10.3389/fmicb.2018.02037

Expression Profile of Glossina pallidipes MicroRNAs During Symptomatic and Asymptomatic Infection With Glossina pallidipes Salivary Gland Hypertrophy Virus (Hytrosavirus)
Cited by: 8
Author(s): Irene K. Meki, İkbal Agah Ince, Henry M. Kariithi, Drion G. Boucias, Orhan Özcan, Andrew G. Parker, Just M. Vlak, Monique M. van Oers, Adly M. M. Abd-Alla
Software Mentions: 4
Published: almost 8 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

10.2196/jmir.6342

Methods for Evaluating Respondent Attrition in Web-Based Surveys
Cited by: 61
Author(s): Camille J. Hochheimer, Roy Sabo, Alex H. Krist, Teresa Day, John Cyrus, Steven H. Woolf
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.67615

Local adaptation and archaic introgression shape global diversity at human structural variant loci
Cited by: 27
Author(s): Shouqing Yan, Rachel M. Sherman, Dylan J. Taylor, Divya R. Nair, Andrew N Bortvin, Michael C. Schatz, Rajiv C. McCoy
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pcbi.1006828

Scalable nonlinear programming framework for parameter estimation in dynamic biological system models
Cited by: 15
Author(s): Sungho Shin, Ophelia S. Venturelli, Ví­ctor M. Zavala
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2020.00982

Functional and Structural Responses of Arctic and Alpine Soil Prokaryotic and Fungal Communities Under Freeze-Thaw Cycles of Different Frequencies
Cited by: 27
Author(s): Carla Perez-Mon, Beat Frey, Aline Frossard
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.47835

Epigenetic silencing of a multifunctional plant stress regulator
Cited by: 25
Author(s): Mark Zander, Björn C. Willige, Yiping He, Thu Anh Nguyen, Amber E. Langford, Ramlah Nehring, Elizabeth D. Howell, Robert B. McGrath, Anna Bartlett, Rosa Castanon, Joseph R. Nery, Huaming Chen, Zhuzhu Zhang, Florian Jupe, Anna N. Stepanova, Robert J. Schmitz, Mathew G. Lewsey, Joanne Chory, Joseph R. Ecker
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj-cs.161

An integrated platform for intuitive mathematical programming modeling using LaTeX
Cited by: 4
Author(s): Charalampos Triantafyllidis, Lazaros G. Papageorgiou
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12974-020-02045-3

Transcriptional heterogeneity between primary adult grey and white matter astrocytes underlie differences in modulation of in vitro myelination
Cited by: 10
Author(s): Inge Werkman, Marissa Dubbelaar, Pieter van der Vlies, Jelkje J. de Boer-Bergsma, Bart J. L. Eggen, Wia Baron
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.53704

Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones
Cited by: 41
Author(s): Anastasia A. Minervina, Mikhail V. Pogorelyy, Ekaterina A. Komech, В. К. Карнаухов, Petra Bächer, Elisa Rosati, André Franke, Dmitriy M. Chudakov, Ilgar Z. Mamedov, Yuri B Lebedev, Thierry Mora, Aleksandra M. Walczak
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-72861-3

Dietary fatty acid intake and gut microbiota determine circulating endocannabinoidome signaling beyond the effect of body fat
Cited by: 48
Author(s): Sophie Castonguay-Paradis, Sébastien Lacroix, Gabrielle Rochefort, Lydiane Parent, Julie Perron, Cyril Martin, Benoît Lamarche, Frédéric Raymond, Nicolas Flamand, Vincenzo Di Marzo, Alain Veilleux
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpsyg.2019.00480

BEEP—Bodily and Emotional Perception of Pain. A Questionnaire to Measure Reaction to Pain in Chronic Pain Disorders
Cited by: 3
Author(s): Antonio Preti, Serena Stocchino, Francesca Pinna, Manuela Deidda, Mario Musu, Federica Sancassiani, Ferdinando Romano, Sérgio Machado, Gabriele Finco, Mauro Giovanni Carta
Software Mentions: 4
Published: over 7 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

