10.1097/MD.0000000000023153

Identification of candidate biomarkers correlated with the pathogenesis and prognosis of breast cancer via integrated bioinformatics analysis
Cited by: 8
Author(s): Shuyu Liu, Xinkui Liu, Jiarui Wu, Wei Zhou, Mengwei Ni, Ziqi Meng, Shanshan Jia, Jingyuan Zhang, Siyu Guo, Shan Lu, Yingfei Li
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-27493-z

A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system
Cited by: 5
Author(s): Nisha Govender, Siju Senan, Zeti‐Azura Mohamed‐Hussein, R Wickneswari V Ratnam
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.ppat.1004959

Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis
Cited by: 16
Author(s): Amber J. Marty, Aimee Teo Broman, Robert Żarnowski, Teigan G. Dwyer, Laura M. Bond, Anissa Lounès-Hadj Sahraoui, Joël Fontaine, James M. Ntambi, Sündüz Keleş, Christina Kendziorski, Gregory M. Gauthier
Software Mentions: 4
Published: about 11 years ago

10.1186/s12874-021-01318-6

High performance implementation of the hierarchical likelihood for generalized linear mixed models: an application to estimate the potassium reference range in massive electronic health records datasets
Cited by: 1
Author(s): Cristian Bologa, V. Shane Pankratz, Mark Unruh, Maria Roumelioti, Vallabh O. Shah, Kamran Shaffi, Soraya Arzhan, John P. Cook, Christos Argyropoulos
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2021.628192

KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs
Cited by: 7
Author(s): Tao Wang, Yuanyuan Guo, Shengwei Liu, Chaoxin Zhang, Tongyan Cui, Kun Ding, Peng Wang, Xibiao Wang, Zhipeng Wang
Software Mentions: 4
Published: over 5 years ago

10.1016/j.dib.2016.06.001

Microarray dataset of Jurkat cells following miR-93 over-expression
Cited by: 0
Author(s): Silvia Gioiosa, Lorena Verduci, Gianluca Azzalin, Claudia Carissimi, Valerio Fulci, Giuseppe Macino
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41421-018-0030-5

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation
Cited by: 64
Author(s): Yuli Li, Ruijia Wang, Xiaogang Xun, Jing Wang, Lisui Bao, Ramesha Thimmappa, Jun Ding, Jingwei Jiang, Liheng Zhang, Tianqi Li, Jia Lv, Chuang Mu, Xiaoli Hu, Lingling Zhang, Jing Liu, Yuqiang Li, Lijie Yao, Wenqian Jiao, Yangfan Wang, Shanshan Lian, Zelong Zhao, Yaoyao Zhan, Xiaoting Huang, Huan Liao, Wang Jia, Hongzhen Sun, Xue Mi, Yu Xia, Qiang Xing, Wei Lü, Anne Osbourn, Zunchun Zhou, Yaqing Chang, Zhenmin Bao, Shi Wang
Software Mentions: 4
Published: about 8 years ago

10.1186/s13059-021-02289-z

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
Cited by: 55
Author(s): David B Bernstein, Snorre Sulheim, Eivind Almaas, Daniel Segrè
Software Mentions: 4
Published: over 5 years ago

10.1186/s12863-019-0790-4

Transcriptome, physiological and biochemical analysis of Triarrhena sacchariflora in response to flooding stress
Cited by: 17
Author(s): Jia Wang, Hao Sun, Jiajin Sheng, Surong Jin, Fangjian Zhou, Zhongli Hu, Youxiang Diao
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.00845

Comprehensive Analysis of mRNA and lncRNA Transcriptomes Reveals the Differentially Hypoxic Response of Preadipocytes During Adipogenesis
Cited by: 3
Author(s): Jinwei Zhang, Jideng Ma, Xiankun Zhou, Silu Hu, Liangpeng Ge, Jing Sun, Penghao Li, Keren Long, Long Jin, Qianzi Tang, Lingyan Liu, Xuewei Li, Surong Shuai, Mingzhou Li
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2015.00531

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire
Cited by: 70
Author(s): Jacob D. Galson, Johannes Trück, Anna Fowler, Márton Münz, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter, Dominic F. Kelly
Software Mentions: 4
Published: almost 11 years ago

10.3390/ijms20143480

Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
Cited by: 34
Author(s): Ziwen Li, Xianghai An, Taotao Zhu, Tingwei Yan, Wu Shu, Youhui Tian, Jinping Li, Xiangyuan Wan
Software Mentions: 4
Published: about 7 years ago

