10.1038/srep25668

Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy
Cited by: 76
Author(s): Konrad J. Dębski, Asla Pitkänen, Noora Puhakka, Anna Bot, Ishant Khurana, K N Harikrishnan, Mark Ziemann, Antony Kaspi, Assam El‐Osta, Katarzyna Łukasiuk, Katja Kobow
Software Mentions: 5
Published: about 10 years ago

10.1038/s41392-020-00221-8

An individualized immune signature of pretreatment biopsies predicts pathological complete response to neoadjuvant chemoradiotherapy and outcomes in patients with esophageal squamous cell carcinoma
Cited by: 17
Author(s): Chaoqi Zhang, Guochao Zhang, Nan Sun, Zhen Zhang, Liyan Xue, Zhihui Zhang, Haijun Yang, Yuejun Luo, Xiaoli Zheng, Yonglei Zhang, Yufen Yuan, Ruixue Lei, Zhaoyang Yang, Bo Zheng, Le Wang, Yun Cao, Feng Wang, Sihui Wang, Shugeng Gao, Qi Xue, Yi Zhang, Jie He
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-017-4007-9

Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components
Cited by: 28
Author(s): Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, C. L. McGivney, K. F. Gough, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pgen.1009213

Gene regulatory effects of a large chromosomal inversion in highland maize
Cited by: 38
Author(s): Taylor M. Crow, James Ta, Saghi Nojoomi, M. Rocío Aguilar-Rangel, Jorge Vladimir Torres Rodríguez, David M. Gates, Rubén Rellán‐Álvarez, Ruairidh J. H. Sawers, Daniel E. Runcie
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2105-14-165

Separate-channel analysis of two-channel microarrays: recovering inter-spot information
Cited by: 28
Author(s): Gordon K. Smyth, Naomi Altman
Software Mentions: 5
Published: about 13 years ago

10.1186/s12864-017-3936-7

Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
Cited by: 35
Author(s): Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D. G. Jones, Matt Clark
Software Mentions: 5
Published: almost 9 years ago

10.15252/msb.20199005

Combinatorial prediction of marker panels from single‐cell transcriptomic data
Cited by: 54
Author(s): Conor P. Delaney, Alexandra Schnell, Louis Cammarata, Aaron Yao-Smith, Aviv Regev, Vijay K. Kuchroo, Meromit Singer
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12859-021-04355-6

Fast and exact quantification of motif occurrences in biological sequences
Cited by: 1
Author(s): Mattia Prosperi, Simone Marini, Christina Boucher
Software Mentions: 5
Published: almost 5 years ago

10.1186/s40168-020-00966-y

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation
Cited by: 10
Author(s): Rajesh Kaushal, Peng Li, Sunil Kumar Singh, Mengrui Zhang, Xinlian Zhang, Juan Ignacio Vílchez, Zhen Wang, Danxia He, Yu Ye, Suhui Lv, Zhongtian Xu, Rafael J. L. Morcillo, Wei Wang, Wei-Chang Huang, Paul W. Paré, Chun‐Peng Song, Jian‐Kang Zhu, Renyi Liu, Wenxuan Zhong, Ping Ma, Huiming Zhang
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.561254

Development and Validation of a Novel Metabolic-Related Signature Predicting Overall Survival for Pancreatic Cancer
Cited by: 5
Author(s): Junyu Huo, Liqun Wu, Yunjin Zang
Software Mentions: 5
Published: about 5 years ago

10.15252/msb.20209844

Integrative characterization of the near‐minimal bacterium <i>Mesoplasma florum</i>
Cited by: 8
Author(s): Dominick Matteau, Jean-Christophe Lachance, Frédéric Grenier, Samuel Gauthier, James M. Daubenspeck, Kevin Dybvig, Daniel Garneau, Thomas F. Knight, Pierre-Étienne Jacques, Sébastien Rodrigue
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-016-1154-y

