Christina Haddad, Le Luo, Jesse Davila‐Calderon, Liang Yuan-Chiu, Christian Shema Mugisha, Adeline G. Monaghan, Andrew Kennedy, Joseph D. Yesselman, Robert R Gifford, Andrew W. Tai, Sebla B. Kutluay, Meiling Li, Gary Brewer, Blanton S. Tolbert, Amanda E. Hargrove
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.pone.0163111
MetaPhinder—Identifying Bacteriophage Sequences in Metagenomic Data Sets
Cited by: 50
Author(s): Vanessa Isabell Jurtz, Julia Villarroel, Ole Lund, Mette Voldby Larsen, Morten Nielsen
Software Mentions: 5
Published: about 8 years ago
10.1093/gbe/evab145
High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly<i>Vanessa cardui</i>
Cited by: 7
Author(s): Linlin Zhang, Rachel Steward, Christopher W. Wheat, Robert D. Reed
Software Mentions: 5
Published: over 3 years ago
10.1111/tpj.14454
Metabolic diversification of nitrogen‐containing metabolites by the expression of a heterologous lysine decarboxylase gene in Arabidopsis
Cited by: 10
Author(s): Y. Shimizu, Amit Rai, Yuko Okawa, Hajime Tomatsu, Masaru Satô, Kota Kera, Hideyuki Suzuki, Kazuki Saito, Mami Yamazaki
Software Mentions: 4
Published: about 5 years ago
10.1002/2211-5463.12705
Analysis of Bn <scp>MTL</scp> , a novel metallothionein‐like protein in the bast fiber crop Ramie ( <i>Boehmeria nivea</i> )
Cited by: 3
Author(s): Gang Gao, Jikang Chen, Ping Chen, Kunmei Chen, Aminu Shehu Abubakar, Chang Yeon Yu, Aiguo Zhu
Software Mentions: 4
Published: over 5 years ago
10.1007/s00251-019-01137-6
The Immune Epitope Database and Analysis Resource Program 2003–2018: reflections and outlook
Cited by: 37
Author(s): Sheridan Martini, Morten Nielsen, Bjoern Peters, Alessandro Sette
Software Mentions: 4
Published: almost 5 years ago
10.18632/aging.202400
A DNA methylation age predictor for zebrafish
Cited by: 27
Author(s): Benjamin Mayne, Darren Korbie, Lisa M Kenchington, Ben J Ezzy, Oliver Berry, Simon Jarman
Software Mentions: 4
Published: almost 4 years ago
10.3389/fpls.2017.01279
Sequence Polymorphisms and Structural Variations among Four Grapevine (Vitis vinifera L.) Cultivars Representing Sardinian Agriculture
Cited by: 23
Author(s): Luca Mercenaro, G. Nieddu, Andrea Porceddu, Mario Pezzotti, Salvatore Camiolo
Software Mentions: 4
Published: over 7 years ago
10.3390/md17030181
Comparative Transcriptome Analyses Provide Potential Insights into the Molecular Mechanisms of Astaxanthin in the Protection against Alcoholic Liver Disease in Mice
Cited by: 12
Author(s): Huilin Liu, Huimin Liu, Liang Zhu, Ziqi Zhang, Xin Zheng, Jingsheng Liu, Xueqi Fu
Software Mentions: 4
Published: over 5 years ago
10.3389/fmicb.2021.723350
Identification and Molecular Characterization of a Novel Hordeivirus Associated With Yellow Mosaic Disease of Privet (Ligustrum vulgare) in Europe
Cited by: 4
Author(s): Jean-Sébastien Reynard, Silvia Turco, Justine Brodard, Isabelle Kellenberger, François Maclot, Olivier Schumpp, P. Gugerli, Mikhail M. Pooggin
Software Mentions: 4
Published: about 3 years ago
10.3390/ijms22031332
The Expression of the Cancer-Associated lncRNA Snhg15 Is Modulated by EphrinA5-Induced Signaling
Cited by: 4
Author(s): Daniel Pensold, Julia Gehrmann, Georg Pitschelatow, Asa Walberg, Kai Braunsteffer, Julia Reichard, Amin Ravaei, Jenice Linde, Angelika Lampert, Ivan G. Costa, Geraldine Zimmer-Bensch
Software Mentions: 4
Published: almost 4 years ago
10.1186/1471-2164-9-333
Structure and properties of transcriptional networks driving selenite stress response in yeasts
Cited by: 74