10.1242/dmm.048090

Integrative genomic analysis of blood pressure and related phenotypes in rats
Cited by: 6
Author(s): Fumihiko Takeuchi, Yi-Qiang Liang, Motohide Isono, Masanori Tajima, Zong Hu Cui, Yoko Ikoma, Takanari Gotoda, Toru Nabika, Norihiro Kato
Software Mentions: 4
Published: over 5 years ago

10.1007/s11356-019-06639-0

Determination of nest occupation and breeding effect of the white stork by human-mediated landscape in Western Poland
Cited by: 22
Author(s): Joanna T. Białas, Łukasz Dylewski, Marcin Tobółka
Software Mentions: 4
Published: over 6 years ago

10.3390/metabo8030041

Unbiased Lipidomic Profiling of Triple-Negative Breast Cancer Tissues Reveals the Association of Sphingomyelin Levels with Patient Disease-Free Survival
Cited by: 27
Author(s): Preeti Purwaha, Franklin Gu, Danthasinghe Waduge Badrajee Piyarathna, Theckelnaycke Rajendiran, Anindita Ravindran, Angela R. Omilian, Sao Jiralerspong, Gokul M. Das, Carl Morrison, Christine B. Ambrosone, Cristian Coarfa, Nagireddy Putluri, Arun Sreekumar
Software Mentions: 4
Published: about 8 years ago

10.18632/oncotarget.25382

Aberration hubs in protein interaction networks highlight actionable targets in cancer
Cited by: 4
Author(s): Mehran Karimzadeh, Pouria Jandaghi, Andreas I. Papadakis, Sebastian Trainor, Johan Rung, Mar Gonzàlez-Porta, Ghislaine Scélo, Naveen S. Vasudev, Alvis Brāzma, Sidong Huang, Rosamonde E. Banks, Mark Lathrop, Hamed S. Najafabadi, Yasser Riazalhosseini
Software Mentions: 4
Published: about 8 years ago

10.1016/j.celrep.2016.06.096

Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins
Cited by: 60
Author(s): Christian Hauer, Jana Sieber, Thomas Schwarzl, Ina Hollerer, Tomaž Curk, Anne-Marie Alleaume, Matthias W. Hentze, Andreas E. Kulozik
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2105-12-139

PeakRanger: A cloud-enabled peak caller for ChIP-seq data
Cited by: 146
Author(s): Xin Feng, Robert L. Grossman, Lincoln Stein
Software Mentions: 4
Published: about 15 years ago

10.1016/j.celrep.2021.109032

Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome
Cited by: 17
Author(s): Alejandro Brenes, Harunori Yoshikawa, Dalila Bensaddek, Bogdan Mirauta, Daniel D Seaton, Jens Hukelmann, Hao Jiang, Oliver Stegle, Angus I. Lamond
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-8-337

Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs
Cited by: 124
Author(s): Mamoon Rashid, Sudipto Saha, Gajendra P. S. Raghava
Software Mentions: 4
Published: almost 19 years ago

10.1038/s41598-021-82362-6

Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet
Cited by: 11
Author(s): Kelsey E. Witt, Karthik Yarlagadda, Julie M. Allen, Alyssa C. Bader, Mary Simon, Seppe Kuehn, Kelly S. Swanson, Tzu Wen L. Cross, Kristin M. Hedman, Stanley H. Ambrose, Ripan S. Malhi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-28986-7

A monocyte gene expression signature in the early clinical course of Parkinson’s disease
Cited by: 35
Author(s): J Schlachetzki, Iryna Prots, Jenhan Tao, Hyun Bae Chun, Kaoru Saijo, David Gosselin, Beate Winner, Christopher K. Glass
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-019-2732-6

The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation
Cited by: 4
Author(s): Yance Feng, Sheng Zhang, Liang Li, Lei M. Li
Software Mentions: 4
Published: over 7 years ago

10.1128/mSphere.00451-20

Assessing the Variation within the Oral Microbiome of Healthy Adults
Cited by: 43
Author(s): Jacob T. Nearing, Vanessa DeClercq, Johan Van Limbergen, Morgan G. I. Langille
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12915-018-0585-5

Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions
Cited by: 8
Author(s): Xinyi Yang, Martin Vingron
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2018.00093

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method
Cited by: 17
Author(s): Yonggang Yan, Qin Jiang, Jian-Gong Wang, Ting Zhu, Bin Zou, Qiongfen Qiu, Zhe‐Xue Quan
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-021-95544-z