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016
Cited by: 0
Author(s): Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park, Xueyuan Cao, Stanley Pounds, Susana C. Raimondi, James R. Downing, Raul C. Ribeiro, Jeffery Rubnitz, Jatinder K. Lamba, Bernie J. Daigle, Deborah C. Hay Burgess, Stephanie Gehrlich, John C. Carmen, Nicholas Johnson, Chandrakanth Emani, Kalpani De Silva, Michael P. Heaton, Theodore S. Kalbfleisch, Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun T. Ajayi, Fatih Şen, Eunice Y. Huang, Mohammad Mohebbi, Luaire Florian, Douglas Jackson, John Naber, Akm Sabbir, Sally R. Ellingson, Yuping Lu, Charles Phillips, Michael A. Langston, Rahul Kumar Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui, Mohammed Sayed, Jing Wang, Qi Liu, Yu Shyr, Xiaofei Zhang, Naresh Prodduturi, Gavin R. Oliver, Diane E. Grill, Jie Na, Jeanette E. Eckel‐Passow, Eric W. Klee, Michael M. Goodin, Mark L. Farman, Harrison A Inocencio, Chanyong Jang, Jerzy W. Jaromczyk, Neil Moore, Kelly L Sovacool, Leon Dent, Mike Izban, Sammed N. Mandape, Shruti S. Sakhare, Siddharth Pratap, Dana Marshall, M Scotty DePriest, James N. MacLeod, H. Marblestone Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Smalter Hall, Philip Kreisle, Jessica Lasher, B.K. Oakes, Allison Speer, Maximilian Valentine, Naga Satya V Rao Nagisetty, Rony Jose, Robert J. Rooney, David S. Hains
Software Mentions: 5
Published: almost 10 years ago

10.1186/s12874-020-01201-w

Re-evaluation of the comparative effectiveness of bootstrap-based optimism correction methods in the development of multivariable clinical prediction models
Cited by: 33
Author(s): Katsuhiro Iba, Tomohiro Shinozaki, Kazushi Maruo, Hisashi Noma
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2020.595361

Identification of Hub Prognosis-Associated Oxidative Stress Genes in Pancreatic Cancer Using Integrated Bioinformatics Analysis
Cited by: 8
Author(s): Xin Qiu, Qin-Han Hou, Qiuyue Shi, Haixing Jiang, Shanyu Qin
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-92838-0

Light intensity and spectral composition drive reproductive success in the marine benthic diatom Seminavis robusta
Cited by: 4
Author(s): Gust Bilcke, Lore Van Craenenbroeck, Alexandre Castagna, Cristina Maria Osuna-Cruz, Klaas Vandepoele, Koen Sabbe, Lieven De Veylder, Wim Vyverman
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0227860

Fungal diversity in canopy soil of silver beech, Nothofagus menziesii (Nothofagaceae)
Cited by: 4
Author(s): Andy R. Nilsen, Suliana Teasdale, P. L. Guy, Tina C. Summerfield, David A. Orlovich
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2018.01309

A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative Genomics
Cited by: 17
Author(s): Chuanmei Zhu, Jiani Yang, Mathew S. Box, Elizabeth A. Kellogg, Andrea L. Eveland
Software Mentions: 5
Published: almost 8 years ago

10.3389/fninf.2019.00053

A Comparison of Shallow and Deep Learning Methods for Predicting Cognitive Performance of Stroke Patients From MRI Lesion Images
Cited by: 52
Author(s): Sucheta Chauhan, Lovekesh Vig, Michele De Filippo De Grazia, Maurizio Corbetta, Shandar Ahmad, Marco Zorzi
Software Mentions: 5
Published: almost 7 years ago

10.1186/1471-2105-10-S10-S5

KA-SB: from data integration to large scale reasoning
Cited by: 3
Author(s): María del Mar Roldán‐García, Ismael Navas‐Delgado, Amine Kerzazi, Othmane Chniber, Joaquin J. Molina-Castro, José F. Aldana‐Montes
Software Mentions: 5
Published: almost 17 years ago

10.1186/s13036-018-0112-9

Machine learning analysis of microbial flow cytometry data from nanoparticles, antibiotics and carbon sources perturbed anaerobic microbiomes
Cited by: 10
Author(s): Abhishek S. Dhoble, Pratik Lahiri, Kaustubh Bhalerao
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pgen.1005693

Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome
Cited by: 24
Author(s): Luke Isbel, Richa Srivastava, Harald Oey, Alex Spurling, Lucia Daxinger, Hamsa Puthalakath, Emma Whitelaw
Software Mentions: 5
Published: over 10 years ago

10.1098/rsos.200792

Tissue-specific developmental regulation and isoform usage underlie the role of<i>doublesex</i>in sex differentiation and mimicry in<i>Papilio</i>swallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: almost 6 years ago

10.1111/jcmm.16799

Comprehensive characterization of pathological stage‐related genes of papillary thyroid cancer along with survival prediction
Cited by: 1
Author(s): Lei Xu, Liang Feng, Haiyan Li, Menglong Li, Yongmei Xie, Zhihui Li, Yanzhi Guo
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0235117

