Scientific Papers with Software Mentions

10.3389/fgene.2020.00440

The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus
Cited by: 38
Author(s): Ronghua Li, Weijia Zhang, Junkai Lu, Zhouyi Zhang, Changkao Mu, Weiwei Song, Hervé Migaud, Michaël Bekaert
Software Mentions: 1
Published: over 6 years ago

10.3389/fonc.2019.00450

Utility of Immunophenotypic Measurable Residual Disease in Adult Acute Myeloid Leukemia—Real-World Context
Cited by: 12
Author(s): Nikhil Patkar, Chinmayee Kakirde, Prasanna Bhanshe, Shalik Ram Joshi, Shruti Chaudhary, Yajamanam Badrinath, Sitaram Ghoghale, Nilesh Deshpande, Shraddha Kadechkar, Gaurav Chatterjee, Sadhana Kannan, Dhanalaxmi Shetty, Anant Gokarn, Sachin Punatkar, Avinash Bonda, Lingaraj Nayak, Hasmukh Jain, Bhausaheb Bagal, Hari Menon, Manju Sengar, Syed Khizer Hasan, Navin Khattry, Prashant Tembhare, Sumeet Gujral, Papagudi Ganesan Subramanian
Software Mentions: 1
Published: over 7 years ago

10.3389/fpls.2018.00724

Red Clover (Trifolium pratense) and Zigzag Clover (T. medium) – A Picture of Genomic Similarities and Differences
Cited by: 18
Author(s): Jana Dluhošová, Jan Ištvánek, J. Nedêlník, Jana Řepková
Software Mentions: 1
Published: over 8 years ago

10.3389/fpls.2016.02055

Simultaneous Identification of Multiple Causal Mutations in Rice
Cited by: 35
Author(s): Yan Wang, Zhufeng Chen, Jian Lü, Chengpei Xu, Gang Xie, Yiqi Li, Xing Wang Deng, Hang He, Xiaoyan Tang
Software Mentions: 1
Published: almost 10 years ago

10.3389/fvets.2019.00175

Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth Brucella sp. BCCN84.3
Cited by: 10
Author(s): Caterina Guzmán-Verri, Marcela Suárez-Esquivel, Nazareth Ruíz-Villalobos, Michel S. Zygmunt, Mathieu Gonnet, Elena Campos, Eunice Víquez-Ruiz, Carlos Chacón-Díaz, Beatriz Aragón-Aranda, Raquel Conde-Álvarez, Ignacio Moriyón, J.M. Blasco, Pilar M. Muñoz, Kate S. Baker, Nicholas R. Thomson, Axel Cloeckaert, Edgardo Moreno
Software Mentions: 1
Published: over 7 years ago

10.1186/cc9260

Intensive care diaries reduce new onset post traumatic stress disorder following critical illness: a randomised, controlled trial
Cited by: 388
Author(s): Christina Jones, Carl Bäckman, Maurizia Capuzzo, Ingrid Egerod, Hans Flaatten, Cristina Granja, Christian Rylander, Richard D. Griffiths
Software Mentions: 1
Published: almost 17 years ago

10.1186/gb-2005-6-5-r47

Cited by: 263
Author(s): Ilya G. Goldberg, Chris Allan, Jean‐Marie Burel, Doug Creager, Andrea Falconi, Harry Hochheiser, Josiah Johnston, Jeff Mellen, Peter K. Sorger, Jason R. Swedlow
Software Mentions: 1
Published: almost 22 years ago

10.1186/2047-217X-2-5

Sequence squeeze: an open contest for sequence compression
Cited by: 14
Author(s): Richard Holland, Nick Lynch
Software Mentions: 1
Published: over 13 years ago

10.3390/s21155160

Energy and Performance Analysis of Lossless Compression Algorithms for Wireless EMG Sensors
Cited by: 7
Author(s): Giorgio Biagetti, Paolo Crippa, Laura Falaschetti, Ali Mansour, Claudio Turchetti
Software Mentions: 1
Published: about 5 years ago

10.2196/13559

Development and Implementation of the Portable Operating Room Tracker App With Vital Signs Streaming Infrastructure: Operational Feasibility Study
Cited by: 6
Author(s): Matthias Görges, Nicholas West, Chris Petersen, J. Mark Ansermino
Software Mentions: 1
Published: about 7 years ago

10.1107/S1600577520007353

Impact of lossy compression of X-ray projections onto reconstructed tomographic slices
Cited by: 0
Author(s): Federica Marone, Jakob Vogel, Marco Stampanoni
Software Mentions: 1
Published: about 6 years ago

