10.1172/JCI129115

Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia
Cited by: 29
Author(s): Alhomidi Almotiri, Hamed Ahmad A. Alzahrani, Juan Bautista Menendez-Gonzalez, Ali Abdelfattah, Badi Alotaibi, Lubaid Saleh, Adelle Greene, Mia R. F. Georgiou, Alex Gibbs, Amani Salem Alsayari, Sarab Taha, Leigh-anne Thomas, Dhruv Shah, Sarah Edkins, Peter Giles, Marc P. Stemmler, Simone Brabletz, Thomas Brabletz, Ashleigh S. Boyd, Florian A. Siebzehnrübl, Neil P. Rodrigues
Software Mentions: 1
Published: over 5 years ago

10.1186/s13021-017-0078-9

Current remote sensing approaches to monitoring forest degradation in support of countries measurement, reporting and verification (MRV) systems for REDD+
Cited by: 167
Author(s): A. R. Mitchell, Åke Rosenqvist, B. Mora
Software Mentions: 1
Published: over 9 years ago

10.1093/jxb/ert397

Overexpression of<i>PYL5</i>in rice enhances drought tolerance, inhibits growth, and modulates gene expression
Cited by: 178
Author(s): Hyun-Mi Kim, Kyeyoon Lee, Hyunsik Hwang, Nikita Bhatnagar, Dool Yi Kim, In Sun Yoon, Myung-Ok Byun, Sun Tae Kim, Ki‐Hong Jung, Beom-Gi Kim
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0025913

Spreading of Alu Methylation to the Promoter of the MLH1 Gene in Gastrointestinal Cancer
Cited by: 16
Author(s): Xiyin Wang, Jing Fan, Dong Liu, Shanlin Fu, Sigurður Ingvarsson, Huiping Chen
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0087494

Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism
Cited by: 6
Author(s): A Acevedo, Germán Aroca, Raúl Conejeros
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.ppat.1000529

Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Cited by: 74
Author(s): Roy R. Chaudhuri, Sarah Peters, Stephen J. Pleasance, Helen Northen, Chrissie Willers, Gavin K. Paterson, Danielle B. Cone, Andrew G. Allen, Paul Owen, Gil Shalom, Dov J. Stekel, Ian G. Charles, Duncan J. Maskell
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-7-282

Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring
Cited by: 44
Author(s): Joern Toedling, Peter Rhein, Richard Ratei, Leonid Karawajew, Rainer Spang
Software Mentions: 1
Published: about 20 years ago

10.1371/journal.ppat.1003083

A Strong Immune Response in Young Adult Honeybees Masks Their Increased Susceptibility to Infection Compared to Older Bees
Cited by: 70
Author(s): James C. Bull, Eugene V. Ryabov, Gill Prince, Andrew Mead, Cunjin Zhang, Laura Baxter, J. K. Pell, Juliet L. Osborne, Dave Chandler
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.ppat.1005469

In Vivo Molecular Dissection of the Effects of HIV-1 in Active Tuberculosis
Cited by: 44
Author(s): Lucy Bell, Gabriele Pollara, Pascoe Mellissa, Gillian S. Tomlinson, Rannakoe Lehloenya, Jennifer Roe, Richard Meldau, R F Miller, Alan D. Ramsay, Benjamin M. Chain, Keertan Dheda, Mahdad Noursadeghi
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-9-425

Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems
Cited by: 21
Author(s): Yu‐Shuen Tsai, Chin‐Teng Lin, George C. Tseng, I‐Fang Chung, Nikhil R. Pal
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0070386

Hypomethylation of Alu Elements in Post-Menopausal Women with Osteoporosis
Cited by: 63
Author(s): Pornrutsami Jintaridth, Rungsunn Tungtrongchitr, Sangchai Preutthipan, Apiwat Mutirangura
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0239820

Structural equation modeling approach to explore the influence of childhood maltreatment in adults
Cited by: 9
Author(s): Kuniyoshi Toyoshima, Takeshi Inoue, Jiro Masuya, Yota Fujimura, Shinji Higashi, Hajime Tanabe, Ichiro Kusumi
Software Mentions: 1
Published: almost 6 years ago