Using structured pathology data to predict hospital-wide mortality at admission
Cited by: 6
Author(s): Mieke Deschepper, Willem Waegeman, Dirk Vogelaers, Kristof Eeckloo
Software Mentions: 5
Published: about 6 years ago

10.1186/s12983-016-0178-5

Development of foraging skills in two orangutan populations: needing to learn or needing to grow?
Cited by: 36
Author(s): Caroline Schuppli, Sofia Forss, Ellen Meulman, Nicole Zweifel, Kevin C. Lee, Evasari Rukmana, Erin R. Vogel, Maria A. van Noordwijk, Carel P. van Schaik
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0204920

Predicting acute kidney injury at hospital re-entry using high-dimensional electronic health record data
Cited by: 8
Author(s): Samuel J. Weisenthal, Caroline M. Quill, Samir A. Farooq, Henry Kautz, Martin S. Zand
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.60100

Sequential perturbations to mouse corticogenesis following in utero maternal immune activation
Cited by: 15
Author(s): Cesar P Canales, Myka L. Estes, Karol Cichewicz, Kartik Angara, John Paul Aboubechara, Scott A. Cameron, Kathryn Prendergast, Linda Su-Feher, Iva Zdilar, Ellie J Kreun, Emma C Connolly, Jin Myeong Seo, Jack B Goon, Kathleen Farrelly, Tyler W. Stradleigh, Deborah van der List, Lori Haapanen, Judy Van de Water, Daniel Vogt, A. Kimberley McAllister, A. Nord
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2020.548618

Microbiome in Healthy Women Between Two Districts With Different Air Quality Index
Cited by: 8
Author(s): Yinhua Wu, Zujin Wang, Yu Zhang, Li-Ming Ruan, Ang Li, Xiaoyan Liu
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0254514

Reaching to inhibit a prepotent response: A wearable 3-axis accelerometer kinematic analysis
Cited by: 2
Author(s): Alessia Angeli, Irene Valori, Teresa Farroni, Gustavo Marfia
Software Mentions: 5
Published: about 5 years ago

10.1186/s13014-020-01699-w

Imaging biomarkers of contrast-enhanced computed tomography predict survival in oesophageal cancer after definitive concurrent chemoradiotherapy
Cited by: 4
Author(s): Chengbing Zeng, Tian‐Tian Zhai, Jianzhou Chen, Longjia Guo, Bao-Tian Huang, Hong Guo, Guozhi Lv, Tingting Zhuang, Weitong Liu, Ting Luo, Yanxuan Wu, Guopeng Peng, Derui Li, Chuangzhen Chen
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-85669-6

Transcriptome of rhesus macaque (Macaca mulatta) exposed to total-body irradiation
Cited by: 12
Author(s): Yaoxiang Li, Jatinder Singh, Rency S. Varghese, Yubo Zhang, Oluseyi O. Fatanmi, Amrita K. Cheema, Vijay K. Singh
Software Mentions: 5
Published: over 5 years ago

10.1098/rsos.201795

Understanding spatial patterns in rape reporting delays
Cited by: 5
Author(s): Konstantin Klemmer, Daniel B. Neill, Stephen A. Jarvis
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0241993

Association of small, dense LDL-cholesterol concentration and lipoprotein particle characteristics with coronary heart disease: A systematic review and meta-analysis
Cited by: 52
Author(s): Lathan Liou, Stephen Kaptoge
Software Mentions: 5
Published: over 5 years ago

10.3389/fnut.2019.00058

Integrated Analysis of Human Milk Microbiota With Oligosaccharides and Fatty Acids in the CHILD Cohort
Cited by: 66
Author(s): Shirin Moossavi, Faisal Atakora, Kozeta Miliku, Shadi Sepehri, Bianca Robertson, Qing Duan, Allan B. Becker, Piushkumar J. Mandhane, Stuart E. Turvey, Theo J. Moraes, Diana L. Lefebvre, Malcolm R. Sears, Padmaja Subbarao, Catherine J. Field, Lars Bode, Ehsan Khafipour, Meghan B. Azad
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-021-84497-y

Gut microbiota resilience in horse athletes following holidays out to pasture
Cited by: 15
Author(s): Núria Mach, Léa Lansade, David Bars-Cortina, Sophie Dhorne–Pollet, Aline Foury, Marie‐Pierre Moisan, Alice Ruet
Software Mentions: 5
Published: over 5 years ago

