10.3389/fmolb.2018.00082

Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package
Cited by: 29
Author(s): Paula P. Navarro, Henning Stahlberg, Daniel Castaño-Díez
Software Mentions: 8
Published: almost 8 years ago

10.1186/s12866-021-02222-1

Patterns of yeast diversity distribution and its drivers in rhizosphere soil of Hami melon orchards in different regions of Xinjiang
Cited by: 7
Author(s): Shanshan Zhu, Yonghui Lei, Chong Wang, Yu‐Mei Wei, Chuncheng Wang, Yanfei Sun
Software Mentions: 8
Published: about 5 years ago

10.1186/s12862-015-0570-3

Phylogenetic analyses suggest that diversification and body size evolution are independent in insects
Cited by: 19
Author(s): James Rainford, Michael Hofreiter, Peter J. Mayhew
Software Mentions: 8
Published: over 10 years ago

10.1038/s41392-021-00729-7

Technological advances in cancer immunity: from immunogenomics to single-cell analysis and artificial intelligence
Cited by: 34
Author(s): Ying Xu, Guan-Hua Su, Ding Ma, Yi Xiao, Zhi-Ming Shao
Software Mentions: 8
Published: almost 5 years ago

10.1002/elsc.202000053

Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard
Cited by: 3
Author(s): Marc Porr, F. Lange, Daniel Marquard, Laura Niemeyer, Patrick Lindner, Thomas Scheper, Sascha Beutel
Software Mentions: 8
Published: over 5 years ago

10.3390/cancers12102802

Comparison of the Tree-Based Machine Learning Algorithms to Cox Regression in Predicting the Survival of Oral and Pharyngeal Cancers: Analyses Based on SEER Database
Cited by: 31
Author(s): Mi Du, Dandara Haag, John Lynch, Murthy Mittinty
Software Mentions: 8
Published: over 5 years ago

10.1155/2018/3719703

Quantitative Assessment of the Physiological Parameters Influencing QT Interval Response to Medication: Application of Computational Intelligence Tools
Cited by: 2
Author(s): Sebastian Polak, Barbara Wiśniowska, Aleksander Mendyk, Adam Pacławski, Jakub Szlęk
Software Mentions: 8
Published: over 8 years ago

10.1186/s12859-021-04130-7

Correlation AnalyzeR: functional predictions from gene co-expression correlations
Cited by: 35
Author(s): Henry E. Miller, Alexander J.R. Bishop
Software Mentions: 8
Published: about 5 years ago

10.1111/2041-210X.12490

hext , a software supporting tree‐based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test
Cited by: 4
Author(s): Kevin Schneider, Stephan Koblmüller, Kristina M. Sefc
Software Mentions: 8
Published: over 10 years ago

10.1099/mgen.0.000337

Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes
Cited by: 39
Author(s): Morteza M. Saber, B. Jesse Shapiro
Software Mentions: 8
Published: over 6 years ago

10.1002/ece3.7269

3D genital shape complexity in female marine mammals
Cited by: 15
Author(s): Dara N. Orbach, Charlotte A. Brassey, James Gardiner, Patricia L. R. Brennan
Software Mentions: 8
Published: over 5 years ago

10.3389/fdata.2021.693674

A Benchmark for Data Imputation Methods
Cited by: 41
Author(s): Sebastian Jäger, Arndt Allhorn, Felix Bießmann
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41597-021-00870-6

The Amsterdam Open MRI Collection, a set of multimodal MRI datasets for individual difference analyses
Cited by: 45
Author(s): Lukas Snoek, Maite M. van der Miesen, Tinka Beemsterboer, Andries van der Leij, Annemarie Eigenhuis, H. Steven Scholte
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0143970

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome
Cited by: 37
Author(s): Katherine James, Shereen Al-Ali, Jessica Tarn, Simon Cockell, Colin S. Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin Pease, Paul Emery, Peter Lanyon, John Hunter, Monica Gupta, Michèle Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert J. Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, Anil Wipat, Julia L. Newton, David Jones, John D. Isaacs, Jennifer Hallinan, Wan‐Fai Ng
Software Mentions: 8
Published: over 10 years ago

10.1186/s12859-021-04124-5

Popularity and performance of bioinformatics software: the case of gene set analysis
Cited by: 21
Author(s): Chengshu Xie, Shaurya Jauhari, Antonio M. Mora
Software Mentions: 8
Published: about 5 years ago

10.1016/j.isci.2021.102762

NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cells
Cited by: 9
Author(s): Azzurra Codino, Tomasz W. Turowski, Louie N. van de Lagemaat, Ivayla Ivanova, Andrea Tavosanis, Christian Much, Tania Auchynnikava, Lina Vasiliauskaitė, Marcos Morgan, Juri Rappsilber, Robin Allshire, Kamil R. Kranc, David Tollervey, Dónal O’Carroll
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12864-021-07760-6

UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Cited by: 31
Author(s): Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime A Castro-Mondragón, Anthony Mathelier
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0000737

ADaCGH: A Parallelized Web-Based Application and R Package for the Analysis of aCGH Data
Cited by: 26
Author(s): Ramón Díaz‐Uriarte, Oscar M. Rueda
Software Mentions: 8
Published: almost 19 years ago

10.3389/fonc.2020.558596

Development and Validation of Autophagy-Related Gene Signature and Nomogram for Predicting Survival in Oral Squamous Cell Carcinoma
Cited by: 25
Author(s): Chen Hou, Hao Cai, Yue Zhu, Shuojin Huang, Song Fan, Jinsong Hou
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0179623

Estimating the basic reproduction rate of HFMD using the time series SIR model in Guangdong, China
Cited by: 28
Author(s): Zhicheng Du, Wangjian Zhang, Dingmei Zhang, Shicheng Yu, Yuantao Hao
Software Mentions: 8
Published: almost 9 years ago

10.18632/oncotarget.10834

Dysregulated long intergenic non-coding RNA modules contribute to heart failure
Cited by: 15
Author(s): Lin Pang, Jing Hu, Guanxiong Zhang, Xiang Li, Xinxin Zhang, Fulong Yu, Yujia Lan, Jiu Hua Xu, Bo Pang, Dong Han, Yun Xiao, Xia Li
Software Mentions: 8
Published: almost 10 years ago

10.1186/s12864-020-07123-7

Illuminating the dark side of the human transcriptome with long read transcript sequencing
Cited by: 76
Author(s): Richard Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. Brown, Jacqueline Smith, Alan Archibald, David W. Burt
Software Mentions: 8
Published: over 5 years ago

10.1186/s12967-021-02981-5

N6-Methyladenosine RNA modification in cerebrospinal fluid as a novel potential diagnostic biomarker for progressive multiple sclerosis
Cited by: 14
Author(s): Fei Ye, Tianzhu Wang, Xiaoxin Wu, Jie Liang, Jiaoxing Li, Wenli Sheng
Software Mentions: 8
Published: almost 5 years ago

10.3389/fmicb.2018.01868

Exposure to Yeast Shapes the Intestinal Bacterial Community Assembly in Zebrafish Larvae
Cited by: 29
Author(s): Prabhugouda Siriyappagouder, Jorge Galindo-Villegas, Jep Lokesh, Victoriano Mulero, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 8
Published: almost 8 years ago

10.1007/s00442-018-04329-1

Coping with climate change: limited behavioral responses to hot weather in a tropical carnivore
Cited by: 34
Author(s): Daniella Rabaiotti, Rosie Woodroffe
Software Mentions: 8
Published: over 7 years ago

10.3390/microorganisms8091265

Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change
Cited by: 10
Author(s): Young Hun Jung, Setu Bazie Tagele, HyunWoo Son, Jerald Conrad Ibal, Dorsaf Kerfahi, Hyunju Yun, Bora Lee, Clara Yongjoo Park, Eun Soo Kim, Sang-Jun Kim, Jae‐Ho Shin
Software Mentions: 8
Published: almost 6 years ago

10.3389/fmicb.2020.594928

Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity
Cited by: 45
Author(s): Sunil K. Raghav, Arup Ghosh, Jyotirmayee Turuk, Satish Kumar, Atimukta Jha, Swati Madhulika, Manasi Priyadarshini, Viplov Kumar Biswas, P. Sushree Shyamli, Balveer Singh, Neha Singh, Deepika Singh, Ankita Datey, Kiran Avula, Shuchi Smita, Jyotsnamayee Sabat, Debdutta Bhattacharya, Jaya Singh Kshatri, Dileep Vasudevan, Amol Ratnakar Suryawanshi, Rupesh Dash, Shantibhusan Senapati, Tushar Kant Beuria, Roy Swain, Soma Chattopadhyay, Gulam Hussain Syed, Anshuman Dixit, Punit Prasad, Sanghamitra Pati, Ajay Parida
Software Mentions: 8
Published: over 5 years ago

10.1002/ece3.2641

Convergent evolution in social swallows (Aves: Hirundinidae)
Cited by: 12
Author(s): Allison E. Johnson, Jonathan S. Mitchell, Mary Bomberger Brown
Software Mentions: 8
Published: over 9 years ago

10.3389/fcell.2021.677697

Single-Cell RNA-Sequencing Portraying Functional Diversity and Clinical Implications of IFI6 in Ovarian Cancer
Cited by: 7
Author(s): Hongyu Zhao, Zhefeng Li, Yan Gao, Jie Li, Xiaoting Zhao, Wentao Yue
Software Mentions: 8
Published: almost 5 years ago