Seasonal and geographic variation in packed cell volume and selected serum chemistry of platypuses
Cited by: 0
Author(s): J.W.B. Stewart, Gilad Bino, Tahneal Hawke, Richard T. Kingsford
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0192947

Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men
Cited by: 26
Author(s): Kathryn Burton, Grégory Pimentel, Nadine Zangger, Nathalie Vionnet, Jocelyne Drai, P. G. McTernan, François P. Pralong, Mauro Delorenzi, Guy Vergères
Software Mentions: 4
Published: over 8 years ago

10.1016/j.stem.2017.03.003

H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Cited by: 85
Author(s): Eva Hörmanseder, Angela Simeone, George E. Allen, Charles R. Bradshaw, Magdalena Figlmüller, J. B. Gurdon, Jérôme Jullien
Software Mentions: 4
Published: about 9 years ago

10.1128/mSphere.00227-21

Microbiome Analysis Reveals Diversity and Function of <i>Mollicutes</i> Associated with the Eastern Oyster, <i>Crassostrea virginica</i>
Cited by: 16
Author(s): Zachary T. Pimentel, Keith Dufault‐Thompson, Kayla T. Russo, Abigail K. Scro, Roxanna Smolowitz, Marta Gómez-Chiarri, Ying Zhang
Software Mentions: 4
Published: about 5 years ago

10.1016/j.stem.2019.09.008

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
Cited by: 71
Author(s): Stephanie Z. Xie, Laura García‐Prat, Véronique Voisin, Raffaele Ferrari, Olga I. Gan, Elvin Wagenblast, Kerstin B. Kaufmann, Andy G.X. Zeng, Shin‐ichiro Takayanagi, Ishita Patel, Esther K. Lee, Joseph Jargstorf, Gareth D. Holmes, Guy Romm, Kristele Pan, Michelle Shoong, Aditi Vedi, Chiara Luberto, Mark D. Minden, Gary D. Bader, Elisa Laurenti, John E. Dick
Software Mentions: 4
Published: almost 7 years ago

10.1099/mic.0.034538-0

Cholesterol utilization in mycobacteria is controlled by two TetR-type transcriptional regulators: kstR and kstR2
Cited by: 143
Author(s): Sharon L. Kendall, Philippa Burgess, Ricardo Balhana, Mike Withers, Annemieke Ten Bokum, J.S. Lott, Chen Gao, Iria Uhia-Castro, Neil G. Stoker
Software Mentions: 4
Published: over 16 years ago

10.3389/fphys.2017.00734

Distinct Subfamilies of Odorant Binding Proteins in Locust (Orthoptera, Acrididae): Molecular Evolution, Structural Variation, and Sensilla-Specific Expression
Cited by: 15
Author(s): Xingcong Jiang, Jürgen Krieger, Heinz Breer, Pablo Pregitzer
Software Mentions: 4
Published: almost 9 years ago

10.3389/fphys.2020.00311

Exercise Reverses the Alterations in Gut Microbiota Upon Cold Exposure and Promotes Cold-Induced Weight Loss
Cited by: 8
Author(s): Yan Meng, Lina Chen, Lin Wei, Hongjuan Wang, Guangming Xu, Xiquan Weng
Software Mentions: 4
Published: over 6 years ago

10.5808/GI.2020.18.1.e6

Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples
Cited by: 2
Author(s): Sonali P. Barwe, Anilkumar Gopalakrisnapillai, Nitin Mahajan, Todd E. Druley, E. Anders Kolb, Erin L. Crowgey
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pbio.1002146

The Structure of an NDR/LATS Kinase–Mob Complex Reveals a Novel Kinase–Coactivator System and Substrate Docking Mechanism
Cited by: 45
Author(s): Gergő Gógl, Kyle D. Schneider, Brian J. Yeh, Alam Nashida, Alex N Nguyen Ba, Alan M. Moses, Csaba Hetényi, Attila Reményi, Eric L. Weiss
Software Mentions: 4
Published: about 11 years ago

10.1186/s12864-019-6384-8

Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach
Cited by: 6
Author(s): Frédéric Jehl, Colette Désert, Christophe Klopp, M. Brenet, Andrea Rau, Sophie Leroux, Morgane Boutin, Laëtitia Lagoutte, Kévin Muret, Yuna Blum, Diane Esquerré, David Gourichon, Thierry Burlot, Anne Collin, Frédérique Pitel, Alexandre Bénani, Tatiana Zerjal, Sandrine Lagarrigue
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.27840

miR-708-5p enhances erlotinib/paclitaxel efficacy and overcomes chemoresistance in lung cancer cells
Cited by: 13
Author(s): Nicholas J. Monteleone, Carol S. Lutz
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1006090