10.3389/fpsyt.2019.00896

Population Survey Data Informing the Therapeutic Potential of Classic and Novel Phenethylamine, Tryptamine, and Lysergamide Psychedelics
Cited by: 28
Author(s): James D Sexton, Charles D. Nichols, Peter S. Hendricks
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0136980

Selfies of Imperial Cormorants (Phalacrocorax atriceps): What Is Happening Underwater?
Cited by: 16
Author(s): Agustina Gómez‐Laich, Ken Yoda, Carlos B. Zavalaga, Flavio Quintana
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pcbi.1007348

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting
Cited by: 64
Author(s): Alex X. Lu, Oren Kraus, Sam Cooper, Alan M. Moses
Software Mentions: 4
Published: almost 7 years ago

10.2196/26749

Data Missing Not at Random in Mobile Health Research: Assessment of the Problem and a Case for Sensitivity Analyses
Cited by: 13
Author(s): Simon B. Goldberg, Daniel M. Bolt, Richard J. Davidson
Software Mentions: 4
Published: about 5 years ago

10.18632/oncotarget.12818

Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21
Cited by: 32
Author(s): Yosr Hamdi, Penny Soucy, Véronique Adoue, Kyriaki Michailidou, Sander Canisius, Audrey Lemaçon, Arnaud Droit, Irene L. Andrulis, Hoda Anton‐Culver, Volker Arndt, Caroline Baynes, Carl Blomqvist, Natalia Bogdanova, Stig E. Bojesen, Manjeet K. Bolla, Bernardo Bonanni, Anne‐Lise Børresen‐Dale, Judith S. Brand, Hiltrud Brauch, Hermann Brenner, Annegien Broeks, Barbara Burwinkel, Jenny Chang–Claude, Fergus J. Couch, Angela Cox, Simon S. Cross, Kamila Czene, Hatef Darabi, Joe Dennis, Peter Devilee, Thilo Dörk, Isabel dos‐Santos‐Silva, Mikael Eriksson, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Montserrat García‐Closas, Graham G. Giles, Mark S. Goldberg, Anna González‐Neira, Grethe Irene Grenaker-Alnæs, Pascal Guénel, Lothar Haeberle, Christopher A. Haiman, Ute Hamann, Emily Hallberg, Maartje J. Hooning, John L. Hopper, Anna Jakubowska, Michael E. Jones, Maria Kabisch, Vesa Kataja, Diether Lambrechts, Loı̈c Le Marchand, Annika Lindblom, Jan Lubiński, Arto Mannermaa, Mel Maranian, Sara Margolin, Frederik Marmé, Roger L. Milne, Susan L. Neuhausen, Heli Nevanlinna, Patrick Neven, Curtis Olswold, Julian Peto, Dijana Plaseska‐Karanfilska, Katri Pylkäs, Paolo Radice, Anja Rudolph, Elinor J. Sawyer, Marjanka K. Schmidt, Xiao‐Ou Shu, Melissa C. Southey, Anthony Swerdlow, Rob A.E.M. Tollenaar, Ian Tomlinson, Diana Torres, Thérèse Truong, Celine M. Vachon, Ans M.W. van den Ouweland, Qin Wang, Robert Winqvist, _ kConFab, Aocs Investigators, Wei Zheng, Javier Benı́tez, Georgia Chenevix-Trench, Alison M. Dunning, Paul D.P. Pharoah, Vessela N. Kristensen, Per Hall, Douglas F. Easton, Tomi Pastinen, Silje Nord, Jacques Simard
Software Mentions: 4
Published: almost 10 years ago

10.1080/19768354.2019.1675759

Predicting climate-driven shifts in the breeding phenology of Varied Tits (Sittiparus various) in South Korean forests
Cited by: 1
Author(s): Min-Su Jeong, Chang-Young Choi, Hankyu Kim, Woo-Shin Lee
Software Mentions: 4
Published: almost 7 years ago

10.2196/mhealth.6474

Analyzing mHealth Engagement: Joint Models for Intensively Collected User Engagement Data
Cited by: 57
Author(s): Emily A. Scherer, Dror Ben‐Zeev, Zhigang Li, John M. Kane
Software Mentions: 4
Published: over 9 years ago