10.1186/s13024-021-00481-0

Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer’s disease brains
Cited by: 9
Author(s): Julio Barrera, Lingyun Song, Julia Gamache, Melanie E. Garrett, Alexias Safi, Young Won Yun, Ivana Premasinghe, Daniel J. Sprague, Danielle Chipman, Jeffrey Li, Hélène Fradin, Karen Soldano, Raluca Gordân, Allison Ashley‐Koch, Gregory E. Crawford, Ornit Chiba‐Falek
Software Mentions: 5
Published: almost 5 years ago

10.18632/oncotarget.13252

Prognostic and predictive values of CDK1 and MAD2L1 in lung adenocarcinoma
Cited by: 81
Author(s): Yuan-Xiang Shi, Tao Zhu, Ting Zou, Wei Zhuo, Yixin Chen, Ma-Sha Huang, Wei Zheng, Chenjing Wang, Xi Li, Xiao‐Yuan Mao, Wei Zhang, Hong‐Hao Zhou, Ji‐Ye Yin, Zhao‐Qian Liu
Software Mentions: 5
Published: over 9 years ago

10.1186/1756-0500-6-358

Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins
Cited by: 1
Author(s): John C. Whitin, Srinivasa Rangan, Harvey J. Cohen
Software Mentions: 5
Published: almost 13 years ago

10.12688/wellcomeopenres.16075.2

A reproducible picture of open access health facility data in Africa and R tools to support improvement
Cited by: 4
Author(s): Andy South, Ahmadou Dicko, Mark Herringer, Peter M. Macharia, Joseph Maina, Emelda A. Okiro, Robert W. Snow, Van der Walt Anelda
Software Mentions: 5
Published: over 5 years ago

10.1111/jcmm.14556

A prognostic 10‐lncRNA expression signature for predicting the risk of tumour recurrence in breast cancer patients
Cited by: 16
Author(s): Jianing Tang, Jiangbo Ren, Qiuxia Cui, Dan Zhang, Deguang Kong, Xing Liao, Mengxin Lü, Yan Gong
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0055635

Functional-Network-Based Gene Set Analysis Using Gene-Ontology
Cited by: 6
Author(s): Billy Chang, Rafal Kustra, Weidong Tian
Software Mentions: 5
Published: over 13 years ago

10.2196/27110

Prediction Model of Anastomotic Leakage Among Esophageal Cancer Patients After Receiving an Esophagectomy: Machine Learning Approach
Cited by: 3
Author(s): Ziran Zhao, Xi Cheng, Xiao Sun, Shanrui Ma, Hao Feng, Liang Zhao
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-020-80557-x

Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)
Cited by: 33
Author(s): Esteban Góngora, Kyle H. Elliott, Lyle G. Whyte
Software Mentions: 5
Published: over 5 years ago

10.1186/s40462-015-0063-4

Reproductive constraints influence habitat accessibility, segregation, and preference of sympatric albatross species
Cited by: 21
Author(s): Michelle A. Kappes, Scott A. Shaffer, Yann Tremblay, David G. Foley, Daniel M. Palacios, Steven J. Bograd, Daniel P. Costa
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12964-019-0363-1

Systematic expression analysis of ligand-receptor pairs reveals important cell-to-cell interactions inside glioma
Cited by: 31
Author(s): Dongsheng Yuan, Yiran Tao, Geng Chen, Tieliu Shi
Software Mentions: 5
Published: about 7 years ago

10.1038/s41396-019-0543-4

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands
Cited by: 124
Author(s): Selma Vieira, Johannes Sikorski, Sophie Dietz, Katharina Herz, Marion Schrumpf, Helge Bruelheide, Dierk Scheel, Michael W. Friedrich, Jörg Overmann
Software Mentions: 5
Published: over 6 years ago

10.1534/genetics.119.302138

Proteostasis Environment Shapes Higher-Order Epistasis Operating on Antibiotic Resistance
Cited by: 28
Author(s): Rafael F. Guerrero, Samuel V. Scarpino, João V. Rodrigues, Daniel L. Hartl, C. Brandon Ogbunugafor
Software Mentions: 5
Published: about 7 years ago

10.7717/peerj.3712

PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages
Cited by: 15
Author(s): Yulong Niu, Chengcheng Liu, Shayan Moghimyfiroozabad, Yi Yang, Kambiz N. Alavian
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0138726

The Relationship of Immune Cell Signatures to Patient Survival Varies within and between Tumor Types
Cited by: 24
Author(s): Peter S. Linsley, Damien Chaussabel, Cate Speake
Software Mentions: 5
Published: almost 11 years ago