10.3390/genes12030444

Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity
Cited by: 9
Author(s): Amanda T S Albanaz, Evgeny S. Gerasimov, Jeffrey Jon Shaw, Jovana Sádlová, Julius Lukeš, Petr Volf, Frederik Opperdoes, Alexei Y. Kostygov, Anzhelika Butenko, Vyacheslav Yurchenko
Software Mentions: 8
Published: over 5 years ago

10.1186/s40168-018-0468-6

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate
Cited by: 44
Author(s): Pål Trosvik, Eric J. de Muinck, Eli Knispel Rueness, Peter J. Fashing, Evan C. Beierschmitt, Kadie R. Callingham, Jacob B. Kraus, Thomas H. Trew, Amera Moges, Addisu Mekonnen, Vivek V. Venkataraman, Nga Nguyen
Software Mentions: 8
Published: about 8 years ago

10.3389/fpls.2019.00382

The Potential of Liming to Improve Drought Tolerance of Norway Spruce [Picea abies (L.) Karst.]
Cited by: 6
Author(s): M. Köhler, Jörg Kunz, Johannes Herrmann, Peter Hartmann, Lelde Jansone, Heike Puhlmann, Klaus von Wilpert, Jürgen Bauhus
Software Mentions: 8
Published: about 7 years ago

10.3389/fpsyg.2020.00810

Validation of the Toronto Empathy Questionnaire (TEQ) Among Medical Students in China: Analyses Using Three Psychometric Methods
Cited by: 10
Author(s): Richard Huan Xu, Eliza Lai Yi Wong, Sabrina Yu jun Lu, Ling-Ming Zhou, Jing Chang, Dong Wang
Software Mentions: 8
Published: about 6 years ago

10.1093/cid/ciz060

Global Review of the Age Distribution of Rotavirus Disease in Children Aged <5 Years Before the Introduction of Rotavirus Vaccination
Cited by: 35
Author(s): Mateusz Hasso-Agopsowicz, Chandresh N Ladva, Benjamin A. Lopman, Colin Sanderson, Adam L. Cohen, Jacqueline E. Tate, Ximena Riveros, Ana María Henao-Restrepo, Andrew Clark, Míriam Alkorta, Christina Atchison, Salem Banajeh, Sylvia Becker‐Dreps, Mohammed Benhafid, Nita Bhandari, Ladaporn Bodhidatta, Tessa Braeckman, Josephine Bwogi, Rita de Cássia Compagnoli Carmona, Gustavo Cilla, Ingrid L. Contreras-Roldan, Barbara S. Coulson, Nigel A. Cunliffe, Ron Dagan, N. Givon, Juan Ignacio Degiuseppe, Shaveta Dhiman, Zhang Dian, Jenna Diaz, Shubha Ranjan Dutta, Triveni Krishnan, Byomkesh Manna, Stephanie Fletcher-Lartey, Chuanxi Fu, D. Gendrel, Khalifa Sifaw Ghenghesh, G. Gonzalez Mago, Simona De Grazia, Keith Grimwood, Michelle Groome, Md. Ahshanul Haque, Ulrich Heininger, Eric R. Houpt, Miren Iturriza‐Gómara, Daniel Hungerford, Claudia Jarquín, John P. McCracken, I. L. Contreras, Celia Cordón-Rosales, Petra Kaiser-Labusch, Gagandeep Kang, Sumit Kar, Nicholas M. Kiulia, Karen L. Kotloff, Renat Latipov, Alexandre da Costa Linhares, Mathie Lorrot, Marcelo Gastón Mandile, Christine Mast, M. A. Mathew, F. Matinon-Torres, Jelle Matthijnssens, Z. Mladenova, Marina Monini, Milagrosa Montes, Ainara Arana, Mohammad Motamedifar, Akram Najafi, Tell Nelson, James Nokes, Francine Ntoumi, Kei Numazaki, Ciara E. O’Reilly, Theresa J. Ochoa, Nicola Page, Anne‐Laure Page, Céline Langendorf, Alexander T. Podkolzin, Caroline Quach, Maria Lúcia Rácz, Alexis de Rougemont, Guillermo M. Ruíz-Palacios, Samir K. Saha, Samir K. Saha, Syed Moinuddin Satter, L. Soares, Subijanto Marto Sudarmo, Katsumi Shigemura, Toshihiko Shirakawa, Alpha Fardah Athiyyah, Beckie Nnenna Tagbo, Phillip I. Tarr, Eileen J. Klein, Donna M. Denno, Ann Turner, Ezeonwu Bertilla Uzoma, R. R. Vatosoa, Ernest Apondi Wandera, Mary E. Wikswo, Daniel C. Payne, Huang Yhu-Chering, Tetsushi Yoshikawa, Ken Sugata, Qianqian Yuan, Liang LiYing, Khalequ Zaman, Xiaofang Zhou, S. X. Zhang, Wei Xu, Fatima Serhan, Tomoka Nakamura, Sébastien Antoni, Mary Agócs, Jillian Murray, Thomas Cherian, Jason M. Mwenda, Goitom Weldegebriel, Joseph Nsiari-Muzeyi Biey, Dah Cheikh, Nadia Teleb, Hossam Abdel Rahman, Hinda Ahmed, Danni Daniels, Dovile Videbaek, Annemarie Wasley, Simarjit Singh, Lúcia de Oliveira, Gloria Rey-Benito, N. Jennifer Sanwogou, Jayantha Liyanage, Pushpa Ranjan Wijesinghe, Batmunkh Nyambat, Varja Grabovac, Kimberley Fox, Fem Julia Paladin, Nicholas Henschke
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pbio.3001172

