pypi: Archive | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-11-187

Artificial and natural duplicates in pyrosequencing reads of metagenomic data
Cited by: 236
Author(s): Beifang Niu, Li‐Chen Fu, Sheng Sun, Weizhong Li
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-019-3124-7

Identifying Alzheimer’s disease-related proteins by LRRGD
Cited by: 14
Author(s): Tianyi Zhao, Yang Hu, Tianyi Zang, Cheng Liang
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-7-4

Application of machine learning in SNP discovery
Cited by: 42
Author(s): Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik‐Young Choi, Perry B. Cregan, Curtis P. Van Tassell
Software Mentions: 1
Published: almost 19 years ago

10.1186/s12859-020-03810-0

Multi-view feature selection for identifying gene markers: a diversified biological data driven approach
Cited by: 3
Author(s): Sudipta Acharya, Laizhong Cui, Yi Pan
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2105-8-151

Tracembler – software for in-silico chromosome walking in unassembled genomes
Cited by: 14
Author(s): Qunfeng Dong, Matthew D. Wilkerson, Volker Brendel
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-7-479

HybGFS: a hybrid method for genome-fingerprint scanning
Cited by: 1
Author(s): Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga, Masaru Tomita
Software Mentions: 1
Published: about 18 years ago

10.1186/s12859-020-03694-0

“METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI’s sequence read archive”
Cited by: 15
Author(s): Mariam Quiñones, David Liou, Conrad Shyu, Wongyu Kim, Ivan Vujkovic-Cvijin, Yasmine Belkaid, Darrell E. Hurt
Software Mentions: 1
Published: about 4 years ago

10.1186/s12862-019-1359-6

Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales
Cited by: 20
Author(s): Mark S. Springer, Christopher A. Emerling, John Gatesy, Jason G. Randall, Matthew A. Collin, Nikolai Hecker, Michael Hiller, Frédéric Delsuc
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12862-020-01701-9

Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution
Cited by: 20
Author(s): Chris Kay, Tom A. Williams, Wendy Gibson
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12863-016-0333-1

Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
Cited by: 15
Author(s): Yongyi Yuan, Xue Gao, Bangqing Huang, Jingqiao Lü, Guojian Wang, Xiaobo Lin, Yan Qü, Pu Dai
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-020-07159-9

FishDB: an integrated functional genomics database for fishes
Cited by: 5
Author(s): Liandong Yang, Zetan Xu, Honghui Zeng, Ning Sun, Baosheng Wu, Cheng Wang, Bo Jing, Lin Li, Yang Dong, Shunping He
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2164-13-616

Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome
Cited by: 20
Author(s): Chen Cai, Ralf Bundschuh
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-016-3255-4

Comparative analysis of Corynebacterium glutamicum genomes: a new perspective for the industrial production of amino acids
Cited by: 36
Author(s): Junjie Yang, Sheng Yang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-020-07178-6

Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis
Cited by: 15
Author(s): Guislaine Refrégier, Christophe Sola, Christophe Guyeux
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12866-019-1520-9

Determining antimicrobial susceptibility in Salmonella enterica serovar Typhimurium through whole genome sequencing: a comparison against multiple phenotypic susceptibility testing methods
Cited by: 19
Author(s): Nana E. Mensah, Yue Tang, Shaun Cawthraw, Manal AbuOun, Jackie Fenner, Nicholas R. Thomson, Alison E. Mather, Liljana Petrovska
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-03134-y

JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen
Cited by: 8
Author(s): Cong Liu, Qiuyi Shen, Xiang Cai, Danni Lai, Ling-Shang Wu, Han Zhao, Tianlun Zhao, Donghong Chen, Jinping Si
Software Mentions: 1
Published: over 3 years ago

10.1186/1746-6148-3-28

Canine candidate genes for dilated cardiomyopathy: annotation of and polymorphic markers for 14 genes
Cited by: 8
Author(s): Anje C Wiersma, P.A.J. Leegwater, B.A. van Oost, William Ollier, J. Dukes‐McEwan
Software Mentions: 1
Published: almost 18 years ago

10.3897/BDJ.2.e1079

The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth
Cited by: 148
Author(s): Cynthia Parr, Nevin Wilson, Patrick Leary, Katja Schulz, Kristen D. Lans, Walley Lisa, Jennifer Hammock, Anthony Goddard, Jeremy J. Rice, Marie Studer, Jeffrey T. G. Holmes, Robert J. Corrigan
Software Mentions: 1
Published: over 10 years ago

10.3897/BDJ.3.e4507

Vascular plant community composition from the campos rupestres of the Itacolomi State Park, Brazil
Cited by: 2
Author(s): Markus Gastauer, Werner Leyh, Angela Silva Miazaki, João Augusto Alves Meira‐Neto
Software Mentions: 1
Published: over 9 years ago