10.1073/pnas.1912109117

The circadian clock protein REVERBα inhibits pulmonary fibrosis development
Cited by: 50
Author(s): Peter Cunningham, P. J. J. De Meijer, Alicja Nazgiewicz, Simon Anderson, Lee A. Borthwick, James Bagnall, Gareth Kitchen, Monika Lodyga, Nicola Begley, Rajamiyer Venkateswaran, Rajesh Shah, Paul F. Mercer, Hannah J. Durrington, Neil C. Henderson, Karen Piper Hanley, Andrew J. Fisher, Rachel C. Chambers, David A. Bechtold, Julie Gibbs, A. S. I. Loudon, Martin K. Rutter, Boris Hinz, David Ray, John Blaikley
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-016-1185-4

Prediction of redox-sensitive cysteines using sequential distance and other sequence-based features
Cited by: 16
Author(s): Miao‐Kun Sun, Qing Zhang, Yejun Wang, Wei Ge, Dianjing Guo
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2105-14-S14-S15

Data mining tools for Salmonella characterization: application to gel-based fingerprinting analysis
Cited by: 16
Author(s): Wen Zou, Hailin Tang, Weizhong Zhao, Joe Meehan, Steven L. Foley, Wei‐Jen Lin, Hung-Chia Chen, Hong Fang, Rajesh Nayak, James J. Chen
Software Mentions: 1
Published: almost 13 years ago

10.1186/1748-717X-5-25

MicroRNA expression after ionizing radiation in human endothelial cells
Cited by: 135
Author(s): Mechthild Wagner-Ecker, Christian Schwager, Ute Wirkner, Amir Abdollahi, Peter E. Huber
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0113820

CONSTRICTOR: Constraint Modification Provides Insight into Design of Biochemical Networks
Cited by: 8
Author(s): Keesha E. Erickson, Ryan T. Gill, Anushree Chatterjee
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-9-129

Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster
Cited by: 7
Author(s): Wensheng Zhang, Sige Zou, Jiuzhou Song
Software Mentions: 1
Published: over 18 years ago

10.1186/1477-7827-7-133

Fhl5/Act, a CREM-binding transcriptional activator required for normal sperm maturation and morphology, is not essential for testicular gene expression
Cited by: 13
Author(s): Aurélie Lardenois, Frédéric Chalmel, Philippe Demougin, Noora Kotaja, Paolo Sassone‐Corsi, Michael Primig
Software Mentions: 1
Published: over 16 years ago

10.1186/1477-7827-8-154

Profiling spermatogenic failure in adult testes bearing Sox9-deficient Sertoli cells identifies genes involved in feminization, inflammation and stress
Cited by: 11
Author(s): Aurélie Lardenois, Frédéric Chalmel, Francisco Barrionuevo, Philippe Demougin, Gerd Scherer, Michael Primig
Software Mentions: 1
Published: over 15 years ago

10.1186/s13021-016-0066-5

Attribution of net carbon change by disturbance type across forest lands of the conterminous United States
Cited by: 50
Author(s): Nancy L. Harris, Stephen Hagen, Sassan Saatchi, T. Pearson, Christopher W. Woodall, Grant M. Domke, B. H. Braswell, Brian F. Walters, Sandra Brown, William Salas, Alexander Fore, Yifan Yu
Software Mentions: 1
Published: over 9 years ago

10.1186/1742-4690-11-59

Microarray analysis reveals global modulation of endogenous retroelement transcription by microbes
Cited by: 45
Author(s): George R. Young, Bettina Mavrommatis, George Kassiotis
Software Mentions: 1
Published: about 12 years ago

10.1186/s12284-015-0059-0

Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice
Cited by: 26
Author(s): Hinako Takehisa, Yutaka Satō, Baltazar A. Antonio, Yoshiaki Nagamura
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0115607

Delayed Contrast Enhancement Imaging of a Murine Model for Ischemia Reperfusion with Carbon Nanotube Micro-CT
Cited by: 2
Author(s): Laurel Burk, Ko Han Wang, John Matthew Wait, Eunice Kang, Monte S. Willis, Jianping Lu, Otto Zhou, Yueh Z. Lee
Software Mentions: 1
Published: over 11 years ago

10.1186/s12885-016-2183-7

Evaluation of serum and tissue levels of VAP-1 in colorectal cancer
Cited by: 11
Author(s): Steve Ward, Chris J. Weston, Emma L. Shepherd, Rahul Hejmadi, Tariq Ismail, David H. Adams
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0183357

Terminal differentiation of T cells is strongly associated with CMV infection and increased in HIV-positive individuals on ART and lifestyle matched controls
Cited by: 34
Author(s): Thijs Booiman, Ferdinand W. N. M. Wit, Arginell F. Girigorie, Irma Maurer, Davide De Francesco, Caroline Sabin, Agnes M. Harskamp, Maria Prins, Claudio Franceschi, Steven G. Deeks, Alan Winston, Peter Reiss, Neeltje A. Kootstra
Software Mentions: 1
Published: almost 9 years ago