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
Cited by: 12
Author(s): Sneha Mitra, Anushua Biswas, Leelavati Narlikar
Software Mentions: 4
Published: over 8 years ago

10.3390/microorganisms9020459

A Mucoralean White Collar-1 Photoreceptor Controls Virulence by Regulating an Intricate Gene Network during Host Interactions
Cited by: 6
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Carlos Lax, Marta Silva, Javier Capilla, Eusebio Navarro, Victoriano Garre
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1007988

Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases
Cited by: 7
Author(s): Bojan Krtenic, Adrian Drazic, Thomas Arnesen, Nathalie Reuter
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-05949-y

Enhanced differential expression statistics for data-independent acquisition proteomics
Cited by: 29
Author(s): Tomi Suomi, Laura L. Elo
Software Mentions: 4
Published: about 9 years ago

10.3389/fmicb.2018.01188

Canola Root–Associated Microbiomes in the Canadian Prairies
Cited by: 67
Author(s): Chih Ying Lay, Terrence H. Bell, Chantal Hamel, K. Neil Harker, Ramona M. Mohr, Charles W. Greer, Étienne Yergeau, Marc St‐Arnaud
Software Mentions: 4
Published: about 8 years ago

10.3390/cells7120275

Activation of Polyamine Catabolism by N1,N11-Diethylnorspermine in Hepatic HepaRG Cells Induces Dedifferentiation and Mesenchymal-Like Phenotype
Cited by: 12
Author(s): О. Н. Иванова, Anastasiya V. Snezhkina, George S. Krasnov, Vladimir T. Valuev-Elliston, Olga A. Khomich, Alexey Khomutov, Tuomo A. Keinänen, Leena Alhonen, Birke Bartosch, Anna V. Kudryavtseva, Sergey N. Kochetkov, Alexander Ivanov
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms20236040

Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-37284-1

A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status
Cited by: 12
Author(s): Harry Clifford, Anna Dulneva, Chris P. Ponting, Wilfried Haerty, Esther B. E. Becker
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1009669

Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids
Cited by: 5
Author(s): Romain Durand, Florence Deschênes, Vincent Burrus
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13072-021-00393-9

H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum
Cited by: 10
Author(s): Jessica Connacher, Gabrielle A. Josling, Lindsey M. Orchard, Janette Reader, Manuel Llinás, Lyn‐Marié Birkholtz
Software Mentions: 4
Published: over 5 years ago

10.1155/2018/1243858

Characterization of Transcription Termination-Associated RNAs: New Insights into their Biogenesis, Tailing, and Expression in Primary Tumors
Cited by: 4
Author(s): Ilaria Laudadio, Sara Formichetti, Silvia Gioiosa, Filippos Klironomos, Nikolaus Rajewsky, Giuseppe Macino, Claudia Carissimi, Valerio Fulci
Software Mentions: 4
Published: over 8 years ago

10.1093/gbe/evv149

Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality
Cited by: 127
Author(s): Xiaofan Zhou, Antonis Rokas, Shelley L. Berger, Jürgen Liebig, Anandasankar Ray, Laurence J. Zwiebel
Software Mentions: 4
Published: about 11 years ago

10.7554/eLife.38432

Immune-mediated hookworm clearance and survival of a marine mammal decrease with warmer ocean temperatures
Cited by: 13
Author(s): Mauricio Seguel, Felipe Montalva, Diego Pérez-Venegas, Josefina Gutiérrez, Héctor Pavés, Ananda Müller, Carola Valencia-Soto, Elizabeth W. Howerth, Victoria C Mendiola, Nicole L. Gottdenker
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-020-06789-3

Distinctions between sex and time in patterns of DNA methylation across puberty
Cited by: 11
Author(s): Sarah R. Moore, Kathryn L. Humphreys, Natalie L. Colich, Elena Goetz Davis, David Lin, Julia L. MacIsaac, Michæl S. Kobor, Ian H. Gotlib
Software Mentions: 4
Published: about 6 years ago