10.3897/BDJ.3.e5425

Tree Diversity and Dynamics of the Forest of Seu Nico, Viçosa, Minas Gerais, Brazil
Cited by: 6
Author(s): Markus Gastauer, Werner Leyh, João Augusto Alves Meira‐Neto
Software Mentions: 1
Published: over 9 years ago

10.1093/bioinformatics/btz083

Structured crowdsourcing enables convolutional segmentation of histology images
Cited by: 120
Author(s): Mohamed Amgad, Habiba Elfandy, Hagar Hussein, Lamees A. Atteya, Mai A. T. Elsebaie, Lamia S. Abo Elnasr, Rokia Adel Sakr, Hazem S. E. Salem, A.F. Ismail, Anas M. Saad, Joumana Ahmed, Maha A. T. Elsebaie, Md. Shafiqur Rahman, Inas A. Ruhban, Nada M. Elgazar, Yahya Alagha, Mohammed E. Osman, Ahmed M. Alhusseiny, Mariam M. Khalaf, Abo-Alela F. Younes, Ali Abdulkarim, Duaa M. Younes, Ahmed M. Gadallah, Ahmad M. Elkashash, Yahya Salma, Basma M. Zaki, Jonathan D. Beezley, Deepak Roy Chittajallu, David Manthey, David Gutman, Lee Cooper
Software Mentions: 1
Published: almost 6 years ago

10.6026/97320630013323

Molecular modeling and simulation of three important components of Plant Pathogen Interaction cascade in Vigna mungo
Cited by: 1
Author(s): Pankaj Kumar Singh, Anju Patel, Sayak Ganguli, Amita Pal
Software Mentions: 1
Published: about 7 years ago

10.1093/biolre/ioaa083

CRISPR/Cas9-based genome editing in mice uncovers 13 testis- or epididymis-enriched genes individually dispensable for male reproduction†
Cited by: 20
Author(s): Jiang Sun, Yonggang Lu, Kaori Nozawa, Zoulan Xu, Akane Morohoshi, Julio M Castaneda, Taichi Noda, Haruhiko Miyata, Ferheen Abbasi, Hossam H. Shawki, Satoru Takahashi, Darius J Devlin, Zhifeng Yu, Ryan M. Matzuk, Thomas Garcia, Martin M. Matzuk, Masahito Ikawa
Software Mentions: 1
Published: over 4 years ago

10.1155/2016/6329217

The A, C, G, and T of Genome Assembly
Cited by: 7
Author(s): Bilal Wajid, Muhammad Umar Sohail, Ali Rıza Ekti, Erchin Serpedin
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41375-020-0901-2

S100A6 is a critical regulator of hematopoietic stem cells
Cited by: 17
Author(s): Tan Hooi Min Grahn, Abhishek Niroula, Ákos Végvári, Leal Oburoglu, Maroulio Pertesi, Sarah Warsi, Fatemeh Safi, Natsumi Miharada, Sandra Capellera Garcia, Kavitha Siva, Yang Liu, Emma Rörby, Björn Nilsson, Roman A. Zubarev, Stefán Karlsson
Software Mentions: 1
Published: over 4 years ago

10.3390/life10030030

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.
Cited by: 4
Author(s): Alberto Vangelisti, Flavia Mascagni, Gabriele Usai, Lucia Natali, Tommaso Giordani, Andrea Cavallini
Software Mentions: 1
Published: over 4 years ago

10.1016/j.marenvres.2015.06.017

Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin (TBT): Unravelling the effects from the molecular level to the organism
Cited by: 8
Author(s): Andreia Cruz, Raquel Rodrigues, Miguel Pinheiro, Sónia Mendo
Software Mentions: 1
Published: over 9 years ago

10.1007/s11306-017-1309-5

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it
Cited by: 16
Author(s): Rachel Spicer, Christoph Steinbeck
Software Mentions: 1
Published: almost 7 years ago

10.1099/mgen.0.000062

Quantitative assessment of insertion sequence impact on bacterial genome architecture
Cited by: 47
Author(s): Mark D. Adams, Brian Bishop, Meredith S. Wright
Software Mentions: 1
Published: over 8 years ago

10.1099/mgen.0.000138

Whole-genome sequencing of bloodstream Staphylococcus aureus isolates does not distinguish bacteraemia from endocarditis
Cited by: 23
Author(s): Berit Lilje, Rasmus V. Rasmussen, Anders Dahl, Marc Stegger, Robert Skov, Vance G. Fowler, Kim Lee Ng, Kristoffer Kiil, Anders Rhod Larsen, Andreas Petersen, Helle Krogh Johansen, Henrik Carl Schønheyder, Magnus Arpi, Flemming Schønning Rosenvinge, Eva Korup, Ulla Høst, Christian Hassager, Sabine Gill, Thomas Fritz Hansen, Thor Bech Johannesen, Jesper Smit, Peter Søgaard, Paal Skytt Andersen, Niels Eske-Bruun
Software Mentions: 1
Published: about 7 years ago