10.1038/sdata.2017.125

Precision annotation of digital samples in NCBI’s gene expression omnibus
Cited by: 34
Author(s): Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D. Azad, Mohamad Omar Hadied, S. Mahmood Raza, Benjamin Abhishek Rayikanti, Bin Chen, Harikrishna Paik, Dvir Aran, Jordan Spatz, Daniel S. Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A. Musen, Atul J. Butte
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0014060

Gemcitabine Functions Epigenetically by Inhibiting Repair Mediated DNA Demethylation
Cited by: 42
Author(s): Andrea Schäfer, Lars Schomacher, Guillermo Barreto, Gabi Döderlein, Christof Niehrs
Software Mentions: 1
Published: over 15 years ago

10.1038/sdata.2018.29

Uniform resolution of compact identifiers for biomedical data
Cited by: 49
Author(s): Sarala M. Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A. McMurry, Niall Beard, Rafael C. Jiménez, Jeffrey S. Grethe, Henning Hermjakob, Maryann E. Martone, Tim W. Clark
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0226223

Cross-cultural examination of the Big Five Personality Trait Short Questionnaire: Measurement invariance testing and associations with mental health
Cited by: 14
Author(s): Laura Mezquita, Adrian J. Bravo, Julien Morizot, Angelina Pilatti, Matthew R. Pearson, Manuel I. Ibáñez, Generós Ortet, Cross-Cultural Addictions Study Team
Software Mentions: 1
Published: over 6 years ago

10.1038/sdata.2019.21

The variable quality of metadata about biological samples used in biomedical experiments
Cited by: 48
Author(s): Rafael S. Gonçalves, Mark A. Musen
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-12-614

PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae
Cited by: 19
Author(s): Antonio Palmeri, Pier Federico Gherardini, Polina Tsigankov, Gabriele Ausiello, Gérald F. Späth, Dan Zilberstein, Manuela Helmer-Citterich
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-12-399

A genomic biomarker signature can predict skin sensitizers using a cell-based in vitro alternative to animal tests
Cited by: 113
Author(s): Henrik Johansson, Malin Lindstedt, Ann-Sofie Albrekt, Carl Borrebaeck
Software Mentions: 1
Published: about 15 years ago

10.1038/s41597-019-0152-0

HENA, heterogeneous network-based data set for Alzheimer’s disease
Cited by: 33
Author(s): Elena Sügis, Jérôme Dauvillier, Anna Leontjeva, Priit Adler, Valérie Hindié, Thomas Moncion, Vincent Collura, Rachel Daudin, Yann Loe-Mie, Yann Hérault, Jean‐Charles Lambert, Henning Hermjakob, Tal Pupko, Jean-Christophe Rain, Ioannis Xénarios, Jaak Vilo, Michel Simonneau, Hedi Peterson
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0025634

GSTP1 DNA Methylation and Expression Status Is Indicative of 5-aza-2′-Deoxycytidine Efficacy in Human Prostate Cancer Cells
Cited by: 47
Author(s): Karen Chiam, Margaret M. Centenera, Lisa M. Butler, Wayne D. Tilley, Tina Bianco‐Miotto
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0109478

LINE-1 Hypomethylation in Blood and Tissue Samples as an Epigenetic Marker for Cancer Risk: A Systematic Review and Meta-Analysis
Cited by: 121
Author(s): Martina Barchitta, Annalisa Quattrocchi, Andrea Maugeri, Manlio Vinciguerra, Antonella Agodi
Software Mentions: 1
Published: almost 12 years ago

10.1186/1472-6947-7-41

Using machine learning algorithms to guide rehabilitation planning for home care clients
Cited by: 52
Author(s): Mu Zhu, Zhanyang Zhang, John P. Hirdes, Paul Stolee
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0184435

Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Cited by: 20
Author(s): Yukina Kawada, Shun‐ichiro Asahara, Yumiko Sugiura, Ayaka Sato, Ayuko Furubayashi, Mitsuhiro Kawamura, Alberto Bartolomé, Emi Terashi-Suzuki, Toshihiro Takai, Ayumi Kanno, Maki Koyanagi‐Kimura, Tomokazu Matsuda, Naoko Hashimoto, Yoshiaki Kido
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0113728