Perception of biological motion by jumping spiders
Cited by: 16
Author(s): Massimo De Agrò, Daniela C. Rößler, Kris Kim, Paul S. Shamble
Software Mentions: 8
Published: almost 5 years ago

10.1002/ece3.6172

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)
Cited by: 10
Author(s): Matthew A. Kolmann, Michael D. Burns, Justin Y. K. Ng, Nathan R. Lovejoy, Devin D. Bloom
Software Mentions: 8
Published: over 6 years ago

10.1038/s41598-021-94853-7

Unique chemical parameters and microbial activity lead to increased archaeological preservation at the Roman frontier site of Vindolanda, UK
Cited by: 3
Author(s): Caroline Orr, Rhys Williams, Hrafnhildur Halldórsdóttir, Andrew Birley, Elizabeth M. Greene, Andrew Nelson, T. Komang Ralebitso-Senior, Gillian Taylor
Software Mentions: 8
Published: almost 5 years ago

10.1007/s00122-020-03667-0

Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera ‘Pinot Noir’ and Vitis spp. genotypes
Cited by: 6
Author(s): Robert Richter, Susanne Rossmann, Doreen Gabriel, Reinhard Töpfer, Klaus Theres, Eva Zyprian
Software Mentions: 8
Published: almost 6 years ago

10.1111/jcmm.16712

Cytokeratin 5 and cytokeratin 20 inversely correlate with tumour grading in Ta non‐muscle‐invasive bladder cancer
Cited by: 7
Author(s): Tim Muilwijk, Murat Akand, Frank Van der Aa, Vincent De Coninck, Marc Claessens, Robert Hente, Markus Eckstein, Yves Allory, Louis Libbrecht, Steven Joniau, Thomas Gevaert
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41598-021-93874-6

Factors associated with baseline mortality in Norwegian Atlantic salmon farming
Cited by: 26
Author(s): Victor Henrique Silva de Oliveira, Katharine R. Dean, Lars Qviller, Carsten Kirkeby, Bogi Bech Jensen
Software Mentions: 8
Published: almost 5 years ago

10.15252/msb.20209667

Using single‐plant‐omics in the field to link maize genes to functions and phenotypes
Cited by: 17
Author(s): Daniel Felipe Cruz, Sam Meyer, Joke Ampe, Heike Sprenger, Dorota Herman, Tom Van Hautegem, Jolien De Block, Dirk Inzé, Hilde Nelissen, Steven Maere
Software Mentions: 8
Published: over 5 years ago

10.1186/s13007-021-00744-3

PredCRG: A computational method for recognition of plant circadian genes by employing support vector machine with Laplace kernel
Cited by: 4
Author(s): Prabina Kumar Meher, Ansuman Mohapatra, Subhrajit Satpathy, Anuj Sharma, Isha Saini, Sukanta Kumar Pradhan, Anil Rai
Software Mentions: 8
Published: about 5 years ago

10.3389/fpls.2021.647375

Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae)
Cited by: 11
Author(s): Judith Fehrer, Renata Slavíková, Ladislava Paštová, Jiřina Josefiová, Patrik Mráz, Jindřich Chrtek, Yann Bertrand
Software Mentions: 8
Published: over 5 years ago

10.3389/fpls.2018.00796

An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus
Cited by: 23
Author(s): Hongge Li, Xi Cheng, Liping Zhang, Jihong Hu, Fugui Zhang, Biyun Chen, Kun Xu, Guizhen Gao, Hao Li, Lixia Li, Qian Huang, Zaiyun Li, Guiqin Yan, Xiaoming Wu
Software Mentions: 8
Published: about 8 years ago