10.1038/srep18811

Prognostic nomogram integrated systemic inflammation score for patients with esophageal squamouscell carcinoma undergoing radical esophagectomy
Cited by: 43
Author(s): Yingjie Shao, Zhonghua Ning, Jun Chen, Yiting Geng, Wenjing Gu, Jin Huang, Honglei Pei, Yueping Shen, Jingting Jiang
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-021-95739-4

Assessing effectiveness of exclusion fences in protecting threatened plants
Cited by: 6
Author(s): Juan Lorite, Carlos Salazar-Mendías, Roza Pawlak, Eva M. Cañadas
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0041374

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome
Cited by: 121
Author(s): Hebing Chen, Yao Tian, Wenjie Shu, Xiaochen Bo, Shengqi Wang
Software Mentions: 4
Published: about 14 years ago

10.1038/s41598-021-82866-1

The protective role of daidzein in intestinal health of turbot (Scophthalmus maximus L.) fed soybean meal-based diets
Cited by: 14
Author(s): Guijuan Yu, Yang Liu, Weihao Ou, Jihong Dai, Qinghui Ai, Wenbing Zhang, Kangsen Mai, Yan-Jiao Zhang
Software Mentions: 4
Published: over 5 years ago

10.3390/toxins5122621

Venom Down Under: Dynamic Evolution of Australian Elapid Snake Toxins
Cited by: 54
Author(s): Timothy N. W. Jackson, Kartik Sunagar, Eivind A. B. Undheim, Ivan Koludarov, Angelo H. C. Chan, Kate L. Sanders, Syed Abid Ali, Iwan Hendrikx, Nathan Dunstan, Bryan G. Fry
Software Mentions: 4
Published: over 12 years ago

10.1186/s12931-021-01743-7

RORγt inhibitors block both IL-17 and IL-22 conferring a potential advantage over anti-IL-17 alone to treat severe asthma
Cited by: 11
Author(s): David Lamb, Dorothy De Sousa, Karsten Quast, Katrin Fundel‐Clemens, Jonas Erjefält, Caroline Sandén, Hans Jürgen Hoffmann, Marc Kästle, RM Schmid, Kevin Menden, Denis Delić
Software Mentions: 4
Published: about 5 years ago

10.3389/fphys.2020.609335

Exhaustive Exercise and Post-exercise Protein Plus Carbohydrate Supplementation Affect Plasma and Urine Concentrations of Sulfur Amino Acids, the Ratio of Methionine to Homocysteine and Glutathione in Elite Male Cyclists
Cited by: 8
Author(s): Trond E. Olsen, Ove Sollie, Eha Nurk, Cheryl Turner, Fredrik Jernerén, John L. Ivy, Kathrine J. Vinknes, Matthieu Clauss, Helga Refsum, Jørgen Jensen
Software Mentions: 4
Published: over 5 years ago

10.15252/msb.20209526

Multi‐modal meta‐analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor
Cited by: 6
Author(s): Alok Jaiswal, Prson Gautam, Elina Pietilä, Sanna Timonen, Nora Nordström, Yevhen Akimov, Nina Sipari, Ziaurrehman Tanoli, Thomas Fleischer, Kaisa Lehti, Krister Wennerberg, Tero Aittokallio
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.6924.1

The khmer software package: enabling efficient nucleotide sequence analysis
Cited by: 325
Author(s): Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, R.A. Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan A. Fish, Leonor García-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David M. Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, McDonald Eric, Jessica E. Mizzi, Kevin Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander J. Nederbragt, Humberto Ortíz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N. Russ, Erich M. Schwarz, Camille Scott, Josiah Seaman, Scott Sievert, Jared T. Simpson, Connor T. Skennerton, James Spencer, S. Ramakrishnan, Daniel Standage, James A. Stapleton, Susan R. Steinman, J.J. Stein, Benjamin A. Taylor, W. Trimble, Heather L. Wiencko, Michael J. Wright, Brian Wyss, Zhang Qingpeng, en zyme, C. Titus Brown
Software Mentions: 4
Published: almost 11 years ago

10.1128/mSystems.00332-18

A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome
Cited by: 110
Author(s): Courtney R. Armour, Stephen Nayfach, Katherine S. Pollard, Thomas J. Sharpton
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-018-31170-6