A Pragmatic Approach to Assess the Exposure of the Honey Bee (Apis mellifera) When Subjected to Pesticide Spray
Cited by: 34
Author(s): Yannick Poquet, Laurent Bodin, Marc Tchamitchian, Marion Fusellier, Barbara Giroud, Florent Lafay, Audrey Buleté, Sylvie Tchamitchian, Marianne Cousin, Michel Pélissier, Jean-Luc Brunet, Luc Belzunces
Software Mentions: 1
Published: over 11 years ago

10.1186/s12911-019-0890-0

Applying machine learning to predict future adherence to physical activity programs
Cited by: 24
Author(s): Mo Zhou, Yoshimi Fukuoka, Ken Goldberg, Eric Vittinghoff, Anil Aswani
Software Mentions: 1
Published: almost 7 years ago

10.1038/srep22989

Candida albicans repetitive elements display epigenetic diversity and plasticity
Cited by: 33
Author(s): Verónica Freire-Benéitez, R. Jordan Price, Daniel Tarrant, Judith Berman, Alessia Buscaino
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2288-12-82

Interpreting the concordance statistic of a logistic regression model: relation to the variance and odds ratio of a continuous explanatory variable
Cited by: 190
Author(s): Peter C. Austin, Ewout W. Steyerberg
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0041977

PATHLOGIC-S: A Scalable Boolean Framework for Modelling Cellular Signalling
Cited by: 6
Author(s): Liam G. Fearnley, Lars K. Nielsen
Software Mentions: 1
Published: about 14 years ago

10.1038/srep25975

A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure
Cited by: 24
Author(s): Sayak Mukhopadhyay, Ratan K. Saha, Anbarasi Palanisamy, Madhurima Ghosh, A. Biswas, Saheli Roy, Arijit Pal, Kathakali Sarkar, Sangram Bagh
Software Mentions: 1
Published: about 10 years ago

10.1038/srep26747

Intestinal APCs of the endogenous nanomineral pathway fail to express PD-L1 in Crohn’s disease
Cited by: 26
Author(s): Jack Robertson, Carolin Haas, Laetitia Pele, Tom P. Monie, Charles Charalambos, Miles Parkes, Rachel E. Hewitt, Jonathan J. Powell
Software Mentions: 1
Published: about 10 years ago

10.1038/srep28006

Circulating Plasma microRNAs can differentiate Human Sepsis and Systemic Inflammatory Response Syndrome (SIRS)
Cited by: 92
Author(s): Stefano Caserta, Florian Kern, Jonathan Cohen, Stephen Drage, Sarah F. Newbury, Martin J. Llewelyn
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0139590

Physiologically Shrinking the Solution Space of a Saccharomyces cerevisiae Genome-Scale Model Suggests the Role of the Metabolic Network in Shaping Gene Expression Noise
Cited by: 1
Author(s): Baofang Chi, Shiheng Tao, Yanlin Liu
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep29201

Antibody-Dependent Enhancement of Dengue Virus Infection in Primary Human Macrophages; Balancing Higher Fusion against Antiviral Responses
Cited by: 95
Author(s): Jacky Flipse, Mayra Diosa-Toro, Tabitha E. Hoornweg, Denise P. I. van de Pol, Silvio Urcuqui-Inchima, Jolanda M. Smit
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0176131

InMAP: A model for air pollution interventions
Cited by: 120
Author(s): Christopher W. Tessum, Jason Hill, Julian Marshall
Software Mentions: 1
Published: over 9 years ago

10.1186/s13021-019-0117-9

Forest degradation and biomass loss along the Chocó region of Colombia
Cited by: 22
Author(s): Victoria Meyer, Sassan Saatchi, António Ferraz, Liang Xu, Álvaro Duque, Mariano Garcı́a, Jérôme Chave
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0007099

Lysosomal-Associated Protein Multispanning Transmembrane 5 Gene (LAPTM5) Is Associated with Spontaneous Regression of Neuroblastomas
Cited by: 42
Author(s): Jun Inoue, Akiko Misawa, Yukichi Tanaka, Shizuko Ichinose, Yuriko Sugino, Hajime Hosoi, Tohru Sugimoto, Issei Imoto, Johji Inazawa
Software Mentions: 1
Published: almost 17 years ago