10.3389/fpsyg.2020.00533

Development and Preliminary Validation of a New Type 1 Diabetes Adjustment Scale (DAS-1)
Cited by: 1
Author(s): Teresa Rivas, Mónica Carreira, Marta Domínguez-López, María Soledad Ruiz de Adana, María Teresa Anarte
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1006777

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes
Cited by: 138
Author(s): Romain Blanc-Mathieu, Laetitia Perfus‐Barbeoch, Jean‐Marc Aury, Martine Da Rocha, Jérôme Gouzy, Erika Sallet, Cristina Martín-Jimenez, Marc Bailly‐Bechet, Philippe Castagnone‐Sereno, Jean‐François Flot, Djampa Kozlowski, Julie Cazareth, Arnaud Couloux, Corinne Da Silva, Julie Guy, Yujin Kim, Corinne Rancurel, Thomas Schiex, Pierre Abad, Patrick Wincker, Etienne G. J. Danchin
Software Mentions: 4
Published: about 9 years ago

10.7717/peerj.1066

Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree
Cited by: 33
Author(s): Nagesh A. Kuravadi, Vijay A. Yenagi, Kannan Rangiah, H. B. Mahesh, Anantharamanan Rajamani, Meghana Deepak Shirke, Heikham Russiachand, Ramya Malarini Loganathan, Chandana Shankara Lingu, S Shilpa, Aishwarya Ramamurthy, B. N. Sathyanarayana, Malali Gowda
Software Mentions: 4
Published: about 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

10.18632/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

10.18632/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

10.3390/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

10.1186/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

10.1038/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

10.1007/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

10.1016/j.anbehav.2018.04.017

In wolves, play behaviour reflects the partners' affiliative and dominance relationship
Cited by: 13
Author(s): Simona Cafazzo, Sarah Marshall-Pescini, Jennifer L. Essler, Zsófia Virányi, Kurt Kotrschal, Friederike Range
Software Mentions: 4
Published: about 8 years ago

10.1093/gigascience/giaa027

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C
Cited by: 43
Author(s): Matthew A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva Chan, André E. Minoche, Richard J. Edwards, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanović, Martin A. Smith, E Aiden, Timothy P. L. Smith, Robert A. Zammit, J. William O. Ballard
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0163491

LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines
Cited by: 3
Author(s): Jingting Xu, Hong Hu, Yang Dai
Software Mentions: 4
Published: almost 10 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

10.1038/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

10.3390/ijms21249560

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses
Cited by: 2
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 4
Published: over 5 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

10.1186/1479-5876-12-159

An eight-miRNA signature as a potential biomarker for predicting survival in lung adenocarcinoma
Cited by: 95
Author(s): Xuelian Li, Yunrui Shi, Zhihua Yin, Xiaoxia Xue, Baosen Zhou
Software Mentions: 4
Published: about 12 years ago

10.1186/s12967-021-02991-3

Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus
Cited by: 7
Author(s): Jian Lin, Yuanhua Lu, Bizhou Wang, Peng Jiao, Jie Ma
Software Mentions: 4
Published: about 5 years ago

10.1167/jov.21.5.14

The ability to predict actions of others from distributed cues is still developing in 6- to 8-year-old children
Cited by: 0
Author(s): Emalie McMahon, Daniel Kim, Samuel A. Mehr, Ken Nakayama, Elizabeth S. Spelke, Maryam Vaziri-Pashkam
Software Mentions: 4
Published: about 5 years ago

10.1186/s12915-021-00963-z

Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly
Cited by: 64
Author(s): Mahul Chakraborty, Arunachalam Ramaiah, Adriana Adolfi, Paige Halas, Bhagyashree Kaduskar, Luna Thanh Ngo, Suvratha Jayaprasad, Kiran Paul, Saurabh Whadgar, Subhashini Srinivasan, Suresh Subramani, Ethan Bier, Anthony A. James, J. J. Emerson
Software Mentions: 4
Published: over 5 years ago