10.1128/mBio.00201-16

Status of the Archaeal and Bacterial Census: an Update
Cited by: 117
Author(s): Patrick D. Schloss, R. Girard, Thomas Martin, Joshua Edwards, J. Cameron Thrash
Software Mentions: 5
Published: about 10 years ago

10.1093/gbe/evaa223

Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair
Cited by: 16
Author(s): Mohak Sharda, Anjana Badrinarayanan, Aswin Sai Narain Seshasayee
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-020-07027-6

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome
Cited by: 21
Author(s): Yiqian Li, Wenyan Nong, Tobias Baril, Ho Yin Yip, Thomas Swale, Alexander Hayward, David Ferrier, Jerome H. L. Hui
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-018-4541-0

Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys lethostigma
Cited by: 8
Author(s): Shannon J. O’Leary, Christopher M. Hollenbeck, Robert R. Vega, John R. Gold, David S. Portnoy
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0243395

The applicability of forensic time since death estimation methods for buried bodies in advanced decomposition stages
Cited by: 21
Author(s): Stefan Pittner, Valentina Bugelli, M. Eric Benbow, Bianca Ehrenfellner, Angela Zissler, Carlo Pietro Campobasso, Roelof‐Jan Oostra, Maurice C. G. Aalders, Richard Zehner, Lena Lutz, Fabio Monticelli, Christian Staufer, Katharina Helm, Vilma Pinchi, Joseph P. Receveur, Janine Geißenberger, Peter Steinbacher, Jens Amendt
Software Mentions: 5
Published: over 5 years ago

10.1186/s40104-020-00542-2

Linkage between the intestinal microbiota and residual feed intake in broiler chickens
Cited by: 26
Author(s): Jing Liu, Sydney Stewart, Kelsy Robinson, Qing Yang, Wentao Lyu, Melanie A. Whitmore, Guolong Zhang
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-90797-0

Targeting of the CD80/86 proinflammatory axis as a therapeutic strategy to prevent severe COVID-19
Cited by: 9
Author(s): Antonio Julià, Irene Bonafonte-Pardàs, Antonio Gómez, María López-Lasanta, Mireia López-Corbeto, Sergio H Martínez-Mateu, Jordi Lladós, Iván Rodríguez-Nunez, R Myers, Sara Marsal
Software Mentions: 5
Published: about 5 years ago

10.1111/j.1461-0248.2007.01121.x

Demographic analysis of continuous-time life-history models
Cited by: 60
Author(s): André M. de Roos
Software Mentions: 5
Published: over 18 years ago

10.18632/oncotarget.20405

Cancer cell line specific co-factors modulate the FOXM1 cistrome
Cited by: 8
Author(s): Yue Wang, Matthew Ung, Tian Xia, Wenqing Cheng, Chao Cheng
Software Mentions: 5
Published: almost 9 years ago

10.1128/mSphere.00511-17

Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus
Cited by: 9
Author(s): Tatum D Mortimer, Douglas S. Annis, Mary O’Neill, Lindsey L. Bohr, Tracy M. Smith, Hendrik N. Poinar, Deane F. Mosher, Caitlin S. Pepperell
Software Mentions: 5
Published: over 8 years ago

10.1093/beheco/araa112

Habitat features and colony characteristics influencing ant personality and its fitness consequences
Cited by: 10
Author(s): István Maák, Gema Trigos‐Peral, Piotr Ślipiński, Irena M. Grześ, Gergely Horváth, Magdalena Witek
Software Mentions: 5
Published: over 5 years ago

10.3389/fbioe.2020.00808

Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy
Cited by: 6
Author(s): Keshav Aditya R Premkumar, Ramit Bharanikumar, Ashok Palaniappan
Software Mentions: 5
Published: about 6 years ago

10.1007/s00248-020-01657-9

Identifying Potential Hosts of Short-Branch Microsporidia
Cited by: 3
Author(s): Annemie Doliwa, Micah Dunthorn, Erika Rassoshanska, Frédéric Mahe, David Bass, Camila Duarte Ritter
Software Mentions: 5
Published: over 5 years ago

10.1242/dev.146811

Epigenetic resetting of human pluripotency
Cited by: 210
Author(s): Ge Guo, Ferdinand von Meyenn, Maria Rostovskaya, James Clarke, Sabine Dietmann, Duncan Baker, Anna Sahakyan, Samuel A. Myers, Paul Bertone, Wolf Reik, Kathrin Plath, Austin Smith
Software Mentions: 5
Published: almost 9 years ago