Author(s): Hélène Salin, Vivienne Fardeau, Eugenia Piccini, Gaëlle Lelandais, Véronique Tanty, Sophie Lemoine, Claude Jacq, Frédéric Devaux
Software Mentions: 3
Published: over 16 years ago
10.1007/s00425-021-03606-3
A family of pathogen-induced cysteine-rich transmembrane proteins is involved in plant disease resistance
Cited by: 6
Author(s): Marciel Pereira Mendes, Richard Hickman, Marcel C. Van Verk, Nicole M. Nieuwendijk, Anja Reinstädler, Ralph Panstruga, Corné M. J. Pieterse, Saskia C.M. Van Wees
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2105-13-S17-S5
Multiple virtual screening approaches for finding new Hepatitis c virus RNA-dependent RNA polymerase inhibitors: Structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors
Cited by: 26
Author(s): Mahmoud ElHefnawi, Mohammad ElGamacy, Mohamed Fares
Software Mentions: 3
Published: almost 12 years ago
10.1098/rstb.2012.0503
Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals
Cited by: 50
Author(s): Adam F. Lee, Alison Nolan, Jason Watson, Michael Tristem
Software Mentions: 3
Published: about 11 years ago
10.1186/s12870-018-1501-4
Genome-wide transcriptome analysis reveals small RNA profiles involved in early stages of stolon-to-tuber transitions in potato under photoperiodic conditions
Cited by: 22
Author(s): Kirtikumar R. Kondhare, Nilam N Malankar, Ravi Suresh Devani, Anjan K. Banerjee
Software Mentions: 3
Published: about 6 years ago
10.1128/mSystems.01322-20
Longitudinal Profiling of the Macaque Vaginal Microbiome Reveals Similarities to Diverse Human Vaginal Communities
Cited by: 11
Author(s): Nicholas S Rhoades, Sara M Hendrickson, Danielle R. Gerken, Kassandra Martinez, Ov D. Slayden, Mark K. Slifka, Ilhem Messaoudi
Software Mentions: 3
Published: over 3 years ago
10.1093/gbe/evaa063
An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)
Cited by: 23
Author(s): W. Brian Simison, James F. Parham, Theodore J. Papenfuss, Athena Lam, James Henderson
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-020-58985-6
Facilitating gene editing in potato: a Single-Nucleotide Polymorphism (SNP) map of the Solanum tuberosum L. cv. Desiree genome
Cited by: 33
Author(s): François Sevestre, Maud Facon, Fabrice Wattebled, Nicolas Szydlowski
Software Mentions: 3
Published: almost 5 years ago
10.1186/s13007-019-0437-5
Quantifying cereal crop movement through hemispherical video analysis of agricultural plots
Cited by: 5
Author(s): Alexander Q. Susko, Peter Marchetto, D. Jo Heuschele, Kevin P. Smith
Software Mentions: 3
Published: over 5 years ago
10.3389/fmicb.2016.00645
A Network of Paralogous Stress Response Transcription Factors in the Human Pathogen Candida glabrata
Cited by: 26
Author(s): Jawad Merhej, Antonin Thiébaut, Corinne Blugeon, Juliette Pouch, Mohammed el amine Ali Chaouche, Jean‐Michel Camadro, Stéphane Le Crom, Gaëlle Lelandais, Frédéric Devaux
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0002126
Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance
Cited by: 162
Author(s): David G. Hendrickson, Daniel J. Hogan, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: over 16 years ago
10.1371/journal.pone.0033802
Reconstructing Viral Genomes from the Environment Using Fosmid Clones: The Case of Haloviruses
Cited by: 85
Author(s): Inmaculada García-Heredia, Ana-Belén Martín-Cuadrado, Francisco J. M. Mojica, Fernando Santos, Álex Mira, Josefa Antón, Francisco Rodrı́guez-Valera
Software Mentions: 3
Published: over 12 years ago
10.1371/journal.pone.0059847
Do Changes in the Pace of Events Affect One-Off Judgments of Duration?