10.1186/s12862-019-1466-4

The multi-peak adaptive landscape of crocodylomorph body size evolution
Cited by: 42
Author(s): Pedro Godoy, Roger Benson, Mario Bronzati, Richard J. Butler
Software Mentions: 8
Published: almost 7 years ago

10.3389/fonc.2021.654388

MYD88 Is a Potential Prognostic Gene and Immune Signature of Tumor Microenvironment for Gliomas
Cited by: 13
Author(s): Qinglong Guo, Xing Xiao, Jinsen Zhang
Software Mentions: 8
Published: about 5 years ago

10.3389/fmicb.2018.02621

Elevated CO2 Has Little Influence on the Bacterial Communities Associated With the pH-Tolerant Coral, Massive Porites spp.
Cited by: 18
Author(s): Paul A. O’Brien, Hillary A. Smith, Stewart Fallon, Katharina Fabricius, Bette L. Willis, Kathleen M. Morrow, David G. Bourne
Software Mentions: 8
Published: over 7 years ago

10.3390/microorganisms9071454

First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes
Cited by: 8
Author(s): Julia Moll, Friederike Roy, Claus Bässler, Jacob Heilmann‐Clausen, Martin Hofrichter, Harald Kellner, Doris Krabel, Jan Henrik Schmidt, François Buscot, Björn Hoppe
Software Mentions: 8
Published: almost 5 years ago

10.2196/jmir.5461

What Are We Looking for in Computer-Based Learning Interventions in Medical Education? A Systematic Review
Cited by: 60
Author(s): Tiago Taveira-Gomes, Patrícia Ferreira, Isabel Taveira-Gomes, Mílton Severo, Manuela Ferreira
Software Mentions: 8
Published: almost 10 years ago

10.3389/fgene.2021.602196

AI Aided Design of Epitope-Based Vaccine for the Induction of Cellular Immune Responses Against SARS-CoV-2
Cited by: 4
Author(s): Giovanni Mazzocco, Iga Niemiec, Alexander Myronov, Piotr Skoczylas, Jan Kaczmarczyk, Anna Sanecka-Duin, Katarzyna Gruba, Paulina Król, Michał Drwal, Marian Szczepanik, Krzysztof Pyrć, Piotr Stępniak
Software Mentions: 8
Published: over 5 years ago

10.1097/MD.0000000000026194

Integrated analysis of ceRNA network in hepatocellular carcinoma using bioinformatics analysis
Cited by: 5
Author(s): Yu Luo, Hongjuan Li, Hongli Huang, Ling Xue, Haiwen Li, Li Liu, Haiyan Fu
Software Mentions: 8
Published: about 5 years ago

10.3389/fnhum.2019.00066

Finger Temperature: A Psychophysiological Assessment of the Attentional State
Cited by: 1
Author(s): Rodrigo C. Vergara, Cristóbal Moënne‐Loccoz, Camila Ávalos, Juan Ignacio Egaña, Pedro Maldonado
Software Mentions: 8
Published: over 7 years ago

10.1186/s12920-020-0729-7

ERα-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer
Cited by: 6
Author(s): Chun-Lin Lin, Xueying Tan, Chun-Liang Chen, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ya-Ting Hsu, Chiou‐Miin Wang, Nameer B. Kirma, Ching-Hung Lin, Kate Lathrop, Richard M. Elledge, Virginia Kaklamani, Kohzoh Mitsuya, Tim H.M. Huang
Software Mentions: 8
Published: about 6 years ago

10.1002/ece3.7032

A comparison of two methods for estimating measurement repeatability in morphometric studies
Cited by: 2
Author(s): Zachariah Wylde, Russell Bonduriansky
Software Mentions: 8
Published: over 5 years ago

10.1186/s12864-021-07895-6

Identification of ferroptosis genes in immune infiltration and prognosis in thyroid papillary carcinoma using network analysis
Cited by: 26
Author(s): Rui-Qing Lin, Conor E. Fogarty, Bao‐Qing Ma, Hejie Li, Guoying Ni, Xiaosong Liu, Jing Yuan, Tianfang Wang
Software Mentions: 8
Published: almost 5 years ago

10.1017/S1368980019003239

Four decades of socio-economic inequality and secular change in the physical growth of Guatemalans
Cited by: 14
Author(s): Liina Mansukoski, William Johnson, Katherine Brooke‐Wavell, J. Andres Galvez-Sobral, L.R. Furlan, Tim J. Cole, Barry Bogin
Software Mentions: 8
Published: over 6 years ago

10.1186/s12864-021-07898-3

Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events
Cited by: 4
Author(s): Ümit Akköse, Veysel Oğulcan Kaya, Laura A. Lindsey-Boltz, Zeynep Karagöz, Adam D. Brown, Peter A. Larsen, Anne D. Yoder, Aziz Sancar, Ogün Adebali
Software Mentions: 8
Published: almost 5 years ago