10.1038/srep33924

Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin
Cited by: 17
Author(s): Magdalena B. Rother, Kristin Jensen, Mirjam van der Burg, Fleur S. van de Bovenkamp, Roel Kroek, Wilfred F. J. van IJcken, Vincent H.J. van der Velden, Tom Cupedo, Ole Kristoffer Olstad, Jacques J. M. van Dongen, Menno C. van Zelm
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep34730

Novel population of small tumour-initiating stem cells in the ovaries of women with borderline ovarian cancer
Cited by: 40
Author(s): Irma Virant‐Klun, Martin Štimpfel
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0019862

Methylation Profile of Single Hepatocytes Derived from Hepatitis B Virus-Related Hepatocellular Carcinoma
Cited by: 59
Author(s): Ran Tao, Jun Li, Jiaojiao Xin, Jian Wu, Jing Guo, Liyuan Zhang, Liangliang Jiang, Wu Zhang, Zhe Yang, Lanjuan Li
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0043006

Predictive Potential of Flux Balance Analysis of Saccharomyces cerevisiae Using as Optimization Function Combinations of Cell Compartmental Objectives
Cited by: 14
Author(s): Carlos Eduardo García Sánchez, César Augusto Vargas-García, Rodrigo Torres
Software Mentions: 1
Published: about 14 years ago

10.1038/srep45828

A 3q gene signature associated with triple negative breast cancer organ specific metastasis and response to neoadjuvant chemotherapy
Cited by: 19
Author(s): Jun Qian, Heidi Chen, Xiangming Ji, Rosana Eisenberg, A. Bapsi Chakravarthy, Ingrid A. Mayer, Pierre P. Massion
Software Mentions: 1
Published: over 9 years ago

10.1093/bioinformatics/btu523

Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence
Cited by: 99
Author(s): Niclas Thomas, Katharine Best, Mattia Cinelli, Shlomit Reich-Zeliger, Hilah Gal, Eric Shifrut, Asaf Madi, Nir Friedman, John Shawe‐Taylor, Benjamin M. Chain
Software Mentions: 1
Published: about 12 years ago

10.1038/s41598-017-01156-x

The centrosomal OFD1 protein interacts with the translation machinery and regulates the synthesis of specific targets
Cited by: 35
Author(s): Daniela Iaconis, Maria Monti, Mario Renda, Arianne van Koppen, Roberta Tammaro, Marco Chiaravalli, Flora Cozzolino, Paola Pignata, Claudia Crina, Piero Pucci, Alessandra Boletta, Vincenzo Belcastro, Rachel Giles, Enrico Maria Surace, Simone Gallo, Mario Pende, Brunella Franco
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-04709-2

DACH1 suppresses breast cancer as a negative regulator of CD44
Cited by: 29
Author(s): Hanxiao Xu, Shengnan Yu, Xun Yuan, Jing Xiong, Dong Kuang, Richard G. Pestell, Kongming Wu
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-017-05872-2

Functional and Transcriptomic Characterization of Peritoneal Immune-Modulation by Addition of Alanyl-Glutamine to Dialysis Fluid
Cited by: 12
Author(s): Rebecca Herzog, Lilian Kuster, Julia Powers Becker, Tobias Gluexam, Dietmar Pils, Andreas Spittler, Manoj Bhasin, Seth L. Alper, Andreas Vychytil, Christoph Aufricht, Klaus Kratochwill
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0043658

Distinct DNA Methylation Dynamics of Spermatogenic Cell-Specific Intronless Genes Is Associated with CpG Content
Cited by: 7
Author(s): Yuzuru Kato, Masami Nozaki
Software Mentions: 1
Published: almost 14 years ago

10.3389/fimmu.2021.657950

ATP2C2 Has Potential to Define Tumor Microenvironment in Breast Cancer
Cited by: 9
Author(s): Jiazhou Liu, Yu Wei, Yushen Wu, Jie Li, Jiazheng Sun, Guosheng Ren, Hongzhong Li
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0132837

Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling
Cited by: 13
Author(s): Peter E. Larsen, F. Collart, Yang Dai
Software Mentions: 1
Published: almost 11 years ago

10.1136/jitc-2019-000285

IL-6 promotes PD-L1 expression in monocytes and macrophages by decreasing protein tyrosine phosphatase receptor type O expression in human hepatocellular carcinoma
Cited by: 76
Author(s): Wenjie Zhang, Yang Liu, Zhongyi Yan, Hui Yang, Wei Sun, Yongliang Yao, Yun Chen, Runqiu Jiang
Software Mentions: 1
Published: about 6 years ago