10.1038/s41398-021-01543-z

Network analysis of depressive symptoms in Hong Kong residents during the COVID-19 pandemic
Cited by: 28
Author(s): Teris Cheung, Yu Jin, Simon Ching Lam, Zhaohui Su, Brian J. Hall, Yu‐Tao Xiang, Lorna Kwai Ping Suen, S. M. Chan, H. L. Ho, Hubert Lam, Emma Yun-zhi Huang, Ying Xiao, Fernanda Maria Vieira Pereira-Ávila, Elucir Gir, Menevse Yildirim, Şeyda Seren İntepeler, Tella Lantta, Kyungmi Lee, Nayeon Shin, Ma. Carmen C. Tolabing, Tor Michael Rossing, Ching Yuk Hon, Merissa Tsang, Jessica P. Braz Poeys, Tommy Kwan Hin Fong
Software Mentions: 4
Published: almost 5 years ago

10.1523/ENEURO.0017-18.2018

Tracking Temporal Hazard in the Human Electroencephalogram Using a Forward Encoding Model
Cited by: 26
Author(s): Sophie K. Herbst, Lorenz Fiedler, Jonas Obleser
Software Mentions: 4
Published: over 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

10.1186/s12986-018-0309-4

Bariatric surgery reduces CD36-bearing microvesicles of endothelial and monocyte origin
Cited by: 9
Author(s): Jaco Botha, Mads Nielsen, Maja Høegh Christensen, Henrik Vestergaard, Aase Handberg
Software Mentions: 4
Published: almost 8 years ago

10.3389/fpsyg.2020.609617

The Authenticity Scale: Validation in Russian Culture
Cited by: 7
Author(s): С К Нартова-Бочавер, Sofia Reznichenko, John Maltby
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.00129

Broad and Fine Scale Variability in Bacterial Diversity and Cyanotoxin Quotas in Benthic Cyanobacterial Mats
Cited by: 8
Author(s): Georgia Thomson‐Laing, Jonathan Puddick, Olivier Laroche, Samantha Fulton, Konstanze Steiner, Mark W. Heath, Susanna A. Wood
Software Mentions: 4
Published: over 6 years ago

10.3390/nu12030790

Human Milk Oligosaccharide Profile Variation Throughout Postpartum in Healthy Women in a Brazilian Cohort
Cited by: 39
Author(s): Ana Paula de Lima Ferreira, Ronaldo Alves, Amanda Faria de Figueiredo, Nadya Helena Alves-Santos, Nathalia Freitas-Costa, Mônica Araújo Batalha, Chloe Yonemitsu, Nadia Manivong, Annalee Fürst, Lars Bode, Gilberto Kac
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/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

10.3390/nu9040365

25-Hydroxyvitamin D and Peripheral Immune Mediators: Results from Two Nationwide Danish Pediatric Cohorts
Cited by: 5
Author(s): Sixtus Thorsen, Christian Bressen Pipper, Kristin Skogstrand, Flemming Pociot, Jannet Svensson
Software Mentions: 4
Published: over 9 years ago

10.1128/mSystems.00783-19

Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale
Cited by: 61
Author(s): Kaoping Zhang, Manuel Delgado‐Baquerizo, Yong‐Guan Zhu, Haiyan Chu
Software Mentions: 4
Published: about 6 years ago

10.1002/1878-0261.12776

Fine‐needle aspiration as an alternative to core needle biopsy for tumour molecular profiling in precision oncology: prospective comparative study of next‐generation sequencing in cancer patients included in the SHIVA02 trial
Cited by: 9
Author(s): Célia Dupain, Julien Masliah‐Planchon, Céline Gu, Elodie Girard, Pierre Gestraud, Pauline du Rusquec, Édith Borcoman, Diana Bello, Francesco Ricci, Ségolène Hescot, Marie‐Paule Sablin, Patricia Tresca, Alexandre de Moura, Delphine Loirat, Maxime Frélaut, Anne Vincent‐Salomon, Charlotte Lecerf, Céline Callens, Samantha Antonio, Coralie Franck, Odette Mariani, Ivan Bièche, Maud Kamal, Christophe Le Tourneau, Vincent Servois
Software Mentions: 4
Published: almost 6 years ago