10.1007/978-3-319-35072-1_9

Applications of the BLEND Software to Crystallographic Data from Membrane Proteins
Cited by: 7
Author(s): Pierre Aller, Tao Geng, Gwyndaf Evans, James Foadi
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-015-1377-8

Genomic factors related to tissue tropism in Chlamydia pneumoniae infection
Cited by: 9
Author(s): Thomas Weinmaier, Jonathan Hoser, Sebastian Eck, Inga Kaufhold, Kensuke Shima, Tim M. Strom, Thomas Rattei, Jan Rupp
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0232781

Bacillus subtilis PB6 based probiotic supplementation plays a role in the recovery after the necrotic enteritis challenge
Cited by: 21
Author(s): Mashael R. Aljumaah, Manal M. Alkhulaifi, Alaeldein M. Abudabos, Riyadh S. Aljumaah, Asma N. Alsaleh, Dragana Stanley
Software Mentions: 1
Published: over 6 years ago

10.3390/molecules25194398

Anthocyanin Intake and Physical Activity: Associations with the Lipid Profile of a US Working Population
Cited by: 7
Author(s): María Soledad Hershey, Mercedes Sotos-Prieto, Miguel Ruiz‐Canela, Miguel Ángel Martínez‐González, Aedín Cassidy, Steven Moffatt, Stefanos N. Kales
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0070495

The Influence of Relatives on the Efficiency and Error Rate of Familial Searching
Cited by: 22
Author(s): Rori V. Rohlfs, Erin Murphy, Yun S. Song, Montgomery Slatkin
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0222589

Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model
Cited by: 15
Author(s): Yoshitomo Morinaga, Yuki Take, Daisuke Sasaki, Kenji Ota, Norihito Kaku, Naoki Uno, Kei Sakamoto, Kosuke Kosai, Taiga Miyazaki, Hiroo Hasegawa, Koichi Izumikawa, Hiroshi Mukae, Katsunori Yanagihara
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0081739

Functional and Phylogenetic Relatedness in Temporary Wetland Invertebrates: Current Macroecological Patterns and Implications for Future Climatic Change Scenarios
Cited by: 40
Author(s): Albert Ruhí, Dani Boix, Stéphanie Gascón, Jordi Sala, Darold P. Batzer
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0159368

Polychaete Community of a Marine Protected Area along the West Coast of India—Prior and Post the Tropical Cyclone, Phyan
Cited by: 11
Author(s): Soniya Sukumaran, Tejal Vijapure, Priti Kubal, Jyoti Mulik, M. A. Rokade, Shailesh Salvi, Jubin Thomas, V.S. Naidu
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0091161

Towards Improved Management of Tropical Invertebrate Fisheries: Including Time Series and Gender
Cited by: 58
Author(s): Sara Fröcklin, Maricela de la Torre‐Castro, Elin Håkansson, Anna Carlsson, M. Magnusson, Narriman Jiddawi
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0039808

Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis
Cited by: 35
Author(s): Rohit Vashisht, Anupam Mondal, Akanksha Jain, Anup Shah, Priti Vishnoi, Priyanka Priyadarshini, Kausik Bhattacharyya, Harsha Rohira, Ashwini G. Bhat, Anurag Passi, Krishanu Mukherjee, Kumari Sonal Choudhary, Vikas Kumar, Anshula Arora, Prabhakaran Munusamy, Ahalyaa Subramanian, Aparna Venkatachalam, S. Gayathri, Sweety Raj, V. Chitra, Kaveri Verma, Salman Zaheer, J Balaganesh, Malarvizhi Gurusamy, Mohammed Razeeth, Ilamathi Raja, Madhumohan Thandapani, Vishal Mevada, Raviraj Soni, Shruti Rana, Girish Muthagadhalli Ramanna, Swetha Raghavan, Sunil N. Subramanya, Trupti Kholia, Rajesh Patel, Varsha Bhavnani, Lakavath Chiranjeevi, Sukalyan Sengupta, Pankaj Kumar Singh, Naresh Atray, S. M. Gandhi, Suma Tiruvayipati, Shefin Nisthar, Meenakshi Anurag, Pratibha Sharma, Yasha Hasija, Debasis Dash, Arun Sharma, Vinod Scaria, Zakir Thomas, Nagasuma Chandra, Samir K. Brahmachari, Anshu Bhardwaj
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-018-2408-7

ISU FLUture: a veterinary diagnostic laboratory web-based platform to monitor the temporal genetic patterns of Influenza A virus in swine
Cited by: 46
Author(s): Michael A. Zeller, Tavis K. Anderson, Rasna W Walia, Amy L. Vincent, Phillip C. Gauger
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0241283