10.1002/mbo3.734

Comparative study of gut microbiota in wild and captive Malaysian Mahseer (<i>Tor tambroides</i>)
Cited by: 18
Author(s): Chun Keat Tan, Natrah Fatin Mohd Ikhsan, Iswan B. Suyub, Marilyn Jaoi Edward, Nazrien Kaman, Anjas Asmara Samsudin
Software Mentions: 1
Published: about 6 years ago

10.1128/MRA.00760-21

Complete Genome Sequence of Streptococcus oralis 34
Cited by: 0
Author(s): Justin Kaspar
Software Mentions: 1
Published: about 3 years ago

10.1128/MRA.00650-19

Whole-Genome Sequence of Enterobacter sp. Strain MF024, Isolated from Soil in Shanghai, China
Cited by: 0
Author(s): Shaofeng Rong, Jin Dan Wu, Qianqian Li, Shuo Zhang, Baoguo Cai, Shiyou Guan
Software Mentions: 1
Published: about 5 years ago

10.1128/MRA.00290-19

Genome Sequences of Three Cluster C Mycobacteriophages, Bipolarisk, Bread, and FudgeTart
Cited by: 0
Author(s): Dane M. Bowder, Brandon W. Gannon, Kathryn J. Grint, Jason T. Iltz, Teryn M. Koch, Kaitlyn S. Mahnke, Brea D. Murnan, Alexandria M. Osborn, Danielle M. Schreiber, Grace Su, Jaime G. Troester, Erin L. Doyle
Software Mentions: 1
Published: over 5 years ago

10.1128/MRA.00393-21

Draft Genome Sequence of Novel Filterable <i>Rhodospirillales</i> Bacterium Strain TMPK1, Isolated from Soil
Cited by: 1
Author(s): Ryosuke Nakai, Hiroyuki Kusada, Fumihiro Sassa, Susumu Morigasaki, Hideharu Hayashi, Naoki Takaya, Hideyuki Tamaki
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.01268-20

Complete Genome Sequence of Neonatal Clinical Group B Streptococcal Isolate CJB111
Cited by: 9
Author(s): Brady L. Spencer, Anushila Chatterjee, Breck A. Duerkop, Carol J. Baker, Kelly S. Doran
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00432-20

Sequencing and Annotation of Duggie and Hocus, Two Subcluster B1 Mycobacteriophages
Cited by: 0
Author(s): Erin L. Doyle, Alexis N. Burke, Samuel J. Coy, Haley R. Miller, Lilly M. Shatford-Adams, Reagan M. Petersen, Kade B. Wehrs, Dane M. Bowder
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.00769-20

Complete Genome Sequence of Bartonella alsatica Strain IBS 382 (CIP 105477)
Cited by: 0
Author(s): Arno Thibau, Tilman Schultze, Wibke Ballhorn, Volkhard A. J. Kempf
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms8010087

Whole Genome Sequencing for Studying Bacillus anthracis from an Outbreak in the Abruzzo Region of Italy
Cited by: 8
Author(s): Alexandra Chiaverini, Mostafa Y. Abdel-Glil, Jörg Linde, Domenico Galante, Valeria Rondinone, Antonio Fasanella, Cesare Cammà, Nicola D’Alterio, Giuliano Garofolo, Herbert Tomaso
Software Mentions: 1
Published: almost 5 years ago

10.3390/microorganisms8020161

Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae
Cited by: 20
Author(s): Max L. Cummins, Mohammad Hamidian, Steven P. Djordjevic
Software Mentions: 1
Published: almost 5 years ago

10.3390/microorganisms8101576

Early Inoculation of Microbial Suspension in Suckling Piglets Affects the Transmission of Maternal Microbiota and the Associated Antibiotic Resistance Genes
Cited by: 3
Author(s): Catherine Achard, Véronique Dupouy, Laurent Cauquil, Nathalie Arpaillange, Alain Bousquet‐mélou, Nathalie Le Floc'H, Olivier Zemb
Software Mentions: 1
Published: about 4 years ago

10.1080/23802359.2018.1450671

The complete mitochondrial genome sequence of the sakura shrimp, Sergia lucens (Crustacea, Decapoda, Sergestidae)
Cited by: 0
Author(s): Satoshi Kawato, Reiko Nozaki, Hidehiro Kondo, Ikuo Hirono
Software Mentions: 1
Published: almost 7 years ago

10.3390/molecules25184259

Cytotoxicity of Oleandrin Is Mediated by Calcium Influx and by Increased Manganese Uptake in Saccharomyces cerevisiae Cells
Cited by: 3
Author(s): Lavinia L. Ruţă, Claudia Popa, Ileana C. Fărcăşanu
Software Mentions: 1
Published: about 4 years ago