Cited by: 8
Author(s): H.M. Darlow, Alexandra S. Dylman, Ana I. Gheorghiu, William J. Matthews
Software Mentions: 3
Published: over 11 years ago
10.1038/s41598-021-93495-z
The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas
Cited by: 6
Author(s): Tanvi Sharma, Nitesh Kumar Sharma, Prakash P. Kumar, Ganesh Panzade, Tanuja Rana, Mohit Kumar Swarnkar, Anil Kumar Singh, Dharam Singh, Ravi Shankar, Sanjay Kumar
Software Mentions: 3
Published: over 3 years ago
10.7717/peerj.3692
The complete mitochondrial genome of the grooved carpet shell,<i>Ruditapes decussatus</i>(Bivalvia, Veneridae)
Cited by: 14
Author(s): Fabrizio Ghiselli, Liliana Milani, Mariangela Iannello, Emanuele Procopio, Peter L. Chang, Sergey V. Nuzhdin, Marco Passamonti
Software Mentions: 2
Published: over 7 years ago
10.3892/ol.2014.1967
Expression of TSG101 protein and LSF transcription factor in HPV-positive cervical cancer cells
Cited by: 9
Author(s): Justyna Broniarczyk, Alicja Warowicka, Anna Kwaśniewska, Maria Wohuń-Cholewa, Wojciech Kwaśniewski, Anna Goździcka-Józefiak
Software Mentions: 2
Published: over 10 years ago
10.1093/jncics/pkz060
Cathepsin D Expression and Gemcitabine Resistance in Pancreatic Cancer
Cited by: 4
Author(s): Ujjwal Mukund Mahajan, Elisabetta Goni, Enno Langhoff, Qi Li, Eithne Costello, William Greenhalf, Stephan Krüger, Steffen Ormanns, Christopher Halloran, Paula Ganeh, Manuela Marron, Felix Lämmerhirt, Yue Zhao, Georg Beyer, Florian Weiß, Matthias Sendler, Christiane Bruns, Thomas Kohlmann, Thomas Kirchner, Jens Werner, Jan DʼHaese, Michael von Bergwelt‐Baildon, Volker Heinemann, John P. Neoptolemos, Markus W. Büchler, Claus Belka, Stefan Boeck, Markus M. Lerch, Julia Mayerle
Software Mentions: 2
Published: over 5 years ago
10.1186/s12864-016-3223-z
A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae
Cited by: 12
Author(s): Christina Schilde, Hajara M. Lawal, Angelika A. Noegel, Ludwig M. Eichinger, Pauline Schaap, Gernot Glöckner
Software Mentions: 2
Published: about 8 years ago
10.1186/s40425-016-0183-4
Unraveling the role of preexisting immunity in prostate cancer patients vaccinated with a HER-2/neu hybrid peptide
Cited by: 11
Author(s): Ioannis F. Voutsas, Eleftheria A. Anastasopoulou, Panagiotis Tzonis, Michael Papamichail, Sonia A. Perez, Constantin N. Baxevanis
Software Mentions: 2
Published: about 8 years ago
10.1186/s12864-016-3163-7
Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron
Cited by: 31
Author(s): William J Gammerdinger, Matthew A. Conte, Jean‐François Baroiller, Hélèna D'Cotta, Thomas D. Kocher
Software Mentions: 2
Published: about 8 years ago
10.1002/humu.24005
AG‐exclusion zone revisited: Lessons to learn from 91 intronic NF1 3′ splice site mutations outside the canonical AG‐dinucleotides
Cited by: 20
Author(s): Katharina Wimmer, Esther Schamschula, Annekatrin Wernstedt, Pia Traunfellner, Albert Amberger, Johannes Zschocke, Peter M. Kroisel, Yunjia Chen, Tom Callens, Ludwine Messiaen
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-019-50978-4
Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers
Cited by: 28
Author(s): Ayako Suda, Issei Nishiki, Yoshiaki Iwasaki, Aiko Matsuura, Tetsuya Akita, Nobuaki Suzuki, Atushi Fujiwara
Software Mentions: 2
Published: about 5 years ago
10.1038/s41598-018-20971-4
Molecular dynamic simulations reveal structural insights into substrate and inhibitor binding modes and functionality of Ecto-Nucleoside Triphosphate Diphosphohydrolases