10.3390/nu12113450

Metabolomic and Metataxonomic Fingerprinting of Human Milk Suggests Compositional Stability over a Natural Term of Breastfeeding to 24 Months
Cited by: 7
Author(s): Natalie Shenker, Alvaro Perdones‐Montero, Adam Burke, Sarah Stickland, Julie A. K. McDonald, Kate Alexander-Hardiman, James M. Flanagan, Zoltan Takáts, Simon Cameron
Software Mentions: 4
Published: over 5 years ago

10.1523/JNEUROSCI.0860-21.2021

Spinal Cord Injury Induces Permanent Reprogramming of Microglia into a Disease-Associated State Which Contributes to Functional Recovery
Cited by: 21
Author(s): Ramil Hakim, Vasilios Zachariadis, Sreenivasa Raghavan Sankavaram, Jinming Han, Robert A. Harris, Lou Brundin, Martin Enge, Mikael Svensson
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSystems.00098-20

Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems
Cited by: 12
Author(s): Robert Danczak, Rebecca A. Daly, Mikayla A. Borton, James C. Stegen, Simon Roux, Kelly Wrighton, Michael J. Wilkins
Software Mentions: 4
Published: over 6 years ago

10.3389/fmed.2018.00034

Beyond Enumeration: Functional and Computational Analysis of Circulating Tumor Cells to Investigate Cancer Metastasis
Cited by: 10
Author(s): Francesc Castro-Giner, Manuel C. Scheidmann, Nicola Aceto
Software Mentions: 4
Published: over 8 years ago

10.18632/oncotarget.8239

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
Cited by: 13
Author(s): Su‐Jin Baek, Mirang Kim, Donghyuck Bae, Jeong‐Hwan Kim, Hee‐Jin Kim, Myoung‐Eun Han, Sae‐Ock Oh, Yong‐Sung Kim, Seon‐Young Kim
Software Mentions: 4
Published: over 10 years ago

10.1186/s13104-017-2839-7

Item response theory analysis of the Utrecht Work Engagement Scale for Students (UWES-S) using a sample of Japanese university and college students majoring medical science, nursing, and natural science
Cited by: 11
Author(s): Takashi Tsubakita, Kazuyo Shimazaki, Hiroshi Ito, Nobuo Kawazoe
Software Mentions: 4
Published: almost 9 years ago

10.1128/mSystems.00522-20

Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants
Cited by: 69
Author(s): John Leech, Raúl Cabrera‐Rubio, Aaron M. Walsh, Guerrino Macori, Calum J. Walsh, Wiley Barton, Laura Finnegan, Fiona Crispie, Órla O’Sullivan, Marcus J. Claesson, Paul D. Cotter
Software Mentions: 4
Published: over 5 years ago

10.18632/oncotarget.11788

Identification of candidate anti-cancer molecular mechanisms of Compound Kushen Injection using functional genomics
Cited by: 64
Author(s): Zhibo Qu, Jingang Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qi Feng, Joy M. Raison, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: almost 10 years ago

10.18632/oncotarget.12180

The transcriptional signature of human ovarian carcinoma macrophages is associated with extracellular matrix reorganization
Cited by: 72
Author(s): Florian Finkernagel, Silke Reinartz, Sonja Lieber, Till Adhikary, Annika Wortmann, Nathalie Hoffmann, Tim Bieringer, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller‐Brüsselbach, Rolf Müller
Software Mentions: 4
Published: almost 10 years ago

10.18632/aging.103753

Eight immune-related genes predict survival outcomes and immune characteristics in breast cancer
Cited by: 2
Author(s): Xu Han, Gangjian Wang, Lili Zhu, Liu Hong, Bingjie Li
Software Mentions: 4
Published: about 6 years ago

10.3389/fnins.2018.00006

Group Analysis in MNE-Python of Evoked Responses from a Tactile Stimulation Paradigm: A Pipeline for Reproducibility at Every Step of Processing, Going from Individual Sensor Space Representations to an across-Group Source Space Representation
Cited by: 17
Author(s): Lau M. Andersen
Software Mentions: 4
Published: over 8 years ago