10.3897/zookeys.209.3486

Nomenclatural benchmarking: the roles of digital typification and telemicroscopy
Cited by: 15
Author(s): Quentin D. Wheeler, Thierry Bourgoin, Jonathan A. Coddington, Timothy Gostony, Andy Hamilton, Roy Larimer, Andrew Polaszek, Michael E. Schauff, M. Alma Solís
Software Mentions: 1
Published: over 12 years ago

10.3897/zookeys.306.5289

Iberian Odonata distribution: data of the BOS Arthropod Collection (University of Oviedo, Spain)
Cited by: 7
Author(s): Antonio Torralba Burrial, Francisco J. Ocharan
Software Mentions: 1
Published: over 11 years ago

10.3897/zookeys.306.4898

FORMIDABEL: The Belgian Ants Database
Cited by: 4
Author(s): Dimitri Brosens, François Vankerkhoven, David Ignace, Philippe Wegnez, Nicolas Noé, André Heughebaert, Jeannine Bortels, Wouter Dekoninck
Software Mentions: 1
Published: over 11 years ago

10.3897/zookeys.341.6130

Harvestmen of the BOS Arthropod Collection of the University of Oviedo (Spain) (Arachnida, Opiliones)
Cited by: 3
Author(s): Izaskun Merino-Sáinz, Araceli Anadôn, Antonio Torralba Burrial
Software Mentions: 1
Published: about 11 years ago

10.3897/zookeys.360.4742

Checklist of beetles (Coleoptera) of Canada and Alaska. Second edition
Cited by: 112
Author(s): Yves Bousquet, Patrice Bouchard, Anthony Davies, Derek S. Sikes
Software Mentions: 1
Published: almost 11 years ago

10.3897/zookeys.408.5633

AnthWest, occurrence records for wool carder bees of the genus Anthidium (Hymenoptera, Megachilidae, Anthidiini) in the Western Hemisphere
Cited by: 4
Author(s): Terry Griswold, Víctor H. González, Harold Ikerd
Software Mentions: 1
Published: over 10 years ago

10.3897/zookeys.466.8523

A Dataset of Deep-Sea Fishes Surveyed by Research Vessels in the Waters around Taiwan
Cited by: 0
Author(s): Kwang‐Tsao Shao, Jack Yung-Chang Lin, Hsin‐Ming Yeh, Mao-Yin Lee, Lee-Sea Chen, Hen-Wei Lin
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13071-019-3558-9

Transcriptome-based molecular systematics: Rhodnius montenegrensis (Triatominae) and its position within the Rhodnius prolixus–Rhodnius robustus cryptic–species complex
Cited by: 13
Author(s): Raíssa N. Brito, Juliana Assis Geraldo, Fernando A. Monteiro, Cristiano Lazoski, Rita C. M. Souza, Fernando Abad‐Franch
Software Mentions: 1
Published: over 5 years ago

10.3390/pathogens9100848

Sequencing of Historical Isolates, K-mer Mining and High Serological Cross-Reactivity with Ross River Virus Argue against the Presence of Getah Virus in Australia
Cited by: 10
Author(s): Daniel J. Rawle, Wilson Nguyen, Troy Dumenil, Rhys Parry, David Warrilow, Bing Tang, Thuy T. Le, Andrii Slonchak, Alexander A. Khromykh, Viviana P. Lutzky, Kexin Yan, Andreas Suhrbier
Software Mentions: 1
Published: about 4 years ago

10.3390/pathogens8030157

Evolutionary Insight into the Trypanosomatidae Using Alignment-Free Phylogenomics of the Kinetoplast
Cited by: 8
Author(s): Alexa Kaufer, Damien Stark, John Ellis
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.10005

Transcriptomic analysis reveals insights into the response to Hop stunt viroid (HSVd) in sweet cherry (Prunus avium L.) fruits
Cited by: 3
Author(s): Li Xu, Xiaojuan Zong, J. Wang, Hairong Wei, Xin Chen, Qingzhong Li
Software Mentions: 1
Published: about 4 years ago

10.3390/pharmaceutics13020212

Utilizing Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) to Analyze Interstitial Fluid Flow and Transport in Glioblastoma and the Surrounding Parenchyma in Human Patients
Cited by: 10
Author(s): Krishnashis Chatterjee, Naciye Atay, Daniel Abler, Saloni Bhargava, Prativa Sahoo, Russell C. Rockne, Jennifer M. Munson
Software Mentions: 1
Published: almost 4 years ago