Spatio-temporal variations in bacterial and fungal community associated with dust aerosol in Kuwait
Cited by: 18
Author(s): Fadila Al Salameen, Nazima Habibi, Saif Uddin, Khalil Al Mataqi, Vinod Kumar, Bashayer Al Doaij, Sami Al Amad, Ebtisam Al Ali, Faiz Shirshikhar
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0137725

Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection
Cited by: 151
Author(s): Joshua S. Son, Ling J. Zheng, Leahana Rowehl, Xinyu Tian, Yuanhao Zhang, Wei Zhu, Leighann Litcher‐Kelly, Kenneth D. Gadow, Grace Gathungu, Charles E. Robertson, Diana Ir, Daniel N. Frank, Ellen Li
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0187935

Contrasts in the marine ecosystem of two Macaronesian islands: A comparison between the remote Selvagens Reserve and Madeira Island
Cited by: 25
Author(s): Alan M. Friedlander, Enric Ballesteros, Sabrina Clemente, Emanuel João Gonçalves, Andy Estep, Paul Rose, Enric Sala
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0049437

Effects of Reef Proximity on the Structure of Fish Assemblages of Unconsolidated Substrata
Cited by: 28
Author(s): Arthur L. Schultz, Hamish A. Malcolm, Daniel J Bucher, Stephen Smith
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0205307

Burn injury alters the intestinal microbiome’s taxonomic composition and functional gene expression
Cited by: 24
Author(s): Nadine Beckmann, Amanda M. Pugh, Charles C. Caldwell
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0115454

Did Androgen-Binding Protein Paralogs Undergo Neo- and/or Subfunctionalization as the Abp Gene Region Expanded in the Mouse Genome?
Cited by: 9
Author(s): Robert C. Karn, Amanda Chung, Christina M. Laukaitis
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-020-68103-1

The influence of age and gender on emu (Dromaius novaehollandiae) fat
Cited by: 6
Author(s): Mateusz Bucław, D. Majewska, D. Szczerbińska, M. Ligocki
Software Mentions: 1
Published: over 6 years ago

10.3390/dj6020006

Effect of Violet-Blue Light on Streptococcus mutans-Induced Enamel Demineralization
Cited by: 4
Author(s): Grace F. Gomez, Frank Lippert, Masahiro Ando, Andréa Ferreira Zandoná, George J. Eckert, Richard L. Gregory
Software Mentions: 1
Published: over 8 years ago

10.9745/GHSP-D-20-00324

Applying the Community Health Worker Coverage and Capacity Tool for Time-Use Modeling for Program Planning in Rwanda and Zanzibar
Cited by: 6
Author(s): Melanie Morrow, Eric Sarriot, Allyson R. Nelson, Felix Sayinzoga, Beatrice Mukamana, Evariste Kayitare, Halima Khamis, Omar Abdalla, William Winfrey
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.4640

A public dataset of overground and treadmill walking kinematics and kinetics in healthy individuals
Cited by: 142
Author(s): Claudiane A. Fukuchi, Reginaldo K. Fukuchi, Marcos Duarte
Software Mentions: 1
Published: over 8 years ago

10.1038/s41597-020-00627-7

An Asian-centric human movement database capturing activities of daily living
Cited by: 10
Author(s): Phyllis Liang, Patrick W.H. Kwong, Ananda Sidarta, Chin Chong Yap, Winson Jianhong Tan, Lek Syn Lim, Pui Yee Chan, Christopher Wee Keong Kuah, Seng Kwee Wee, Karen Sui Geok Chua, Colin Quek, Wei Tech Ang
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-69065-0

Simultaneous FDG-PET/MRI detects hippocampal subfield metabolic differences in AD/MCI
Cited by: 8
Author(s): Mackenzie Carlson, Phillip DiGiacomo, Audrey P. Fan, Maged Goubran, Mohammad Mehdi Khalighi, Steven Chao, Minal Vasanawala, Max Wintermark, Elizabeth C. Mormino, Greg Zaharchuk, Michelle L. James, Michael Zeineh
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-10-S11-S13

Automatic identification of angiogenesis in double stained images of liver tissue
Cited by: 15
Author(s): Mutlu Mete, Leah Hennings, Horace J. Spencer, Ümit Topaloğlu
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0249613

Multisite evaluation of phenotypic plasticity for specialized metabolites, some involved in carrot quality and disease resistance
Cited by: 6
Author(s): Wilfried Chevalier, Sitti-Anlati Moussa, Miguel Medeiros Netto Ottoni, Cécile Dubois-Laurent, Sébastien Huet, Christophe Aubert, Elsa Desnoues, B. Navez, V. Cottet, Guillaume Chalot, Michel Jost, Laure Barrot, Gerald Freymark, Maarten Uittenbogaard, François Chaniet, Anita Suel, Marie-Hélène Bouvier Merlet, Latifa Hamama, Valérie Le Clerc, Mathilde Briard, Didier Peltier, Emmanuel Geoffriau
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0176419