Mitochondrial transcription factor A (TFAM) shapes metabolic and invasion gene signatures in melanoma
Cited by: 36
Author(s): Luíza Ferreira de Araújo, Ádamo Davi Diógenes Siena, Jéssica Rodrigues Plaça, Danielle Barbosa Brotto, Isabela Ichihara de Barros, Bruna Rodrigues Muys, Carlos Alberto Oliveira de Biagi, Kamila Chagas Peronni, Josane F. Sousa, Greice Andreotti de Molfetta, Laura Ciaccia West, A. Phillip West, Andréia Machado Leopoldino, Enilza Maria Espreáfico, W. A. Silva
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13018-021-02658-1

Potential genes and pathways associated with heterotopic ossification derived from analyses of gene expression profiles
Cited by: 5
Author(s): Zhanyu Yang, Delong Liu, Rui Guan, Li X, Yiwei Wang, Bin Sheng
Software Mentions: 4
Published: almost 5 years ago

10.18632/aging.202170

A three-gene signature based on tumour microenvironment predicts overall survival of osteosarcoma in adolescents and young adults
Cited by: 10
Author(s): Chun-Kai Wen, Hongxue Wang, Han Wang, Hao Yuan Mo, Weiying Zhong, Jing Tang, Yuefeng Lu, Wenxian Zhou, Aihua Tan, Yan Liu, Weimin Xie
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2021.666936

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction
Cited by: 5
Author(s): Najoua Mghazli, Laila Sbabou, Rachid Hakkou, Ahmed Ouhammou, Mariam El Adnani, Odile Bruneel
Software Mentions: 4
Published: about 5 years ago

10.1186/s12882-020-1701-7

Effect of low-dose atrial natriuretic peptide in critically ill patients with acute kidney injury: a retrospective, single-center study with propensity-score matching
Cited by: 3
Author(s): Keita Saito, Shigehiko Uchino, Tomoko Fujii, Shinjiro Saito, Masanori Takinami, Shoichi Uezono
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.104134

The value of a metabolic reprogramming-related gene signature for pancreatic adenocarcinoma prognosis prediction
Cited by: 12
Author(s): Zhen Tan, Yubin Lei, Jin Xu, Si Shi, Jie Hua, Bo Zhang, Qingcai Meng, Jiang Liu, Yiyin Zhang, Miaoyan Wei, Xianjun Yu, Chen Liang
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.102556

Robust immunoscore model to predict the response to anti-PD1 therapy in melanoma
Cited by: 14
Author(s): Run‐Cong Nie, Shu Qiang Yuan, Yun Wang, Yan Yu Cai, Shi Chen, Shu Man Li, Jie Zhou, Guo Ming Chen, Tian Qi Luo, Zhi Wei Zhou, Yuan Fang Li
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21082966

Differential Expression and Function of Bicellular Tight Junctions in Skin and Oral Wound Healing
Cited by: 20
Author(s): Trevor R. Leonardo, Junhe Shi, Dandan Chen, Harsh M. Trivedi, Lin Chen
Software Mentions: 4
Published: over 6 years ago

10.3389/fcell.2018.00164

The Transcriptome of Human Endometrial Mesenchymal Stem Cells Under TGFβR Inhibition Reveals Improved Potential for Cell-Based Therapies
Cited by: 31
Author(s): Shanti Gurung, Sarah Williams, James A. Deane, Jerome A. Werkmeister, Caroline E. Gargett
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-28939-0

Agulhas Current properties shape microbial community diversity and potential functionality
Cited by: 10
Author(s): Sandra Phoma, Surendra Vikram, Janet Jansson, Isabelle Ansorge, Don A. Cowan, Yves Van de Peer, Thulani P. Makhalanyane
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.ppat.1008671

Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection
Cited by: 44
Author(s): Jiayi Sun, J. Cristobal Vera, Jenny Drnevich, Yen Ting Lin, Ruian Ke, Christopher B. Brooke
Software Mentions: 4
Published: about 6 years ago

10.1128/mSystems.01178-20

Systems Analysis of Gut Microbiome Influence on Metabolic Disease in HIV-Positive and High-Risk Populations
Cited by: 6
Author(s): Abigail J. S. Armstrong, Kevin Quinn, Jennifer Fouquier, Sam X. Li, Jennifer M. Schneider, Nichole M. Nusbacher, Katrina Doenges, Suzanne Fiorillo, Tyson Marden, Janine Higgins, Nichole Reisdorph, Thomas Campbell, Brent E. Palmer, Catherine Lozupone
Software Mentions: 4
Published: about 5 years ago

10.1016/j.biocon.2019.05.011

1980s–2010s: The world's largest mangrove ecosystem is becoming homogeneous
Cited by: 37
Author(s): Swapan Kumar Sarker, Jason Matthiopoulos, Sonia Mitchell, Zahir Ahmed, Md. Bashirul Al Mamun, Richard Reeve
Software Mentions: 4
Published: about 7 years ago