10.3389/fonc.2021.663556

Identification of a Three-RNA Binding Proteins (RBPs) Signature Predicting Prognosis for Breast Cancer
Cited by: 14
Author(s): Yang Liu, Hefen Sun, Xuan Li, Qiqi Liu, Yuanyuan Zhao, Liangdong Li, Baojin Xu, Yifeng Hou, Wei Jin
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.644516

G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data
Cited by: 5
Author(s): Simone Rampelli, Marco Fabbrini, Marco Candela, Elena Biagi, Patrizia Brigidi, Silvia Turroni
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-020-07183-9

A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants
Cited by: 7
Author(s): Sophie Dhorne–Pollet, Éric Barrey, Nicolas Pollet
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0097277

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads
Cited by: 6
Author(s): Andrea Manconi, Alessandro Orro, Elias Manca, Giuliano Armano, Luciano Milanesi
Software Mentions: 5
Published: about 12 years ago

10.1242/dev.131664

Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β‑catenin recruitment
Cited by: 99
Author(s): Yukio Nakamura, Eduardo Rodrigues Alves, Gert Jan C. Veenstra, Stefan Hoppler
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0151127

MiRComb: An R Package to Analyse miRNA-mRNA Interactions. Examples across Five Digestive Cancers
Cited by: 35
Author(s): María Vila-Casadesús, Meritxell Gironella, Juan José Lozano
Software Mentions: 5
Published: over 10 years ago

10.1126/sciadv.aau4578

Fungal diversity regulates plant-soil feedbacks in temperate grassland
Cited by: 134
Author(s): Marina Semchenko, Jonathan W. Leff, Yudi M. Lozano, Sirgi Saar, John Davison, Anna Wilkinson, Benjamin G. Jackson, William J. Pritchard, Jonathan R. De Long, Simon Oakley, Kelly E. Mason, Nicholas J. Ostle, Elizabeth M. Baggs, David Johnson, Noah Fierer, Richard D. Bardgett
Software Mentions: 5
Published: over 7 years ago

10.1007/s00401-020-02228-5

Mosaic trisomy of chromosome 1q in human brain tissue associates with unilateral polymicrogyria, very early-onset focal epilepsy, and severe developmental delay
Cited by: 27
Author(s): Katja Kobow, Samir Jabari, Tom Pieper, Manfred Kudernatsch, Tilman Polster, Friedrich G. Woermann, Thilo Kalbhenn, Hajo M. Hamer, Karl Rössler, Angelika Mühlebner, Wim G.M. Spliet, Martha Feucht, Yanghao Hou, Damian Stichel, Andrey Korshunov, Felix Sahm, Roland Coras, Ingmar Blümcke, Andreas von Deimling
Software Mentions: 5
Published: almost 6 years ago

10.15252/emmm.202012105

Neuron type‐specific increase in lamin B1 contributes to nuclear dysfunction in Huntington’s disease
Cited by: 23
Author(s): Rafael Alcalá-Vida, Marta Garcia‐Forn, Carla Castany‐Pladevall, Jordi Creus-Muncunill, Yoko Itō, Enrique Blanco, Arantxa Golbano, Kilian Crespí-Vázquez, Aled Parry, Guy Slater, Shamith A. Samarajiwa, Sandra Peiró, Luciano Di Croce, Masashi Narita, Esther Pérez‐Navarro
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers12030628

tRNA Queuosine Modification Enzyme Modulates the Growth and Microbiome Recruitment to Breast Tumors
Cited by: 35
Author(s): Jilei Zhang, Rong Lü, Yongguo Zhang, Żaneta Matuszek, Wen Zhang, Yinglin Xia, Tao Pan, Jun Sun
Software Mentions: 5
Published: over 6 years ago

10.15252/embr.202050932

Foxm1 regulates neural progenitor fate during spinal cord regeneration
Cited by: 6
Author(s): Diane Pelzer, Lauren S. Phipps, Raphaël Thuret, Carlos J Gallardo-Dodd, Syed Murtuza Baker, Karel Dorey
Software Mentions: 5
Published: almost 5 years ago

10.1002/1878-0261.12070

Synergistic activity of everolimus and 5-aza-2′-deoxycytidine in medullary thyroid carcinoma cell lines
Cited by: 23
Author(s): Giovanna Mantovani, Alessandra Dicitore, Daniele Pepe, Davide Gentilini, Elisa Grassi, Maria Orietta Borghi, Giulia Gelmini, Maria Celeste Cantone, Germano Gaudenzi, Gabriella Misso, Anna Maria Di Blasio, Leo J. Hofland, Michele Caraglia, Luca Persani
Software Mentions: 5
Published: about 9 years ago