10.3389/fnhum.2021.713114

Visual Field Reconstruction in Hemianopia Using fMRI Based Mapping Techniques
Cited by: 1
Author(s): Hinke N. Halbertsma, Holly Bridge, Joana Carvalho, Frans W. Cornelissen, Sara Ajina
Software Mentions: 4
Published: almost 5 years ago

10.12688/f1000research.9453.2

Method-centered digital communities on protocols.io for fast-paced scientific innovation
Cited by: 0
Author(s): Lori Kindler, Alexei Stoliartchouk, Leonid Teytelman, Bonnie Hurwitz
Software Mentions: 4
Published: about 9 years ago

10.18632/oncotarget.15807

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease
Cited by: 39
Author(s): Magnus Tobiasson, Hani Abdulkadir, Andreas Lennartsson, Shintaro Katayama, Francesco Marabita, Annick De Paepe, Mohsen Karimi, Kaarel Krjutškov, Elisabet Einarsdottir, Michael Grövdal, Monika Jansson, Asmaa Ben Azenkoud, Lina Corddedu, Sören Lehmann, Karl Ekwall, Juha Kere, Eva Hellström‐Lindberg, Johanna Ungerstedt
Software Mentions: 4
Published: over 9 years ago

10.18632/oncotarget.22878

Identification of cancer prognosis-associated functional modules using differential co-expression networks
Cited by: 10
Author(s): Wenshuai Yu, Shengjie Zhao, Yongcui Wang, Brian Nlong Zhao, Weiling Zhao, Xiaobo Zhou
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-019-39733-x

HER2 and p95HER2 differentially regulate miRNA expression in MCF-7 breast cancer cells and downregulate MYB proteins through miR-221/222 and miR-503
Cited by: 15
Author(s): Andrej Gorbatenko, Rolf Søkilde, Ester E. Sørensen, Inga Newie, Helena Persson, Beatriz Morancho, Joaquı́n Arribas, Thomas Litman, Carlos Rovira, Stine Falsig Pedersen
Software Mentions: 4
Published: over 7 years ago

10.1128/mSystems.01048-20

Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest
Cited by: 3
Author(s): Kaitlyn N. Myers, Daniel Conn, Amanda M. V. Brown
Software Mentions: 4
Published: over 5 years ago

10.18632/oncotarget.23638

YAP-associated chromosomal instability and cholangiocarcinoma in mice
Cited by: 41
Author(s): Sumera Rizvi, Samantha R. Fischbach, Steven F. Bronk, Petra Hirsova, Anuradha Krishnan, Renumathy Dhanasekaran, James B. Smadbeck, Rory L. Smoot, George Vasmatzis, Gregory J. Gores
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2015.01511

High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes
Cited by: 43
Author(s): Marion Stagars, S. Emil Ruff, Rudolf Amann, Katrin Knittel
Software Mentions: 4
Published: over 10 years ago

10.18632/oncotarget.24898

Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets
Cited by: 17
Author(s): Rosemarie Weikard, Frieder Hadlich, H.M. Hammon, D. Frieten, C. Gerbert, Christian Koch, G. Dusel, Christa Kühn
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1009227

Relating simulation studies by provenance—Developing a family of Wnt signaling models
Cited by: 5
Author(s): Kai Budde, Jacob Smith, Pia Wilsdorf, Fiete Haack, Adelinde M. Uhrmacher
Software Mentions: 4
Published: about 5 years ago

10.1186/s12889-018-5234-y

Development and validation of a new knowledge, attitude, belief and practice questionnaire on leptospirosis in Malaysia
Cited by: 24
Author(s): Wan Mohd Zahiruddin, Wan Nor Arifin, Mohd Nazri Shafei, Surianti Sukeri, Zawaha Idris, Rahman Abu Bakar, Rukman Awang Hamat, Malina Osman, Tengku Zetty Maztura Tengku Jamaludin, Arumugam Pathman, Ab Rahman Mas-Harithulfadhli-Agus, Norazlin Idris, Binti Samsudin Suhailah, Siti Nor Sakinah Saudi, Nor Liza Abdullah, Noramira Nozmi, Abdul Wahab Zainuddin, Aziah Daud
Software Mentions: 4
Published: over 8 years ago