Impact of life history traits on gene flow: A multispecies systematic review across oceanographic barriers in the Mediterranean Sea
Cited by: 110
Author(s): Marta Pascual, Borja Rives, Celia Schunter, Enrique Macpherson
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0111889

Differences in Life-Histories Refute Ecological Equivalence of Cryptic Species and Provide Clues to the Origin of Bathyal Halomonhystera (Nematoda)
Cited by: 24
Author(s): Jelle Van Campenhout, Sofie Derycke, Tom Moens, Ann Vanreusel
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0232689

Effect of age and the individual on the gastrointestinal bacteriome of ponies fed a high-starch diet
Cited by: 5
Author(s): Philippa K. Morrison, C. J. Newbold, Eleanor Jones, Hilary J. Worgan, Dai Grove‐White, Alex Dugdale, Clare Barfoot, Patricia A. Harris, Caroline McG. Argo
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0080536

Bleaching Susceptibility and Recovery of Colombian Caribbean Corals in Response to Water Current Exposure and Seasonal Upwelling
Cited by: 36
Author(s): Elisa Bayraktarov, Valeria Pizarro, Corvin Eidens, Thomas Wilke, Christian Wild
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0101701

Within-Otolith Variability in Chemical Fingerprints: Implications for Sampling Designs and Possible Environmental Interpretation
Cited by: 15
Author(s): Antonio Franco, Fabio Bulleri, Antonio Pennetta, Giuseppe E. De Benedetto, K.R. Clarke, Paolo Guidetti
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0047561

Global Change and Response of Coastal Dune Plants to the Combined Effects of Increased Sand Accretion (Burial) and Nutrient Availability
Cited by: 34
Author(s): Silvia Frosini, Claudio Lardicci, Elena Balestri
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2105-10-407

Protein-protein docking using region-based 3D Zernike descriptors
Cited by: 152
Author(s): Vishwesh Venkatraman, Yuxin Yang, Lee Sael, Daisuke Kihara
Software Mentions: 1
Published: almost 17 years ago

10.1186/1472-6807-10-5

Modeling of loops in proteins: a multi-method approach
Cited by: 36
Author(s): Michał H. Jamróz, Andrzej Koliński
Software Mentions: 1
Published: almost 17 years ago

10.1093/bioinformatics/btz185

CABS-dock standalone: a toolbox for flexible protein–peptide docking
Cited by: 47
Author(s): Mateusz Kurciński, Maciej Pawel Ciemny, Tymoteusz Oleniecki, Aleksander Kuriata, Aleksandra E. Badaczewska-Dawid, Andrzej Koliński, Sebastian Kmiecik
Software Mentions: 1
Published: over 7 years ago

10.1186/s12938-017-0363-6

A protocol for CABS-dock protein–peptide docking driven by side-chain contact information
Cited by: 7
Author(s): Mateusz Kurciński, Maciej Błaszczyk, Maciej Pawel Ciemny, Andrzej Koliński, Sebastian Kmiecik
Software Mentions: 1
Published: about 9 years ago

10.1093/bib/bby080

Protein–peptide docking using CABS-dock and contact information
Cited by: 29
Author(s): Maciej Błaszczyk, Maciej Pawel Ciemny, Andrzej Koliński, Mateusz Kurciński, Sebastian Kmiecik
Software Mentions: 1
Published: about 8 years ago

10.3390/molecules26113293

Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking
Cited by: 6
Author(s): M. Zalewski, Sebastian Kmiecik, Michał Koliński
Software Mentions: 1
Published: over 5 years ago

10.1073/pnas.1915372116

Reactivation of Epstein–Barr virus by a dual-responsive fluorescent EBNA1-targeting agent with Zn <sup>2+</sup> -chelating function
Cited by: 19
Author(s): Lijun Jiang, Hong Lok Lung, Tao Huang, Rongfeng Lan, Shuai Zha, Lai Sheung Chan, Waygen Thor, Tik Hung Tsoi, Ho Fai Chau, Cecilia Boreström, Steven L. Cobb, Sai Wah Tsao, Zhao Xiang Bian, Ga Lai Law, Wing Tak Wong, William Tai, Wai Yin Chau, Yujun Du, Lucas Tang, Alan Kwok Shing Chiang, Jaap M. Middeldorp, Kwok Wai Lo, Nai Ki Mak, Nicholas J. Long, Ka Leung Wong
Software Mentions: 1
Published: almost 7 years ago