Cited by: 18
Author(s): Jamshed Iqbal, Syed Jawad Ali Shah
Software Mentions: 2
Published: almost 7 years ago
10.1186/s40814-018-0352-y
Supporting general practitioner-based care for poorly controlled type 2 diabetes mellitus (the DECIDE study): feasibility study and protocol for a pilot cluster randomised controlled trial
Cited by: 4
Author(s): Mark Murphy, Molly Byrne, Fiona Boland, Derek Corrigan, Paddy Gillespie, Tom Fahey, Susan M. Smith
Software Mentions: 2
Published: about 6 years ago
10.1155/2019/5913491
Positive Selection of Squalene Synthase in Cucurbitaceae Plants
Cited by: 9
Author(s): Jiang Qian, Yong Liu, Chunyan Ma, Naixia Chao, Qicong Chen, Yangmei Zhang, Yukun Luo, Dan-Zhao Cai, Yaosheng Wu
Software Mentions: 2
Published: over 5 years ago
10.1002/glia.24032
Regulation of aquaporin‐4 expression in the central nervous system investigated using M23‐AQP4 null mouse
Cited by: 10
Author(s): Francesco Pisani, Laura Simone, Maria Grazia Mola, Manuela De Bellis, Antonio Frigeri, Grazia Paola Nicchia, María Svelto
Software Mentions: 2
Published: over 3 years ago
10.1186/s13073-017-0456-7
Interrogating the “unsequenceable” genomic trinucleotide repeat disorders by long-read sequencing
Cited by: 66
Author(s): Qian Liu, Peng Zhang, Depeng Wang, Wei Gu, Kai Wang
Software Mentions: 2
Published: over 7 years ago
10.1080/19490976.2021.1882927
The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases
Cited by: 82
Author(s): Farideh Hosseinkhani, Almut Heinken, Ines Thiele, Petrus W. Lindenburg, Amy C. Harms, Thomas Hankemeier
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12870-017-1220-2
Identification of AUXIN RESPONSE FACTOR gene family from Prunus sibirica and its expression analysis during mesocarp and kernel development
Cited by: 14
Author(s): Jun Niu, Quanxin Bi, Shuya Deng, Huiping Chen, Haiyan Yu, Libing Wang, Senjie Lin
Software Mentions: 2
Published: almost 7 years ago
10.1186/1471-2164-10-210
Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2
Cited by: 19
Author(s): Alan L. Kwan, Linya Li, David Kulp, Susan K. Dutcher, Gary D. Stormo
Software Mentions: 2
Published: over 15 years ago
10.1128/genomeA.01271-17
Complete Genome Sequence of Bacillus velezensis L-1, Which Has Antagonistic Activity against Pear Diseases
Cited by: 5
Author(s): Pu Sun, Jianchao Cui, Xiaoyun Jia, Wenhui Wang
Software Mentions: 2
Published: almost 7 years ago
10.3389/fvets.2018.00281
Capsular Switching and ICE Transformation Occurred in Human Streptococcus agalactiae ST19 With High Pathogenicity to Fish
Cited by: 3
Author(s): Rui Wang, Liping Li, Ting Huang, Weiyi Huang, Aiying Lei, Ming Chen
Software Mentions: 2
Published: about 6 years ago
10.3390/genes12081185
Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)
Cited by: 2
Author(s): Wenqian Wang, Huan Zhang, Jérôme Constant, Charles R. Bartlett, Dao‐Zheng Qin
Software Mentions: 2
Published: over 3 years ago
10.1128/mBio.00452-20
Toxin-Antitoxin Gene Pairs Found in Tn <i>3</i> Family Transposons Appear To Be an Integral Part of the Transposition Module
Cited by: 22
Author(s): Gipsi Lima‐Mendez, Danillo Oliveira Alvarenga, Karen Ross, Bernard Hallet, Laurence Van Melderen, Alessandro M. Varani, Michaël Chandler
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2164-15-545
A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements
Cited by: 106
Author(s): Hong-Seok Ha, Jimin Song, Shuoguo Wang, Aurélie Kapusta, Cédric Feschotte, Kevin C. Chen, Jinchuan Xing