10.18632/oncotarget.27488

MAGE-A inhibit apoptosis and promote proliferation in multiple myeloma through regulation of BIM and p21Cip1
Cited by: 10
Author(s): Anna Mei, Kaity Tung, Jessie Han, Deepak Perumal, Alessandro Laganà, Jonathan J. Keats, Daniel Auclair, Ajai Chari, Sundar Jagannath, Samir Parekh, Hearn Jay Cho
Software Mentions: 4
Published: over 6 years ago

10.3389/fcvm.2021.628885

Single-Cell Transcriptome Analysis Decipher New Potential Regulation Mechanism of ACE2 and NPs Signaling Among Heart Failure Patients Infected With SARS-CoV-2
Cited by: 13
Author(s): Mengqiu Ma, Yanhua Xu, Yang Su, Sang‐Bing Ong, Xingdong Hu, Min Chai, Maojun Zhao, Hong Li, Xiaojuan Fan, Yingjie Chen, Dan Xu, Xiaojiang Xu
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj-cs.156

Comparison and benchmark of name-to-gender inference services
Cited by: 197
Author(s): L. Santamaría, Helena Mihaljević
Software Mentions: 4
Published: about 8 years ago

10.1098/rsob.160224

Interplay between RNA interference and heat shock response systems in <i>Drosophila melanogaster</i>
Cited by: 9
Author(s): S. Yu. Funikov, Sergei Ryazansky, Alexander Kanapin, Maria D. Logacheva, Aleksey A. Penin, А. В. Снежкина, Victoria Shilova, Д. Г. Гарбуз, Michael B. Evgen’ev, Olga G. Zatsepina
Software Mentions: 4
Published: almost 10 years ago

10.1038/s42003-020-1028-8

Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures
Cited by: 31
Author(s): Åsa Wallén-Mackenzie, Sylvie Dumas, Maria Papathanou, Mihaela M. Martis, Bianca Vlcek, Niclas König, Åsa K. Björklund
Software Mentions: 4
Published: about 6 years ago

10.1038/s41422-020-00445-x

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing
Cited by: 88
Author(s): Luca Mazzurana, Paulo Czarnewski, Viktor Jönsson, Leif Wigge, Markus Ringnér, Teresa C. Williams, Avinash Ravindran, Åsa K. Björklund, Jesper Säfholm, Gunnar Nilsson, Sven Erik Dahlén, Ann Charlotte Orre, Mamdoh Al‐Ameri, Charlotte Höög, Charlotte Hedin, Sylwester Szczegielniak, Sven Almér, Jenny Mjösberg
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-40897-9

Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics research
Cited by: 17
Author(s): Lilla Ozgyin, Attila Horváth, Zsuzsanna Hevessy, Bálint László Bálint
Software Mentions: 4
Published: over 7 years ago

10.1186/s12967-021-02846-x

Eleven immune-gene pairs signature associated with TP53 predicting the overall survival of gastric cancer: a retrospective analysis of large sample and multicenter from public database
Cited by: 9
Author(s): Junyu Huo, Liqun Wu, Yunjin Zang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-43591-y

Apoptotic endothelial cells release small extracellular vesicles loaded with immunostimulatory viral-like RNAs
Cited by: 43
Author(s): Marie-Pierre Hardy, Éric Audemard, Francis Migneault, Albert Feghaly, Sylvie Brochu, Patrick Gendron, Éric Boilard, François Major, Mélanie Dieudé, Marie‐Josée Hébert, Claude Perreault
Software Mentions: 4
Published: about 7 years ago

10.1038/s41419-018-0841-1

The detrimental effects of glucocorticoids exposure during pregnancy on offspring’s cardiac functions mediated by hypermethylation of bone morphogenetic protein-4
Cited by: 13
Author(s): Jun Peng, Yuhao Zhou, Zhiyu Zhang, Zhiming Wang, Ling-Tong Gao, Xiao Zhang, Fang Zhou, Guangyao Li, Huaiyan Chen, Hongxing Yang, Lu Gao
Software Mentions: 4
Published: about 8 years ago