10.1155/2018/9485285

PD-L1 Expression Predicts a Distinct Prognosis in Krukenberg Tumor with Corresponding Origins
Cited by: 10
Author(s): Haiyan Tai, Qin Yang, Zhi‐Yong Wu, Sujuan Sun, Rui Cao, Yanfeng Xi, Ran Zhao, Mengyu Zhang, Zhigang Zhang, Congjian Xu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0241330

Sub-national longitudinal and geospatial analysis of COVID-19 tweets
Cited by: 14
Author(s): Raphael Cuomo, Vidya Purushothaman, Jiawei Li, Mingxiang Cai, Tim K. Mackey
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0009937

Targeting of De Novo DNA Methylation Throughout the Oct-4 Gene Regulatory Region in Differentiating Embryonic Stem Cells
Cited by: 64
Author(s): Rodoniki Athanasiadou, Dina De Sousa, Kevin Myant, Cara Merusi, Irina Stancheva, Adrian Bird
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0098760

Biochemical Characterization of Human Gluconokinase and the Proposed Metabolic Impact of Gluconic Acid as Determined by Constraint Based Metabolic Network Analysis
Cited by: 27
Author(s): Neha Rohatgi, T.K. Nielsen, Sara Petersen Bjørn, Ívar Axelsson, Giuseppe Paglia, Bjørn Gunnar Voldborg, Bernhard Ø. Palsson, Óttar Rolfsson
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0108275

A Heuristic Placement Selection of Live Virtual Machine Migration for Energy-Saving in Cloud Computing Environment
Cited by: 29
Author(s): Jia Zhao, Liang Hu, Yan Ding, Gaochao Xu, Ming Hu
Software Mentions: 1
Published: almost 12 years ago

10.1089/omi.2016.0041

Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-Wide DNA Methylation Profiles and RNA Expression
Cited by: 48
Author(s): Emil Nilsson, Adrian Boström, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 1
Published: about 10 years ago

10.3389/fpsyt.2021.591934

Integration of the ICD-11 and DSM-5 Dimensional Systems for Personality Disorders Into a Unified Taxonomy With Non-overlapping Traits
Cited by: 6
Author(s): Fernando Gutiérrez, Josep María Peri, Miguel Gárriz, Gemma Vall, Estela Arqué, Laura Ruíz, Jaume Condomines, Natàlia Calvo, Marc Ferrer, B Sureda
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0200996

Germline single nucleotide polymorphisms in ERBB3 and BARD1 genes result in a worse relapse free survival response for HER2-positive breast cancer patients treated with adjuvant based docetaxel, carboplatin and trastuzumab (TCH)
Cited by: 9
Author(s): Damien Côté, Alex J. Eustace, Sinéad Toomey, Mattia Cremona, Małgorzata Milewska, Simon J. Furney, Aoife Carr, Joanna Fay, Elaine W. Kay, Susan Kennedy, John Crown, Bryan T. Hennessy, Stephen F. Madden
Software Mentions: 1
Published: about 8 years ago

10.1016/j.ophtha.2016.01.009

Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease
Cited by: 110
Author(s): Jamie M Ellingford, Stephanie Barton, Sanjeev S. Bhaskar, Simon G. Williams, Panagiotis I. Sergouniotis, James O’Sullivan, Janine A. Lamb, Rahat Perveen, Georgina Hall, William G. Newman, Paul N. Bishop, Stephen A Roberts, Rick Leach, Rick Tearle, S. C. Bayliss, Simon Ramsden, Andrea H. Németh, Graeme C M Black
Software Mentions: 1
Published: over 10 years ago

10.1016/j.jmb.2012.10.014

Gene Function Hypotheses for the Campylobacter jejuni Glycome Generated by a Logic-Based Approach
Cited by: 18
Author(s): Michael J.E. Sternberg, Alireza Tamaddoni‐Nezhad, Victor I. Lesk, Emily Kay, Paul G. Hitchen, Adrian P. Cootes, Lieke B. van Alphen, Marc P. Lamoureux, Harold C. Jarrell, Christopher J. Rawlings, Evelyn C. Soo, Christine M. Szymanski, Anne Dell, Brendan W. Wren, Stephen Muggleton
Software Mentions: 1
Published: over 13 years ago

10.1016/j.yjmcc.2019.02.006

The cardiomyocyte “redox rheostat”: Redox signalling via the AMPK-mTOR axis and regulation of gene and protein expression balancing survival and death
Cited by: 25
Author(s): Daniel N. Meijles, Georgia Zoumpoulidou, Thomais Markou, Kerry A Rostron, Rishi Patel, Kenneth Lay, Balvinder S. Handa, Bethany Wong, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: over 7 years ago