10.1186/s42523-021-00115-2

Environmentally enriched housing conditions affect pig welfare, immune system and gut microbiota in early life
Cited by: 21
Author(s): Caifang Wen, I.D.E. van Dixhoorn, Dirkjan Schokker, H. Woelders, Norbert Stockhofe-Zurwieden, Johanna M.J. Rebel, Hauke Smidt
Software Mentions: 5
Published: almost 5 years ago

10.3390/ijerph16040614

The Role of Environmental Conditions on Marathon Running Performance in Men Competing in Boston Marathon from 1897 to 2018
Cited by: 20
Author(s): Pantelis Theodoros Nikolaidis, Stefania Di Gangi, Hamdi Chtourou, Christoph Alexander Rüst, Thomas Rosemann, Beat Knechtle
Software Mentions: 5
Published: over 7 years ago

10.1186/s13756-018-0336-y

Estimating the burden of antimicrobial resistance: a systematic literature review
Cited by: 318
Author(s): Nichola R. Naylor, Rifat Atun, Nina Zhu, Kavian Kulasabanathan, Sachin Silva, Anuja Chatterjee, Gwenan M. Knight, Julie V. Robotham
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0151342

Mining Social Entrepreneurship Strategies Using Topic Modeling
Cited by: 23
Author(s): Yanto Chandra, Li Jiang, Chengjun Wang
Software Mentions: 5
Published: over 10 years ago

10.1186/s12859-019-3100-2

RACS: rapid analysis of ChIP-Seq data for contig based genomes
Cited by: 4
Author(s): Marcelo Ponce, Alejandro Saettone, Syed Nabeel‐Shah, Jeffrey Fillingham
Software Mentions: 5
Published: over 6 years ago

10.1186/s13073-017-0493-2

Predicting cancer type from tumour DNA signatures
Cited by: 36
Author(s): Kee Pang Soh, Ewa Szczurek, Thomas Sakoparnig, Niko Beerenwinkel
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2019.02273

Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre
Cited by: 15
Author(s): Daniel Mende, Dominique Le Bœuf, Edward F. DeLong
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0119027

Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant
Cited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: over 11 years ago

10.1038/s41598-019-40375-2

Transcriptome analysis of rumen epithelium and meta-transcriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis
Cited by: 21
Author(s): Wenli Li, S.L. Gelsinger, Andrea Edwards, Christina Riehle, Daniel C. Koch
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.8549

Invasive vegetation affects amphibian skin microbiota and body condition
Cited by: 7
Author(s): Obed Hernández‐Gómez, Allison Q. Byrne, Alex R. Gunderson, Thomas S. Jenkinson, Clay F. Noss, Andrew P. Rothstein, Molly C. Womack, Erica Bree Rosenblum
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-019-39318-8

Identifying Windows of Susceptibility by Temporal Gene Analysis
Cited by: 9
Author(s): Kristin P. Bennett, Elisabeth M. Brown, Hannah De los Santos, Matthew Poegel, Thomas R. Kiehl, Evan W. Patton, Spencer Norris, Sally Temple, John S. Erickson, Deborah L. McGuinness, Nathan C. Boles
Software Mentions: 5
Published: over 7 years ago

10.3389/fpls.2020.570871

Genomic Selection for Prediction of Fruit-Related Traits in Pepper (Capsicum spp.)
Cited by: 15
Author(s): Ju-Pyo Hong, Na-Young Ro, Hea-Young Lee, Geon Woo Kim, Jae-Hoon Kwon, Eiji Yamamoto, Byoung-Cheorl Kang
Software Mentions: 5
Published: over 5 years ago

10.3390/diagnostics10090617

microRNA Expression Profile in Single Hormone Receptor-Positive Breast Cancers Is Mainly Dependent on HER2 Status—A Pilot Study
Cited by: 6
Author(s): Michał Kunc, Marta Popęda, Magdalena Niemira, Anna Szałkowska, Michał Bieńkowski, Rafał Pęksa, Aleksandra Łacko, Barbara Radecka, Marcin Braun, Joanna Pikiel, Maria Litwiniuk, Katarzyna Pogoda, Ewa Iżycka‐Świeszewska, Adam Krętowski, Anna Żaczek, Wojciech Biernat, Elżbieta Senkus
Software Mentions: 5
Published: almost 6 years ago