10.1186/s12888-021-03425-6

The COVID-19 Pandemic Mental Health Questionnaire (CoPaQ): psychometric evaluation and compliance with countermeasures in psychiatric inpatients and non-clinical individuals
Cited by: 19
Author(s): Stephanie Rek, Markus Bühner, Matthias Reinhard, Daniel Freeman, Daniel Keeser, Kristina Adorjan, Peter Falkai, Frank Padberg
Software Mentions: 4
Published: almost 5 years ago

10.3390/molecules24101973

ACPred: A Computational Tool for the Prediction and Analysis of Anticancer Peptides
Cited by: 109
Author(s): Nalini Schaduangrat, Chanin Nantasenamat, Virapong Prachayasittikul, Watshara Shoombuatong
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0181671

Broad-range lytic bacteriophages that kill Staphylococcus aureus local field strains
Cited by: 36
Author(s): Virginia Abatángelo, Natalia Peressutti Bacci, Carina Andrea Boncompain, Ariel Fernando Amadío, Soledad Telma Carrasco, Cristian Alejandro Suárez, Héctor Ricardo Morbidoni
Software Mentions: 4
Published: about 9 years ago

10.1093/gigascience/giz045

A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification
Cited by: 24
Author(s): Ren‐Hua Chung, Chen-Yu Kang
Software Mentions: 4
Published: over 7 years ago

10.1002/pld3.285

Genetic and genomic resources to study natural variation in <i>Brassica rapa</i>
Cited by: 7
Author(s): Ping Lou, Scott Woody, Kathleen Greenham, Robert VanBuren, Marivi Colle, Patrick P. Edger, Ryan C. Sartor, Zheng Yining, Nathan Levendoski, Jan Lim, Calvin So, Brian Stoveken, Timothy Woody, Zhao Jian-jun, Shuxing Shen, Richard M. Amasino, C. Robertson McClung
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pbio.3000382

LATS1/2 suppress NFκB and aberrant EMT initiation to permit pancreatic progenitor differentiation
Cited by: 19
Author(s): Caitlin M. Braitsch, D. Berfin Azizoglu, Yadanar Htike, Haley R. Barlow, Ulrike Schnell, Christopher Chaney, Thomas J. Carroll, Ben Z. Stanger, Ondine Cleaver
Software Mentions: 4
Published: about 7 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

10.1038/s41396-020-0686-3

Ecological succession in the vaginal microbiota during pregnancy and birth
Cited by: 39
Author(s): Morten Arendt Rasmussen, Jonathan Thorsen, Maria Gloria Domínguez-Bello, Martin J. Blaser, Martin Steen Mortensen, Asker Brejnrod, Samir A. Shah, Mathis Hjort Hjelmsø, Jenni Lehtimäki, Urvish Trivedi, Hans Bisgaard, Søren J. Sørensen, Jakob Stokholm
Software Mentions: 4
Published: about 6 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

10.1186/1471-2105-8-337

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

10.1186/s13054-019-2589-0

Relationship of mottling score, skin microcirculatory perfusion indices and biomarkers of endothelial dysfunction in patients with septic shock: an observational study
Cited by: 16
Author(s): Sigita Kazūne, Anastasija Caica, K. Volceka, Oļegs Šuba, Uldis Rubīns, Andris Grabovskis
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41396-019-0581-y

Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink
Cited by: 14
Author(s): Raquel Rodríguez‐Martínez, Guy Leonard, David S. Milner, Sebastian Sudek, Mike Conway, Karen Moore, Theresa Hudson, Frédéric Mahe, Patrick J. Keeling, Alyson E. Santoro, Alexandra Z. Worden, Thomas A. Richards
Software Mentions: 4
Published: over 6 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: over 15 years ago

10.1002/ece3.3288

Marine dock pilings foster diverse, native cryptobenthic fish assemblages across bioregions
Cited by: 20
Author(s): Simon J. Brandl, Jordan M. Casey, Nancy­ Knowlton­, J. Emmett Duffy
Software Mentions: 4
Published: about 9 years ago