10.3897/phytokeys.9.2770

From text to structured data: Converting a word-processed floristic checklist into Darwin Core Archive format
Cited by: 9
Author(s): David Remsen, Sandra Knapp, Teodor Georgiev, Pavel Stoev, Lyubomir Penev
Software Mentions: 1
Published: almost 13 years ago

10.3897/phytokeys.12.2849

Florabank1: a grid-based database on vascular plant distribution in the northern part of Belgium (Flanders and the Brussels Capital region)
Cited by: 17
Author(s): Wouter Van Landuyt, Léo Vanhecke, Dimitri Brosens
Software Mentions: 1
Published: over 12 years ago

10.3897/phytokeys.35.6746

URJC GB dataset: Community-based seed bank of Mediterranean high-mountain and semi-arid plant species at Universidad Rey Juan Carlos (Spain)
Cited by: 0
Author(s): Patricia Alonso, José María Iriondo
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pbio.0020099

Avoiding URL Reference Degradation in Scientific Publications
Cited by: 8
Author(s): Desiree P Kelly, Eric J. Hester, Kathryn R. Johnson, Lauren F. Heilig, Amanda L. Drake, Lisa M. Schilling, Robert P. Dellavalle
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pcbi.1003541

Leadership in Moving Human Groups
Cited by: 28
Author(s): Margarete Boos, Johannes Pritz, Simon Lange, Michael Belz
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1003965

Selection on Plant Male Function Genes Identifies Candidates for Reproductive Isolation of Yellow Monkeyflowers
Cited by: 9
Author(s): Jan Aagaard, Renee D. George, Lila Fishman, Michael J. MacCoss, Willie J. Swanson
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1000931

A MATE-Family Efflux Pump Rescues the Escherichia coli 8-Oxoguanine-Repair-Deficient Mutator Phenotype and Protects Against H2O2 Killing
Cited by: 33
Author(s): Javier R. Guelfo, Alexandro Rodríguez‐Rojas, Ivan Matić, Jesús Blázquez
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pmed.1000167

Five Years of Access and Activism
Cited by: 1
Author(s):
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0003427

Re-Assembly of the Genome of Francisella tularensis Subsp. holarctica OSU18
Cited by: 8
Author(s): Daniela Puiu, Steven L. Salzberg
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0113267

The Effect of Furnishing on Perceived Spatial Dimensions and Spaciousness of Interior Space
Cited by: 23
Author(s): Christoph von Castell, Daniel Oberfeld, Heiko Hecht
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0209706

Fitness cost of a mcr-1-carrying IncHI2 plasmid
Cited by: 38
Author(s): Ke Ma, Yu Feng, Zhiyong Zong
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0248116

Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake
Cited by: 26
Author(s): Tawseef Ahmad, Gaganjot Gupta, Anshul Sharma, Baljinder Kaur, Mohamed A. El-Sheikh, Mohammed Nasser Alyemeni
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0150240

Liver Transcriptome Analysis of the Large Yellow Croaker (Larimichthys crocea) during Fasting by Using RNA-Seq
Cited by: 23
Author(s): Baoying Qian, Liyan Xue, Hongli Huang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0071484

Metagenomic Guilt by Association: An Operonic Perspective
Cited by: 12
Author(s): Gregory Vey
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0240191

Prometheus, an omics portal for interkingdom comparative genomic analyses
Cited by: 1
Author(s): Gun Hwan Ko, In Su Jang, Nam Jin Koo, Seong-Jin Park, Sang Ho Oh, Minseo Kim, Jinhyuk Choi, Hyeong Min Kim, Young Mi Sim, Iksu Byeon, Pan-Gyu Kim, Kye Young Kim, Jong Cheol Yoon, Kyung Lok Mun, Bang Hyuk Lee, Guk Hee Han, Yong Min Kim
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0114520

Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Single-Cell Sequencing
Cited by: 50
Author(s): Minfeng Chen, Pengfei Song, Dan Zou, Xuesong Hu, Shancen Zhao, Shengjie Gao, Fei Ling
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0112541

Correlations of Differentially Expressed Gap Junction Connexins Cx26, Cx30, Cx32, Cx43 and Cx46 with Breast Cancer Progression and Prognosis
Cited by: 67
Author(s): Ivett Teleki, Attila Marcell Szász, Máté E. Maros, Balázs Győrffy, Janina Kulka, Nóra Meggyesházi, Gergő Kiszner, Péter Balla, Samu Aliz, Tibor Krenács
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0031156

Sec12 Binds to Sec16 at Transitional ER Sites
Cited by: 47
Author(s): Elisabeth A. Montegna, Madhura Bhave, Yang Liu, Dibyendu Bhattacharyya, Benjamin S. Glick
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0182259

Oral microbial community assembly under the influence of periodontitis
Cited by: 11
Author(s): Hongju Chen, Shuting Peng, Lin Dai, Quan Zou, Bin Yi, Xiaoyan Yang, Zhanshan Sam
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0149747