10.1098/rstb.2020.0362

Land-use change and rodent-borne diseases: hazards on the shared socioeconomic pathways
Cited by: 13
Author(s): Gabriel E. García‐Peña, André V. Rubio, Hugo Mendoza, Miguel Fernández, Matthew T. Milholland, A. Alonso Aguirre, Gerardo Suzán, Carlos Zambrana‐Torrelio
Software Mentions: 8
Published: almost 5 years ago

10.3390/microorganisms8040485

Characterization of the Duodenal Mucosal Microbiome in Obese Adult Subjects by 16S rRNA Sequencing
Cited by: 33
Author(s): Carmela Nardelli, Ilaria Granata, Valeria D’Argenio, Salvatore Tramontano, Debora Compare, Mario Rosario Guarracino, Gerardo Nardone, Vincenzo Pilone, Lucia Sacchetti
Software Mentions: 8
Published: about 6 years ago

10.3390/microorganisms9061273

Inoculation with Mycorrhizal Fungi and Irrigation Management Shape the Bacterial and Fungal Communities and Networks in Vineyard Soils
Cited by: 8
Author(s): Nazareth Torres, Runze Yu, S. Kaan Kurtural
Software Mentions: 8
Published: about 5 years ago

10.1155/2021/9048375

Nomograms for Predicting Prognosis of Primary Mediastinal Seminoma: A Population-Based Study
Cited by: 2
Author(s): Weining Huang, Jingwen Luo, Xianghong Zhou, Ying Zhao, Tao Zhang, Xuelei Ma
Software Mentions: 8
Published: about 5 years ago

10.1038/s41598-020-76256-2

Selection of sponge-associated bacteria with high potential for the production of antibacterial compounds
Cited by: 11
Author(s): Riyanti, Walter Balansa, Yang Liu, Abha Sharma, Sanja Mihajlović, Christoph Hartwig, Benedikt Leis, Frets Jonas Rieuwpassa, Frans Gruber Ijong, Heike Wägele, Gabriele M. König, Till F. Schäberle
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0180435

White-nose syndrome pathology grading in Nearctic and Palearctic bats
Cited by: 38
Author(s): Jiří Pikula, Sybill K. Amelon, Hana Banďouchová, Tomáš Bartonička, Hana Berková, Jiří Brichta, Sarah E. Hooper, Tomasz Kokurewicz, Miroslav Kolařík, Bernd Köllner, Veronika Kováčová, Petr Linhart, Vladimír Piaček, Gregory G. Turner, Jan Zukal, Natália Martínková
Software Mentions: 8
Published: almost 9 years ago

10.1186/s12859-020-3538-2

CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments
Cited by: 39
Author(s): H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens, Ryan M. O’Connell
Software Mentions: 8
Published: about 6 years ago

10.1002/ece3.5289

Disturbance history mediates climate change effects on subtropical forest biomass and dynamics
Cited by: 16
Author(s): Alexandre F. Souza, Solon Jonas Longhi
Software Mentions: 8
Published: about 7 years ago

10.3389/fgene.2020.573515

SETDB1 Overexpression Sets an Intertumoral Transcriptomic Divergence in Non-small Cell Lung Carcinoma
Cited by: 8
Author(s): Yong‐Kook Kang, Byungkuk Min
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1007358

Seven quick tips for analysis scripts in neuroimaging
Cited by: 11
Author(s): Marijn van Vliet
Software Mentions: 8
Published: over 6 years ago

10.1186/s12917-015-0593-4

A preliminary study of the effect of closed incision management with negative pressure wound therapy over high-risk incisions
Cited by: 14
Author(s): Karen L Perry, Lynda Rutherford, D. Sajik, Mieghan Bruce
Software Mentions: 8
Published: over 10 years ago

10.1038/s41598-018-34019-0

Microbial structure and function in infant and juvenile rhesus macaques are primarily affected by age, not vaccination status
Cited by: 4
Author(s): Yu Hasegawa, Britni Curtis, Vernon Yutuc, Megan Rulien, Kelly Morrisroe, Kristin Watkins, Clayton Ferrier, Chris English, Laura Hewitson, Carolyn M. Slupsky
Software Mentions: 8
Published: over 7 years ago

10.1128/mSphere.00488-17

Novel ITS1 Fungal Primers for Characterization of the Mycobiome
Cited by: 68
Author(s): Mykhaylo Usyk, Christine P. Zolnik, Hitesh D. Patel, Michael H. Levi, Robert D. Burk
Software Mentions: 8
Published: over 8 years ago