10.3390/cancers12123763

Pharmacokinetic Analysis of Dynamic Contrast-Enhanced Magnetic Resonance Imaging at 7T for Breast Cancer Diagnosis and Characterization
Cited by: 3
Author(s): R. Elena Ochoa‐Albiztegui, Varadan Sevilimedu, João V. Horvat, Sunitha B. Thakur, Thomas H. Helbich, Siegfried Trattnig, Elizabeth A. Morris, Jeffrey S. Reiner, Katja Pinker
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.45051

The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity
Cited by: 36
Author(s): Tamara Sirey, Kenny Roberts, Wilfried Haerty, Oscar C. Bedoya-Reina, Sebastian Rogatti-Granados, Jennifer Y. Tan, Nick Li, Lisa C. Heather, Roderick N. Carter, Sarah Cooper, Andrew J. Finch, Jimi Wills, Nicholas M. Morton, Ana C. Marques, Chris P. Ponting
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0204375

Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)
Cited by: 17
Author(s): Hanseol Kim, Sinyeon Kim, Sung Ho Yoon
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1000145

Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus
Cited by: 114
Author(s): Anders M. Lindroth, Yoon Jung Park, Chelsea McLean, Gregoriy A. Dokshin, Jenna Persson, Herry Herman, Diego Pasini, Xavier Miró, Mary E. Donohoe, Jeannie T. Lee, Kristian Helin, Paul D. Soloway
Software Mentions: 1
Published: about 18 years ago

10.7554/eLife.69160

GIV/Girdin, a non-receptor modulator for Gαi/s, regulates spatiotemporal signaling during sperm capacitation and is required for male fertility
Cited by: 5
Author(s): Sequoyah Reynoso, Vanessa Castillo, Gajanan D. Katkar, Inmaculada López-Sánchez, Sahar Taheri, Celia R. Espinoza, Cristina C. Rohena, Debashis Sahoo, Pascal Gagneux, Pradipta Ghosh
Software Mentions: 1
Published: almost 5 years ago

10.1039/c8sc02239a

Chimera: enabling hierarchy based multi-objective optimization for self-driving laboratories
Cited by: 79
Author(s): Florian Häse, Loı̈c M. Roch, Alán Aspuru‐Guzik
Software Mentions: 1
Published: over 8 years ago

10.1002/ece3.3778

Multiscale landscape genomic models to detect signatures of selection in the alpine plant<i>Biscutella laevigata</i>
Cited by: 9
Author(s): Kevin Leempoel, Christian Parisod, Céline Geiser, Stéphane Joost
Software Mentions: 1
Published: over 8 years ago

10.1002/open.202000258

Extremely Low Vapor‐Pressure Data as Access to PC‐SAFT Parameter Estimation for Ionic Liquids and Modeling of Precursor Solubility in Ionic Liquids
Cited by: 7
Author(s): Mark Bülow, Moritz Greive, Dzmitry H. Zaitsau, Sergey P. Verevkin, Christoph Held
Software Mentions: 1
Published: over 5 years ago

10.1111/eva.13076

Genomic selection for resistance to spruce budworm in white spruce and relationships with growth and wood quality traits
Cited by: 17
Author(s): Jean Beaulieu, Simon Nadeau, Chen Ding, José M. Celedón, Aïda Azaiez, Carol Ritland, Jean‐Philippe Laverdière, Marie Deslauriers, Gregory W. Adams, M. S. Fullarton, Jöerg Bohlmann, P. Lenz, Jean Bousquet
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.03743

The transcription factor Pitx2 positions the embryonic axis and regulates twinning
Cited by: 33
Author(s): Angela Torlopp, Mohsin A.F. Khan, Nidia M M Oliveira, Ingrid Lekk, Luz Mayela Soto‐Jiménez, Alona Sosinsky, Claudio D. Stern
Software Mentions: 1
Published: over 11 years ago

10.7554/eLife.09886

Protein kinase C coordinates histone H3 phosphorylation and acetylation
Cited by: 13
Author(s): Zoulfia Darieva, Aaron Webber, Stacey Warwood, Andrew D. Sharrocks
Software Mentions: 1
Published: almost 11 years ago