10.1051/parasite/2020062

Increasing importance of anthelmintic resistance in European livestock: creation and meta-analysis of an open database
Cited by: 89
Author(s): Hannah Rose Vineer, Eric R. Morgan, Hubertus Hertzberg, David J. Bartley, Antonio Bosco, Johannes Charlier, Christophe Chartier, Edwin Claerebout, Theo de Waal, Guy Hendrickx, Barbara Hinney, Johan Höglund, Jožica Ježek, Martin Kašný, Orla M. Keane, María Martínez‐Valladares, Teresa Letra Mateus, Jennifer McIntyre, Marcin Mickiewicz, Ana María Muñoz, Clare J Phythian, H.W. Ploeger, Aleksandra Vergles Rataj, Philip Skuce, Stanislav Simin, Smaragda Sotiraki, Marina Spînu, Snorre Stuen, Stig Milan Thamsborg, Jaroslav Vadlejch, Marián Várady, Georg von Samson‐Himmelstjerna, Laura Rinaldi
Software Mentions: 5
Published: over 6 years ago

10.1002/ece3.6477

Advancing biodiversity assessments with environmental DNA: Long‐read technologies help reveal the drivers of Amazonian fungal diversity
Cited by: 23
Author(s): Camila Duarte Ritter, Micah Dunthorn, Sten Anslan, Vítor Xavier de Lima, Leho Tedersoo, R. Henrik Nilsson, Alexandre Antonelli
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0184471

Genome-wide miRNA response to anacardic acid in breast cancer cells
Cited by: 14
Author(s): David J. Schultz, Penn Muluhngwi, Negin Alizadeh-Rad, Madelyn A. Green, Eric C. Rouchka, Sabine Waigel, Carolyn M. Klinge
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0225180

Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation
Cited by: 10
Author(s): Aisling M. Redmond, Soleilmane Omarjee, Igor Chernukhin, Muriel Le Romancer, Jason S. Carroll
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-018-36768-4

Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets
Cited by: 10
Author(s): Stefan Wyder, Michael T. Raissig, Ueli Grossniklaus
Software Mentions: 5
Published: over 7 years ago

10.1534/g3.119.400770

Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings
Cited by: 10
Author(s): Luke Browne, Alayna Mead, Courtney Horn, Kevin W. Chang, Zeynep A Celikkol, Claudia L. Henriquez, Feiyang Ma, Eric Beraut, Rachel S. Meyer, Victoria L. Sork
Software Mentions: 5
Published: over 6 years ago

10.1128/mSystems.00087-17

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity
Cited by: 43
Author(s): Isabelle Laforest‐Lapointe, Christian Messier, Steven W. Kembel
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0161476

Evolution of the Exon-Intron Structure in Ciliate Genomes
Cited by: 17
Author(s): Vladyslav Bondarenko, Mikhail S. Gelfand
Software Mentions: 5
Published: almost 10 years ago

10.3389/fmicb.2019.00717

Disentangling the Influence of Environment, Host Specificity and Thallus Differentiation on Bacterial Communities in Siphonous Green Seaweeds
Cited by: 23
Author(s): Kathryn Lee Morrissey, Levent Çavaş, Anne Willems, Olivier De Clerck
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-018-36709-1

Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents
Cited by: 27
Author(s): Olumide Ajibola, Aislinn D. Rowan, Clement O. Ogedengbe, Mari B. Mshelia, Damien J. Cabral, Anthonius A. Eze, Stephen K. Obaro, Peter Belenky
Software Mentions: 5
Published: over 7 years ago

10.1016/j.csbj.2021.07.020

MyoData: An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle
Cited by: 3
Author(s): Davide Corso, Francesco Chemello, Enrico Alessio, Ilenia Urso, Giulia Ferrarese, Martina Bazzega, Chiara Romualdi, Gerolamo Lanfranchi, Gabriele Sales, Stefano Cagnin
Software Mentions: 5
Published: over 5 years ago

10.1111/cpr.12968

Systemic transcriptome comparison between early‐ And late‐onset pre‐eclampsia shows distinct pathology and novel biomarkers
Cited by: 15
Author(s): Fang Guo, Zhenan Bao, Hao Yang, Yixi Fu, Yaning Wang, Jianming Huang, Min Cheng, Xiaobo Li, Zhuo Shen, Li Li, Ping He, Andy Peng Xiang, Shuaiyu Wang, Hongbo Zhang
Software Mentions: 5
Published: over 5 years ago