10.3389/fgene.2021.647353

Identification of Hub Genes and Their Correlation With Immune Infiltration Cells in Hepatocellular Carcinoma Based on GEO and TCGA Databases
Cited by: 22
Author(s): Rui Huang, Jinying Liu, Hui Li, Lierui Zheng, Haojun Jin, Yaqing Zhang, Wei Ma, Junhong Su, Min Wang, Kun Yang
Software Mentions: 8
Published: about 5 years ago

10.3389/fninf.2015.00011

Python in neuroscience
Cited by: 51
Author(s): Eilif Müller, James A. Bednar, Markus Diesmann, Marc‐Oliver Gewaltig, Michael L. Hines, Andrew P. Davison
Software Mentions: 8
Published: about 11 years ago

10.1038/s41598-021-97491-1

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
Cited by: 5
Author(s): Kristian Peters, Stephanie Herman, Payam Emami Khoonsari, Joachim Burman, Steffen Neumann, Kim Kultima
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12955-017-0768-8

Psychometric evaluation of the Oswestry Disability Index in patients with chronic low back pain: factor and Mokken analyses
Cited by: 42
Author(s): Chin-Pang Lee, Tsai-Sheng Fu, Chia-Yih Liu, Ching‐I Hung
Software Mentions: 8
Published: over 8 years ago

10.3897/BDJ.5.e20530

red - an R package to facilitate species red list assessments according to the IUCN criteria
Cited by: 44
Author(s): Pedro Cardoso
Software Mentions: 8
Published: over 8 years ago

10.3390/microorganisms9091943

Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network
Cited by: 6
Author(s): Milan Varsadiya, Tim Urich, Gustaf Hugelius, Jiří Bárta
Software Mentions: 8
Published: almost 5 years ago

10.1186/s40168-021-01140-8

Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
Cited by: 18
Author(s): Olga María Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laísa Corrêa Braga Marques, Nathalie Fortin, Ben Shapiro
Software Mentions: 8
Published: over 4 years ago

10.1093/bioinformatics/btaa555

Benchmark of software tools for prokaryotic chromosomal interaction domain identification
Cited by: 3
Author(s): Mikhail D. Magnitov, Veronika S Kuznetsova, Sergey V. Ulianov, Sergey V. Razin, Alexander Tyakht
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-019-48746-5

Gene Expression Predicts Histological Severity and Reveals Distinct Molecular Profiles of Nonalcoholic Fatty Liver Disease
Cited by: 93
Author(s): Stephen A. Hoang, Abdul M. Oseini, Ryan E. Feaver, Banumathi K. Cole, Amon Asgharpour, Robert Vincent, Mohammad Shadab Siddiqui, Mark Lawson, Nathan Day, Justin M. Taylor, Brian R. Wamhoff, Faridoddin Mirshahi, Melissa J. Contos, Michael O. Idowu, Arun J. Sanyal
Software Mentions: 8
Published: almost 7 years ago

10.1002/ece3.5940

Hollow oaks and beetle functional diversity: Significance of surroundings extends beyond taxonomy
Cited by: 11
Author(s): Ross Wetherbee, Tone Birkemoe, Olav Skarpaas, Anne Sverdrup‐Thygeson
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pone.0255849

Literary runaway: Increasingly more references cited per academic research article from 1980 to 2019
Cited by: 1
Author(s): Chaoyang Dai, Chen Quan, Tao Wan, Fan Liu, Ya‐Jun Gong, Qingfeng Wang
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41598-019-47117-4

Using a trait-based approach to understand the efficiency of a selective device in a multispecific fishery
Cited by: 7
Author(s): Maud Mouchet, Manon Poirson, Fabien Morandeau, Camille Vogel, Sonia Méhault, Dorothée Kopp
Software Mentions: 8
Published: almost 7 years ago

10.1523/ENEURO.0339-19.2020

Function, Innervation, and Neurotransmitter Signaling in Mice Lacking Type-II Taste Cells
Cited by: 16
Author(s): Eric D. Larson, Aurélie Vandenbeuch, Catherine B. Anderson, Sue C. Kinnamon
Software Mentions: 8
Published: over 6 years ago

10.1186/1476-072X-14-7

Using geovisual analytics in Google Earth to understand disease distribution: a case study of campylobacteriosis in the Czech Republic (2008–2012)
Cited by: 19
Author(s): L. Marek, Pavel Tuček, Vít Pásztó
Software Mentions: 8
Published: over 11 years ago

10.1093/cz/zoab026

Hormonal modulation of reproduction and fertility signaling in polistine wasps
Cited by: 8
Author(s): Cíntia Akemi Oi, Rafael Carvalho da Silva, I. D. R. Stevens, Helena Mendes Ferreira, Fábio Santos do Nascimento, Tom Wenseleers
Software Mentions: 8
Published: over 5 years ago