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2164-15-945
Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts
Cited by: 25
Author(s): Amanda M. Hulse‐Kemp, Hamid Ashrafi, Xiuting Zheng, Fei Wang, Kevin A. Hoegenauer, Andrea Maeda, Shanshan Yang, Kevin Stoffel, Marta Matvienko, Kimberly Clemons, Joshua A. Udall, Allen Van Deynze, Don C. Jones, David M. Stelly
Software Mentions: 2
Published: about 10 years ago
10.3389/fmicb.2021.630293
Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants
Cited by: 3
Author(s): H. R. Marti, Sankhya Bommana, Timothy D. Read, Theresa Pesch, Barbara Prähauser, Deborah Dean, Nicole Borel
Software Mentions: 2
Published: over 3 years ago
10.1186/s12896-020-00667-2
Characterization of metabolic responses, genetic variations, and microsatellite instability in ammonia-stressed CHO cells grown in fed-batch cultures
Cited by: 8
Author(s): Dylan G. Chitwood, Qinghua Wang, Kathryn Elliott, Aiyana Bullock, Dwon Jordana, Zhigang Li, Cathy H. Wu, Sarah W. Harcum, Christopher Saski
Software Mentions: 2
Published: almost 4 years ago
10.3389/fchem.2017.00051
Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis
Cited by: 19
Author(s): Linda Oyama, Jean-Adrien Crochet, Joan E. Edwards, Susan Elizabeth Girdwood, Alan Cookson, Narcís Fernández-Fuentes, Kai Hilpert, Peter N. Golyshin, Olga V. Golyshina, Florence Privé, Matthias Hess, Hilário Cuquetto Mantovani, Christopher J. Creevey, Sharon Huws
Software Mentions: 2
Published: over 7 years ago
10.1186/1471-2164-13-396
RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans
Cited by: 30
Author(s): Sanjiveeni Dhamgaye, Maria Bernard, Gaëlle Lelandais, Odile Sismeiro, Sophie Lemoine, Jean‐Yves Coppée, Stéphane Le Crom, Rajendra Prasad, Frédéric Devaux
Software Mentions: 2
Published: over 12 years ago
10.3389/fpls.2015.00594
New insights into plant glycoside hydrolase family 32 in Agave species
Cited by: 18
Author(s): Emmanuel Ávila de Dios, Alan Daniel Gomez Vargas, Maura L. Damián Santos, June Simpson
Software Mentions: 2
Published: over 9 years ago
10.3390/insects10020042
Proteomic Analysis of the Venom from the Ruby Ant Myrmica rubra and the Isolation of a Novel Insecticidal Decapeptide
Cited by: 14
Author(s): J. Heep, Alica Klaus, Tobias Kessel, Maximilian Seip, Andreas Vilcinskas, Marisa Škaljac
Software Mentions: 2
Published: almost 6 years ago
10.5936/csbj.201209008
COMPUTER-AIDED PROTEIN DIRECTED EVOLUTION: A REVIEW OF WEB SERVERS, DATABASES AND OTHER COMPUTATIONAL TOOLS FOR PROTEIN ENGINEERING
Cited by: 49
Author(s): Rajni Verma, Ulrich Schwaneberg, Danilo Roccatano
Software Mentions: 2
Published: about 12 years ago
10.1038/s42003-021-02533-z
Rates of contributory de novo mutation in high and low-risk autism families
Cited by: 18
Author(s): Seungtai Yoon, Adriana Muñoz, Boris Yamrom, Yoon-ha Lee, Peter Andrews, Steven C. Marks, Zihua Wang, Catherine Reeves, Lara Winterkorn, Abba M. Krieger, Andreas Buja, Kith Pradhan, Michael Ronemus, Kristin K. Baldwin, Dan Levy, Michael Wigler, Ivan Iossifov
Software Mentions: 2
Published: about 3 years ago
10.1007/s00284-017-1349-0
Complete Genome Sequence of Geobacillus thermodenitrificans T12, A Potential Host for Biotechnological Applications
Cited by: 14
Author(s): Martinus J. A. Daas, Bastienne Vriesendorp, Antonius H. P. van de Weijer, John van der Oost, Richard van Kranenburg
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pone.0143188
CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases
Cited by: 22
Author(s): Alexandar, Pradeep G Nayar, Ram Murugesan, B Goldring Mary, P Darshana, Shiek S. S. J. Ahmed
Software Mentions: 2
Published: almost 9 years ago
10.1186/1471-2148-12-236
The evolution of ultraconserved elements with different phylogenetic origins
Cited by: 21
Author(s): Tae Woo Ryu, Loqmane Seridi, Timothy Ravasi
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0039573
ChIPnorm: A Statistical Method for Normalizing and Identifying Differential Regions in Histone Modification ChIP-seq Libraries
Cited by: 32
Author(s): Nishanth Ulhas Nair, Avinash Sahu, Philipp Bücher, Bernard M. E. Moret
Software Mentions: 2
Published: over 12 years ago
10.1242/dev.133686
Drosophila Condensin II subunit, Chromosome Associated Protein-D3, regulates cell fate determination through non-cell autonomous signaling
Cited by: 5
Author(s): Lindsey R. Klebanow, Emanuela C. Peshel, Andrew Schuster, Kuntal De, Kavitha Sarvepalli, Madeleine E. Lemieux, Jessica J. Lenoir, Adrian W. Moore, Jocelyn A. McDonald, Michelle S. Longworth
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0049127
Fibroblast Growth Factor 10-Fibroblast Growth Factor Receptor 2b Mediated Signaling Is Not Required for Adult Glandular Stomach Homeostasis
Cited by: 9
Author(s): Allison L. Speer, Denise Al Alam, F.G. Sala, Henri R. Ford, Savério Bellusci, Tracy C. Grikscheit
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pone.0143932
The Rho GTPase Family Genes in Bivalvia Genomes: Sequence, Evolution and Expression Analysis
Cited by: 8
Author(s): Xue Li, Ruijia Wang, Xiaogang Xun, Wenqian Jiao, Mengran Zhang, Shuyue Wang, Shi Wang, Lingling Zhang, Xiaoting Huang, Xiaoli Hu, Zhenmin Bao
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0229417
Biochemical, genetic and transcriptional characterization of multibacteriocin production by the anti-pneumococcal dairy strain Streptococcus infantarius LP90
Cited by: 6
Author(s): Cristina Campanero, Estefanía Muñoz-Atienza, Dzung B. Diep, Javier Feito, Sara Arbulu, Rosa del Campo, Ingolf F. Nes, Pablo E. Hernández, Carmen Herranz, Luis M. Cintas
Software Mentions: 2
Published: over 4 years ago
10.3390/medicina55050195
Preliminary Work Towards Finding Proteins as Potential Vaccine Candidates for Vibrio cholerae Pakistani Isolates through Reverse Vaccinology
Cited by: 3
Author(s): Samia Zeb, Amjad Ali, Sardar Muhammad Gulfam, Habib Bokhari
Software Mentions: 2
Published: over 5 years ago
10.1080/23802359.2021.1911712
Diversity and authentication of Rubus accessions revealed by complete plastid genome and rDNA sequences
Cited by: 4
Author(s): Young Sang Park, Jee Young Park, Jae-Mo Kang, Wan Hee Lee, Tae-Jin Yang
Software Mentions: 2
Published: over 3 years ago
10.1186/s12859-016-1096-4
Protein complexes predictions within protein interaction networks using genetic algorithms
Cited by: 19
Author(s): Emad Ramadan, Ahmed Naef, Moataz Ahmed
Software Mentions: 2
Published: over 8 years ago
10.1007/s10585-016-9832-8
The prognostic effect of DDX3 upregulation in distant breast cancer metastases
Cited by: 26
Author(s): Marise R. Heerma van Voss, Willemijne A.M.E. Schrijver, Natalie D. ter Hoeve, Laurien D.C. Hoefnagel, Quirine F. Manson, Elsken van der Wall, Venu Raman, Paul J. van Diest
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12864-019-6049-7
Combining next-generation sequencing and single-molecule sequencing to explore brown plant hopper responses to contrasting genotypes of japonica rice