DsTRD: Danshen Transcriptional Resource Database
Cited by: 23
Author(s): Yang Shao, Jiabo Wei, Fuyong Wu, Haihua Zhang, Dongfeng Yang, Zongsuo Liang, Weibo Jin
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0078786

Clinical Unity and Community Empowerment: The Use of Smartphone Technology to Empower Community Management of Chronic Venous Ulcers through the Support of a Tertiary Unit
Cited by: 17
Author(s): Edel Quinn, Mark Corrigan, John O’Mullane, David Murphy, Elaine Lehane, Patricia Leahy‐Warren, Alice Coffey, Patricia McCluskey, H. P. Redmond, Greg Fulton
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0025258

Completeness and Changes in Registered Data and Reporting Bias of Randomized Controlled Trials in ICMJE Journals after Trial Registration Policy
Cited by: 106
Author(s): Mirjana Huić, Matko Marušić, Ana Marušić
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0096271

Searching for Genomic Region of High-Fat Diet-Induced Type 2 Diabetes in Mouse Chromosome 2 by Analysis of Congenic Strains
Cited by: 17
Author(s): Misato Kobayashi, Tamio Ohno, Kenji Ihara, Atsushi Murai, Mayumi Kumazawa, Hiromi Hoshino, Koichiro Iwanaga, Hiroshi Iwai, Yoshiki Hamana, Makoto Ito, Kinji Ohno, Fumihiko Horio
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0108728

Worldwide Occurrence of Integrative Conjugative Element Encoding Multidrug Resistance Determinants in Epidemic Vibrio cholerae O1
Cited by: 20
Author(s): Michel Abanto, Érica L. Fonseca, Bruno N. Andrade, Adriana C. Cabral, Ana Carolina Paulo Vicente
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0138424

Efficient Nash Equilibrium Resource Allocation Based on Game Theory Mechanism in Cloud Computing by Using Auction
Cited by: 20
Author(s): Amin Nezarat, GH Dastghaibifard
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0242555

Collaborative multicenter logistics delivery network optimization with resource sharing
Cited by: 7
Author(s): Shejun Deng, Yingying Yuan, Yong Wang, Haizhong Wang, Charles Koll
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0235984

The evolutionary history of mariner elements in stalk-eyed flies reveals the horizontal transfer of transposons from insects into the genome of the cnidarian Hydra vulgaris
Cited by: 6
Author(s): Cooper Alastair Grace, Martin Carr
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0123789

A Simple Strategy for Reducing False Negatives in Calling Variants from Single-Cell Sequencing Data
Cited by: 1
Author(s): Jason Cong, Min‐Hua Zong, Xionglei He
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0200738

Reinforcement learning for solution updating in Artificial Bee Colony
Cited by: 9
Author(s): Suthida Fairee, Santitham Prom-on, Booncharoen Sirinaovakul
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0099033

HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis
Cited by: 38
Author(s): Luis V. Santana‐Quintero, Hayley Dingerdissen, Jean Thierry‐Mieg, Raja Mazumder, Vahan Simonyan
Software Mentions: 1
Published: over 10 years ago

10.1038/s41419-018-1086-8

Demethylzeylasteral inhibits glioma growth by regulating the miR-30e-5p/MYBL2 axis
Cited by: 48
Author(s): Kui Zhang, Gang Fu, Guoqing Pan, Chongyang Li, Li Shen, Renjian Hu, Shunqin Zhu, Yibiao Chen, Hongjuan Cui
Software Mentions: 1
Published: about 6 years ago

10.1016/j.chom.2017.07.019

Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses
Cited by: 126
Author(s): Chris Lauber, Stefan Seitz, Simone Matteï, Alexander Suh, Jürgen Beck, Jennifer Herstein, Jacob Börold, Walter Salzburger, Lars Kaderali, John Briggs, Ralf Bartenschlager
Software Mentions: 1
Published: about 7 years ago

10.1038/s42003-020-01501-3

Evolution and expansion of the RUNX2 QA repeat corresponds with the emergence of vertebrate complexity
Cited by: 10
Author(s): Axel H Newton, Andrew J Pask
Software Mentions: 1
Published: almost 4 years ago

10.1007/s00294-015-0537-3

Affected chromosome homeostasis and genomic instability of clonal yeast cultures
Cited by: 17
Author(s): Jagoda Adamczyk, Anna Deręgowska, Anita D. Panek, Ewelina Golec, Anna Lewińska, Maciej Wnuk
Software Mentions: 1
Published: about 9 years ago

10.1007/s10140-017-1575-6

Impact of duplicate CT scan rate after implementation of transfer image repository system at a level 1 trauma center
Cited by: 5
Author(s): C. W. Sheppard, A Groll, Cindy L Austin, Simon Thompson
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41431-021-00859-0

Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases
Cited by: 38
Author(s): Birte Zurek, Kornelia Ellwanger, Lisenka E.L.M. Vissers, Rebecca Schüle, Matthis Synofzik, Ana Töpf, Richarda M. de Voer, Steve Laurie, Leslie Matalonga, Christian Gilissen, Stephan Ossowski, Peter A C ‘t Hoen, Antonio Vitobello, Julia M. Schulze‐Hentrich, Olaf Rieß, Han G. Brunner, Anthony J. Brookes, Ana Rath, Gisèle Bonne, Gülçin Gümüş, Alain Verloes, Nicoline Hoogerbrugge, Teresinha Evangelista, Tina Harmuth, Morris A. Swertz, J. Dylan Spalding, Alexander Hoischen, Sergi Beltrán, Holm Graeßner, Tobias B. Haack, Birte Zurek, Kornelia Ellwanger, German Demidov, Marc Sturm, Christoph Keßler, Melanie Wayand, Carlo Wilke, Andreas Traschütz, Ludger Schöls, Holger Hengel, Peter Heutink, Han G. Brunner, Hans Scheffer, Wouter Steyaert, Karolis Šablauskas, Richarda M. de Voer, Erik‐Jan Kamsteeg, Bart van de Warrenburg, Nienke van Os, Iris te Paske, Erik Janssen, Elke de Boer, Marloes Steehouwer, Burcu Yaldiz, Tjitske Kleefstra, Colin Veal, Spencer Gibson, Marc Wadsley, Mehdi Mehtarizadeh, Umar Riaz, Greg Warren, Farid Yavari Dizjikan, Thomas Shorter, V. Straub, C. Marini Bettolo, Sabine Specht, Jill Clayton‐Smith, Siddharth Banka, Elizabeth Alexander, Adam Jackson, Laurence Faivre, Christel Thauvin, Antonio Vitobello, Dagmar Wieczorek, Yannis Duffourd, Émilie Tisserant, Ange‐Line Bruel, Christine Peyron, Aurore Pélissier, Sergi Beltrán, Ivo Gut, Steve Laurie, Davide Piscia, Leslie Matalonga, Anastasios Papakonstantinou, Gemma Bullich, Alberto Corvò, Carles García, Marcos Fernández-Callejo, Carles Hernández, Daniel Picó, Ida Paramonov, Hanns Lochmüller, Gülçin Gümüş, Virginie Bros-Facer, Marc Hanauer, Annie Olry, David Lagorce, Svitlana Havrylenko, Katia Izem, Fanny Rigour, Giovanni Stévanin, Alexandra Dürr, Claire-Sophie Davoine, Léna Guillot‐Noël, Anna Heinzmann, Giulia Coarelli, Valérie Allamand, Isabelle Nelson, Rabah Ben Yaou, Corinne Métay, B. Eymard, Enzo Cohen, António Atalaia, Tanya Stojkovic, Milan Maçek, Marek Turnovec, Dana Thomasová, Radka Pourová Kremliková, Věra Franková, Markéta Havlovičová, Vlastimil Kremlik, Helen Parkinson, Thomas Keane, Alexander Senf, Peter N. Robinson, Daniel Daniš, Robert Glenn, Alessia Costa, Christine Patch, Mike Hanna, Henry Houlden, Mary Reilly, Jana Vandrovcová, F. Muntoni, Irina Zaharieva, Anna Sárközy, Vincent Timmerman, Jonathan Baets, Liedewei Van de Vondel, Danique Beijer, Peter De Jonghe, Vincenzo Nigro, Sandro Banfi, Annalaura Torella, Francesco Musacchia, Giulio Piluso, Alessandra Ferlini, Rita Selvatici, Rachele Rossi, Marcella Neri, Stefan Aretz, Isabel Spier, Anna Sommer, Sophia Peters, Carla Oliveíra, Jose Garcia Pelaez, Ana Rita Matos, Celina São José, Marta Ferreira, Irene Gullo, Susana Fernandes, Luzia Garrido, Pedro Ferreira, Fátima Carneiro, Morris A. Swertz, Lennart Johansson, Joeri K. van der Velde, Gerben van der Vries, Pieter Neerincx, Dieuwke Roelofs-Prins, Sebastian Köhler, Alison Metcalfe, Alain Verloès, Séverine Drunat, Caroline Rooryck, Aurélien Trimouille, Raffaele Castello, Manuela Morleo, Michele Pinelli, Alessandra Varavallo, Мануел Посада де ла Паз, Eva Bermejo Sánchez, Estrella López Martín, Beatriz Martínez Delgado, F. Javier Alonso García de la Rosa, Andrea Ciolfi, Bruno Dallapiccola, Simone Pizzi, Francesca Clementina Radio, Marco Tartaglia, Alessandra Renieri, Elisa Benetti, Péter Balicza, Mária Judit Molnár, Aleš Maver, Borut Peterlin, Alexander Münchau, Katja Lohmann, Rebecca Herzog, Martje G. Pauly, Alfons Macaya, Anna Marcé‐Grau, Andres Nascimiento Osorio, Daniel Natera de Benito, Hanns Lochmüller, Rachel Thompson, Kiran Polavarapu, David Beeson, Judith Cossins, Pedro M. Rodríguez Cruz, Peter Hackman, Mridul Johari, Marco Savarese, Bjarne Udd, Rita Horváth, Gabriel Capellá, Laura Valle, Elke Holinski‐Feder, Andreas Laner, Verena Steinke‐Lange, Evelin Schröck, Andreas Rump
Software Mentions: 1
Published: over 3 years ago