10.1093/gigascience/gix058

Connections between the human gut microbiome and gestational diabetes mellitus
Cited by: 178
Author(s): Yashu Kuang, Jinhua Lu, Shenghui Li, Junhua Li, Mingyang Yuan, Jianxing He, Niannian Chen, Wan-Qing Xiao, Shi‐Li Shen, Lan Qiu, Yongming Wu, Cui-Yue Hu, Yanyan Wu, Weidong Li, Qiaozhu Chen, Hong‐Wen Deng, Christopher J. Papasian, Huimin Xia, Xiu Qiu
Software Mentions: 4
Published: about 9 years ago

10.3390/cells10030692

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Cited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-02761-6

Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype
Cited by: 27
Author(s): Willian A. da Silveira, Patrícia Vianna Bonini Palma, Renata Danielle Sicchieri, Rolando A R Villacis, Larissa Raquel Mouro Mandarano, Tatiane Oliveira, Heriton Mr Antonio, Jurandyr Moreira de Andrade, Valdair Francisco Muglia, Sílvia Regina Rogatto, Charles Theillet, Stanislas du Manoir, Daniel Guimarães Tiezzi
Software Mentions: 4
Published: about 9 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: about 6 years ago

10.1128/mSystems.00150-18

Marine Sponges as <i>Chloroflexi</i> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade
Cited by: 61
Author(s): Kristina Bayer, Martin T. Jahn, Beate M. Slaby, Lucas Moitinho‐Silva, Ute Hentschel
Software Mentions: 4
Published: almost 8 years ago

10.1099/mgen.0.000426

Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings
Cited by: 4
Author(s): Benjamin J. Perry, John T. Sullivan, Elena Colombi, Riley Murphy, Joshua P. Ramsay, Clive W. Ronson
Software Mentions: 4
Published: almost 6 years ago

10.3390/ani9110894

The Reliability and Accuracy of Palpation, Radiography, and Sonography for the Detection of Keel Bone Damage
Cited by: 15
Author(s): Linnea M. Tracy, S Mieko Temple, Darin C. Bennett, Kim A. Sprayberry, Maja M. Makagon, Richard A. Blatchford
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13613-021-00920-7

Bioreactance reliably detects preload responsiveness by the end-expiratory occlusion test when averaging and refresh times are shortened
Cited by: 3
Author(s): Francesco Gavelli, Alexandra Beurton, Jean–Louis Teboul, Nello De Vita, Danila Azzolina, Rui Shi, Arthur Pavot, Xavier Monnet
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13075-021-02484-0

Deep learning for detection of radiographic sacroiliitis: achieving expert-level performance
Cited by: 30
Author(s): Keno K. Bressem, Janis L. Vahldiek, Lisa C. Adams, Stefan M. Niehues, Hildrun Haibel, V. Rios Rodriguez, Murat Torğutalp, Mikhail Protopopov, Fabian Proft, Judith Rademacher, Joachim Sieper, Martín Rudwaleit, Bernd Hamm, Marcus R. Makowski, Kay-Geert A. Hermann, Denis Poddubnyy
Software Mentions: 4
Published: over 5 years ago

10.1128/JVI.01127-19

Evolutionary Dynamics of Oropouche Virus in South America
Cited by: 14
Author(s): Bernardo Gutierrez, Emma L. Wise, Steven T. Pullan, Christopher Logue, Thomas A. Bowden, Marina Escalera-Zamudio, Gabriel Trueba, Márcio Roberto Teixeira Nunes, Nuno Rodrigues Faria, Oliver G. Pybus
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-33779-z

Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis
Cited by: 34
Author(s): Ye Liu, Jen-Chien Chang, Chung-Chau Hon, Naoshi Fukui, Nobuhiro Tanaka, Zhen Ya Zhang, Ming Ta Michael Lee, Aki Minoda
Software Mentions: 4
Published: almost 8 years ago

10.1128/mSystems.00327-19

Longitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City Sewage
Cited by: 19
Author(s): Susan Joseph, Thomas Battaglia, Julia M. Maritz, Jane M. Carlton, Martin J. Blaser
Software Mentions: 4
Published: almost 7 years ago