Cited by: 13
Author(s): Jing Zhang, Wanqing Guan, Chao Huang, Yinxia Hu, Yu Chen, Jianping Guo, Cong Zhou, Rongzhi Chen, Bo Du, Lili Zhu, Danax Huanhan, Guangcun He
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0006337
Molecular Analysis of Spring Viraemia of Carp Virus in China: A Fatal Aquatic Viral Disease that Might Spread in East Asian
Cited by: 31
Author(s): Nian Zhi Zhang, Li Feng Zhang, Yuan Jiang, Ting Zhang, Chun Xia
Software Mentions: 2
Published: over 15 years ago
10.1371/journal.pone.0005905
Genetic and Proteomic Evidence for Roles of Drosophila SUMO in Cell Cycle Control, Ras Signaling, and Early Pattern Formation
Cited by: 119
Author(s): Minghua Nie, Yongming Xie, Joseph A. Loo, Albert J. Courey
Software Mentions: 2
Published: over 15 years ago
10.1038/leu.2016.149
Cryptic splicing events in the iron transporter ABCB7 and other key target genes in SF3B1-mutant myelodysplastic syndromes
Cited by: 97
Author(s): Hamid Dolatshad, Andrea Pellagatti, Fabio G. Liberante, Miriam Llorian, Emmanouela Repapi, Violetta Steeples, S. Roy, L Scifo, Richard N. Armstrong, Jacqueline Shaw, Bon Ham Yip, Sally Killick, Rajko Kušec, Stephen Taylor, Ken I. Mills, Kienan I. Savage, Christopher W.J. Smith, Jacqueline Boultwood
Software Mentions: 2
Published: over 8 years ago
10.46439/toxicology.2.006
RAD51 Inhibitor Reverses Etoposide-Induced Genomic Toxicity and Instability in Esophageal Adenocarcinoma Cells
Cited by: 5
Author(s): Chengcheng Liao, Jiangning Zhao, Subodh Kumar, Chitraleema Chakraborty, Srikanth Talluri, Nikhil C. Munshi, Masood A. Shammas
Software Mentions: 2
Published: about 4 years ago
10.1186/1471-2164-8-308
Architecture of Burkholderia cepacia complex σ70 gene family: evidence of alternative primary and clade-specific factors, and genomic instability
Cited by: 14
Author(s): Aymeric Menard, Paulina Estrada‐de los Santos, Arnault Graindorge, Benoît Cournoyer
Software Mentions: 2
Published: about 17 years ago
10.1186/s12864-018-4563-7
Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast
Cited by: 11
Author(s): Viktor Tokan, Janka Puterová, Matej Lexa, Eduard Kejnovský
Software Mentions: 2
Published: over 6 years ago
10.1186/1297-9716-43-66
Mycoplasma haemocanis – the canine hemoplasma and its feline counterpart in the genomic era
Cited by: 17
Author(s): Naíla Cannes do Nascimento, Andrea Pires dos Santos, Ana M. S. Guimarães, Phillip SanMiguel, Joanne B. Messick
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pcbi.1000166
Network Inference Algorithms Elucidate Nrf2 Regulation of Mouse Lung Oxidative Stress
Cited by: 83
Author(s): Ron Taylor, George Acquaah‐Mensah, Mudita Singhal, Deepti Malhotra, Shyam Biswal
Software Mentions: 2
Published: about 16 years ago
10.1371/journal.pone.0027316
Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae
Cited by: 54
Author(s): Amit Ghosh, Huimin Zhao, Nathan D. Price
Software Mentions: 2
Published: about 13 years ago
10.2217/epi-2017-0029
Defining baseline epigenetic landscapes in the rat liver
Cited by: 5
Author(s): John P. Thomson, Raffaele Ottaviano, Roland Buesen, Jonathan G. Moggs, Michael Schwarz, Richard R. Meehan
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-017-12959-3
Trios—promising in silico biomarkers for differentiating the effect of disease on the human microbiome network
Cited by: 13
Author(s): Zhanshan Sam, Dandan Ye
Software Mentions: 2
Published: about 7 years ago
10.1186/s12864-016-2362-6
Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by antennal transcriptome analysis
Cited by: 74
Author(s): Binu Antony, Alan Soffan, Jernej Jakše, Mahmoud Abdelazim, Saleh A. Aldosari, Abdulrahman S. Aldawood, Arnab Pain
Software Mentions: 2
Published: almost 9 years ago
10.7717/peerj.6659
Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization
Cited by: 18
Author(s): Shiyan Xu, Jian-Kun Long, Xiang-Sheng Chen
Software Mentions: 2
Published: over 5 years ago
10.7717/peerj.10085
Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast
Cited by: 1
Author(s): Nagarjun Vijay
Software Mentions: 2
Published: about 4 years ago
10.1042/BSR20181156
Hemin induces autophagy in a leukemic erythroblast cell line through the LRP1 receptor
Cited by: 13
Author(s): Rubén Adrián Grosso, Paula Virginia Subirada Caldarone, Marı́a C. Sánchez, Gustavo A. Chiabrando, María Isabel Colombo, Claudio Marcelo Fader
Software Mentions: 1
Published: almost 6 years ago
10.1155/2021/5515692
In Silico Drug Screening Analysis against the Overexpression of PGAM1 Gene in Different Cancer Treatments
Cited by: 6
Author(s): Muhammad Mazhar Fareed, Mohamed A. El‐Esawi, Enas M. El-Ballat, Gaber El‐Saber Batiha, Abdur Rauf, Fatma M. El‐Demerdash, Fahad A. Alhumaydhi, Suliman A. Alsagaby
Software Mentions: 1
Published: over 3 years ago
10.1155/2015/485624
Targeted Next Generation Sequencing Identifies Novel Mutations in<i>RP1</i>as a Relatively Common Cause of Autosomal Recessive Rod-Cone Dystrophy
Cited by: 23
Author(s): Said El Shamieh, Élise Boulanger-Scemama, Marie‐Elise Lancelot, Antonio Arnaiz‐Villena, Vanessa Démontant, Christel Condroyer, Mélanie Letexier, Jean‐Paul Saraiva, Saddek Mohand‐Saïd, José‐Alain Sahel, Isabelle Audo, Christina Zeitz
Software Mentions: 1
Published: almost 10 years ago
10.1155/2020/1824183
Genome Survey and Transcriptome Analysis on Mycelia and Primordia of Agaricus blazei
Cited by: 7
Author(s): Yuanping Lu, Liao JianHua, Zhiyong Guo, Z. Y. Cai, Meiyuan Chen
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12864-020-06912-4
Transcriptome-based selection and validation of optimal house-keeping genes for skin research in goats (Capra hircus)
Cited by: 11
Author(s): Jipan Zhang, Chengchen Deng, Jialu Li, Yongju Zhao
Software Mentions: 1
Published: over 4 years ago
10.1186/1471-213X-11-30
The zebrafish transcriptome during early development
Cited by: 111
Author(s): Liselotte Vesterlund, Hong Jiao, Per Unneberg, Outi Hovatta, Juha Kere
Software Mentions: 1
Published: over 13 years ago
10.1186/1745-6150-9-19
Mycobacteriophage-drived diversification of Mycobacterium abscessus
Cited by: 16
Author(s): Mohamed Sassi, Philippe Gouret, Olivier Chabrol, Pierre Pontarotti, Michel Drancourt
Software Mentions: 1
Published: about 10 years ago
10.1093/bioinformatics/btx500
EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing
Cited by: 26
Author(s): Zachary T. Berndsen, Charles A. Bowman, Haerin Jang, Andrew B. Ward
Software Mentions: 1
Published: over 7 years ago
10.1093/bioinformatics/btz703
Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs
Cited by: 10
Author(s): Tanvir Alam, Meshari Alazmi, Rayan Naser, Franceline Huser, Afaque Ahmad Imtiyaz Momin, Veronica Astro, Seungbeom Hong, Katarzyna Walkiewicz, Christian G. Canlas, Raphaël Huser, Amal J. Ali, Jasmeen S. Merzaban, Antonio Adamo, Mariusz Jaremko, Łukasz Jaremko, Vladimir B. Bajić, Xin Gao, Stefan T. Arold
Software Mentions: 1
Published: about 5 years ago