10.2807/1560-7917.ES.2019.24.36.1800543

Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017
Cited by: 14
Author(s): Anika Meinen, Sandra Simon, Sangeeta Banerji, István Szabó, Burkhard Malorny, Maria Blettner, Sead Hadžiabdić, Natalie Becker, Petra Luber, Dorothee Lohr, Carolin Harms, Anita Plenge‐Bönig, Kassiani Mellou, Georgia Mandilara, Joël Mossong, Catherine Ragimbeau, Pierre Weicherding, Patrick Hau, Daniela Dědičová, Lucie Šafaříková, Satheesh Nair, Timothy J. Dallman, Lesley Larkin, Jacquelyn McCormick, Elizabeth de Pinna, Ettore Severi, Saara Kotila, Taina Niskanen, V. Rizzi, Domenico Deserio, Antje Flieger, Klaus Stark
Software Mentions: 1
Published: about 5 years ago

10.1111/eva.12860

Cyberinfrastructure and resources to enable an integrative approach to studying forest trees
Cited by: 12
Author(s): Jill L. Wegrzyn, Taylor Falk, Emily Grau, Sean Buehler, Risharde Ramnath, Nic Herndon
Software Mentions: 1
Published: about 5 years ago

10.12688/f1000research.14060.1

Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma
Cited by: 28
Author(s): Kenneth W. Witwer
Software Mentions: 1
Published: over 6 years ago

10.3389/fcell.2021.668164

Cancer-Associated Fibroblasts Facilitate Squamous Cell Carcinoma Lung Metastasis in Mice by Providing TGFβ-Mediated Cancer Stem Cell Niche
Cited by: 13
Author(s): Xueke Shi, Jingjing Luo, Kelsey Weigel, Spencer Hall, Dan-Feng Du, Fanglong Wu, Michael C. Rudolph, Hongmei Zhou, Christian D. Young, Xiaojing Wang
Software Mentions: 1
Published: about 3 years ago

10.3389/fcimb.2017.00229

Comparative Genomic and Phylogenetic Analysis of a Shiga Toxin Producing Shigella sonnei (STSS) Strain
Cited by: 14
Author(s): Domonkos Sváb, Balázs Bálint, Bálint Márk Vásárhelyi, Gergely Maróti, István Tóth
Software Mentions: 1
Published: over 7 years ago

10.3389/fncom.2019.00081

Multivariate Analysis of Preoperative Magnetic Resonance Imaging Reveals Transcriptomic Classification of de novo Glioblastoma Patients
Cited by: 5
Author(s): Saima Rathore, Hamed Akbari, Spyridon Bakas, Jared Pisapia, Gaurav Shukla, Jeffrey D. Rudie, Da Xiao, Ramana V. Davuluri, Nadia Dahmane, Donald M. O’Rourke, Christos Davatzikos
Software Mentions: 1
Published: almost 5 years ago

10.3389/fncom.2019.00084

Multi-Disease Segmentation of Gliomas and White Matter Hyperintensities in the BraTS Data Using a 3D Convolutional Neural Network
Cited by: 31
Author(s): Jeffrey D. Rudie, David Weiß, Rachit Saluja, Andreas M. Rauschecker, Jiancong Wang, Leo P. Sugrue, Spyridon Bakas, John B. Colby
Software Mentions: 1
Published: almost 5 years ago

10.3389/fendo.2017.00133

Alternative RNA Splicing in the Pathogenesis of Liver Disease
Cited by: 31
Author(s): Nicholas J. G. Webster
Software Mentions: 1
Published: over 7 years ago

10.3389/fimmu.2012.00371

Defining the molecular blueprint that drives CD8+ T cell differentiation in response to infection
Cited by: 21
Author(s): Brendan E. Russ, Alice E. Denton, Lauren A Hatton, Hayley A Croom, Matthew R. Olson, Stephen J. Turner
Software Mentions: 1
Published: almost 13 years ago

Projects: pypi: Archive

Papers Mentioning Archive 363