10.1007/s10928-020-09730-z

Population pharmacokinetic modeling of intramuscular and oral dexamethasone and betamethasone in Indian women
Cited by: 8
Author(s): Wojciech Krzyzanski, Mark A. Milad, Alan H. Jobe, Thomas Peppard, Robert R. Bies, William J. Jusko
Software Mentions: 4
Published: over 5 years ago

10.1002/vro2.16

Accuracy of heart girth tapes in the estimation of weights of pre‐weaned calves
Cited by: 7
Author(s): Ginny Sherwin, Robert Hyde, Martin A. Green, John Remnant, Emily Payne, Peter Down
Software Mentions: 4
Published: almost 5 years ago

10.3390/cells9112452

Photochemotherapy Induces Interferon Type III Expression via STING Pathway
Cited by: 0
Author(s): Edyta Biskup, Brian D. Larsen, Leonor Rib, Lasse Folkersen, Omid Niazi, Maria R. Kamstrup, Claus Storgaard Sørensen
Software Mentions: 4
Published: over 5 years ago

10.1038/s41426-018-0195-x

Experimental transmission of Zika virus by <i>Aedes japonicus japonicus</i> from southwestern Germany
Cited by: 32
Author(s): Stéphanie Jansen, Anna Heitmann, Renke Lühken, Hanna Jöst, Michelle Helms, Olli Vapalahti, Jonas Schmidt‐Chanasit, Egbert Tannich
Software Mentions: 4
Published: over 7 years ago

10.18632/aging.203079

Identification and validation of a novel eight mutant-derived long non-coding RNAs signature as a prognostic biomarker for genome instability in low-grade glioma
Cited by: 12
Author(s): Aierpati Maimaiti, Xixian Wang, Yinan Pei, Nuerbiye Nuermaimaiti, Abudireheman Tuersunniyazi, Yaeraili Abula, Zhaohai Feng, Lei Jiang, Xin Shi, Maimaitijiang Kasimu
Software Mentions: 4
Published: about 5 years ago

10.3389/fpsyg.2020.00149

Analyzing the Fit of IRT Models With the Hausman Test
Cited by: 5
Author(s): Jochen Ranger, Sören Much
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-016-0911-6

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways
Cited by: 15
Author(s): Tarmo Äijö, Yun Huang, Henrik Mannerström, Lukas Chávez, Ageliki Tsagaratou, Anjana Rao, Harri Lähdesmäki
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2020.01242

Prokaryotic Response to Phytodetritus-Derived Organic Material in Epi- and Mesopelagic Antarctic Waters
Cited by: 6
Author(s): Vincenzo Manna, Francesca Malfatti, Elisa Banchi, Federica Cerino, Fabio De Pascale, Annalisa Franzo, Riccardo Schiavon, Alessandro Vezzi, Paola Del Negro, Mauro Celussi
Software Mentions: 4
Published: about 6 years ago

10.1186/s12920-015-0133-x

Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways
Cited by: 115
Author(s): David Adrian Ewald, Dana Malajian, James G. Krueger, Christopher T. Workman, Tianjiao Wang, Suyan Tian, Thomas Litman, Emma Guttman‐Yassky, Mayte Suárez‐Fariñas
Software Mentions: 4
Published: almost 11 years ago

10.3389/fmicb.2019.01006

Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence
Cited by: 7
Author(s): Beatriz Beamud, María Alma Bracho, Fernando González‐Candelas
Software Mentions: 4
Published: about 7 years ago

10.3389/fpls.2018.00574

The Mating System of the Wild-to-Domesticated Complex of Gossypium hirsutum L. Is Mixed
Cited by: 12
Author(s): Rebeca Velázquez-López, Ana Wegier, Valeria Alavez, Javier Pérez-López, Valeria Vázquez-Barrios, Denise Arroyo-Lambaer, Alejandro Ponce‐Mendoza, William E. Kunin
Software Mentions: 4
Published: about 8 years ago

10.1186/gb-2010-11-9-r96

Multi-species integrative biclustering
Cited by: 35
Author(s): Peter Waltman, Thadeous J. Kacmarczyk, Ashley R. Bate, Daniel B. Kearns, David J Reiss, Patrick Eichenberger, Richard Bonneau
Software Mentions: 4
Published: over 16 years ago

10.1093/gigascience/giy034

Improving the annotation of the Heterorhabditis bacteriophora genome
Cited by: 15
Author(s): Florence McLean, Duncan Berger, Dominik R. Laetsch, Hillel T. Schwartz, Mark Blaxter
Software Mentions: 4
Published: over 8 years ago