10.1534/g3.119.400126

An R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction
Cited by: 38
Author(s): Osval A. Montesinos-L֯ópez, Abelardo Montesinos‐López, Francisco Javier Luna-Vázquez, Fernando H. Toledo, Paulino Pérez‐Rodríguez, Morten Lillemo, J. Crossa
Software Mentions: 8
Published: about 7 years ago

10.3390/biology8040088

Reproductive Biology and Ecology of the Green Mussel Perna viridis: A Multidisciplinary Approach
Cited by: 8
Author(s): Md. Asaduzzaman, Aysha Rahi Noor, Md. Moshiur Rahman, Shirin Akter, Nayeema Ferdausy Hoque, Abrar Shakil, Abdul Wahab
Software Mentions: 8
Published: over 6 years ago

10.3389/fonc.2021.616133

Analysis of Autophagy-Related Signatures Identified Two Distinct Subtypes for Evaluating the Tumor Immune Microenvironment and Predicting Prognosis in Ovarian Cancer
Cited by: 11
Author(s): Xingyu Chen, Hua Lan, Dong He, Zhanwang Wang, Runshi Xu, Jing Yuan, Mengqing Xiao, Yao Zhang, Lian Gong, Songshu Xiao, Ke Cao
Software Mentions: 8
Published: about 5 years ago

10.1007/s10278-017-0037-8

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research
Cited by: 239
Author(s): Ziv Yaniv, Bradley Lowekamp, Hans J. Johnson, Richard Beare
Software Mentions: 8
Published: over 8 years ago

10.7717/peerj-cs.521

LinkPred: a high performance library for link prediction in complex networks
Cited by: 0
Author(s): Said Kerrache
Software Mentions: 8
Published: about 5 years ago

10.1186/s13321-018-0270-2

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
Cited by: 86
Author(s): Jie Dong, Zhi‐Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Aiping Lu, Alex F. Chen, Dong‐Sheng Cao
Software Mentions: 8
Published: over 8 years ago

10.1016/j.ymeth.2015.07.012

Construction of an instant structured illumination microscope
Cited by: 30
Author(s): Alistair Curd, Alexa Cleasby, Katarzyna Makowska, Andrew G. York, Hari Shroff, Michelle Peckham
Software Mentions: 8
Published: over 10 years ago

10.18632/aging.202515

Cell differentiation trajectory predicts patient potential immunotherapy response and prognosis in gastric cancer
Cited by: 18
Author(s): Renshen Xiang, Yuping Rong, Yuhang Ge, Wei Song, Jun Ren, Tao Fu
Software Mentions: 8
Published: over 5 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: about 5 years ago

10.1534/g3.119.400185

ARMOR: An <u>A</u>utomated <u>R</u>eproducible <u>MO</u>dular Workflow for Preprocessing and Differential Analysis of <u>R</u>NA-seq Data
Cited by: 35
Author(s): Stephany Orjuela, Ronald Huang, Katharina Hembach, Mark D. Robinson, Charlotte Soneson
Software Mentions: 8
Published: almost 7 years ago

10.3390/ijms21134630

Self-Repair in Cacti Branches: Comparative Analyses of Their Morphology, Anatomy, and Biomechanics
Cited by: 10
Author(s): Max D. Mylo, Friederike Krüger, Thomas Speck, Olga Speck
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.pone.0248889

Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms
Cited by: 10
Author(s): Jozsef Karman, Jing Wang, Corneliu Bodea, Sherry Cao, Marc C. Levesque
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0197370

Immunity levels to poliovirus in Lao children and adults before the vaccine-derived poliovirus outbreak: A retrospective study
Cited by: 2
Author(s): Maude Pauly, Antony P. Black, Phonepaseuth Khampanisong, Phonethipsavanh Nouanthong, Judith M. Hübschen, Naphavanh Nanthavong, Kong Sayasinh, Prapan Jutavijittum, Bounthome Samountry, Anonh Xeuatvongsa, Sabine Diedrich, Claude P. Muller
Software Mentions: 8
Published: about 8 years ago

10.1371/journal.pcbi.1007666

Methods detecting rhythmic gene expression are biologically relevant only for strong signal
Cited by: 22
Author(s): David Laloum, Marc Robinson‐Rechavi
Software Mentions: 8
Published: over 6 years ago

10.1186/s12967-021-03065-0

Comprehensive analysis of EMT-related genes and lncRNAs in the prognosis, immunity, and drug treatment of colorectal cancer
Cited by: 28
Author(s): Yang Yang, Mingyang Feng, Liangliang Bai, Wei‐Ting Liao, Kaiyu Zhou, Mengxi Zhang, Qiuji Wu, Feng Wen, Wenhua Lei, Pengfei Zhang, Nan Zhang, Jiaxing Huang, Li Qiu
Software Mentions: 8
Published: almost 5 years ago