10.3390/ijms11093397

Practical Application of Toxicogenomics for Profiling Toxicant-Induced Biological Perturbations
Cited by: 21
Author(s): Naoki Kiyosawa, Sunao Manabe, Takashi Yamoto, Atsushi Sanbuissho
Software Mentions: 1
Published: almost 16 years ago

10.3390/ijms151019037

ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates
Cited by: 7
Author(s): Michael Roemer, Linus Backert, Johannes Eichner, Andreas Zell
Software Mentions: 1
Published: almost 12 years ago

10.1007/s00392-020-01731-9

Risk modeling in transcatheter aortic valve replacement remains unsolved: an external validation study in 2946 German patients
Cited by: 12
Author(s): Georg Wolff, Jasmin Shamekhi, Baravan Al‐Kassou, Noriaki Tabata, Claudio Parco, Kathrin Klein, Oliver Maier, Alexander Sedaghat, Amin Polzin, Akira Sugiura, Christian Jung, Eberhard Grube, Ralf Westenfeld, Andrea Icks, Tobias Zeus, Jan–Malte Sinning, Stephan Baldus, Georg Nickenig, Malte Kelm, Verena Veulemans
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms19051369

Meta-Analysis and Experimental Validation Identified FREM2 and SPRY1 as New Glioblastoma Marker Candidates
Cited by: 11
Author(s): Marko Vidak, Ivana Jovčevska, Neja Šamec, Alja Zottel, Mirjana Liović, Damjana Rozman, Sašo Džeroski, Peter Juvan, Radovan Komel
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms19071967

miR-196a Is Able to Restore the Aggressive Phenotype of Annexin A1 Knock-Out in Pancreatic Cancer Cells by CRISPR/Cas9 Genome Editing
Cited by: 26
Author(s): Raffaella Belvedere, Pasquale Saggese, Emanuela Pessolano, Domenico Memoli, Valentina Bizzarro, Francesca Rizzo, Luca Parente, Alessandro Weisz, Antonello Petrella
Software Mentions: 1
Published: about 8 years ago

10.1186/1752-0509-2-85

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
Cited by: 75
Author(s): Maxime Durot, François Le Fèvre, Véronique de Berardinis, Annett Kreimeyer, David Vallenet, Cyril Combe, Serge Smidtas, Marcel Salanoubat, Jean Weissenbach, Vincent Schächter
Software Mentions: 1
Published: almost 18 years ago

10.3390/ijms20225783

Genome-Wide Identification and Characterization of ABC Transporters in Nine Rosaceae Species Identifying MdABCG28 as a Possible Cytokinin Transporter linked to Dwarfing
Cited by: 19
Author(s): Yi Feng, Qiran Sun, Guifen Zhang, Ting Wu, Xinzhong Zhang, Xuefeng Xu, Zhenhai Han, Yi Wang
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21061941

Fighting Against Promoter DNA Hyper-Methylation: Protective Histone Modification Profiles of Stress-Resistant Intestinal Stem Cells
Cited by: 1
Author(s): Torsten Thalheim, Lydia Hopp, Maria Herberg, Susann Siebert, Christiane Kerner, Marianne Quaas, Michal R. Schweiger, Gabriela Aust, Joerg Galle
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2016.00126

PD1-Expressing T Cell Subsets Modify the Rejection Risk in Renal Transplant Patients
Cited by: 21
Author(s): Rebecca Pike, Niclas Thomas, Sarita Workman, Lyn Ambrose, David Sánchez-Migallón Guzman, S Sivakumaran, Margaret Johnson, Douglas Thorburn, Mark Harber, Benjamin M. Chain, Hans J. Stauss
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms17030402

A Novel Pretreatment-Free Duplex Chamber Digital PCR Detection System for the Absolute Quantitation of GMO Samples
Cited by: 20
Author(s): Pengyu Zhu, Chenguang Wang, Kunlun Huang, Yunbo Luo, Wentao Xu
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms21113749

17-Aminogeldanamycin Inhibits Constitutive Nuclear Factor-Kappa B (NF-κB) Activity in Patient-Derived Melanoma Cell Lines
Cited by: 7
Author(s): Mariusz L. Hartman, Magdalena Rogut, Aleksandra Mielczarek-Lewandowska, Michal Wozniak, Małgorzata Czyż
Software Mentions: 1
Published: about 6 years ago

10.3389/fnins.2017.00470

Interhemispheric Resting-State Functional Connectivity Predicts Severity of Idiopathic Normal Pressure Hydrocephalus
Cited by: 12
Author(s): Yuji Ogata, Akihiko Ozaki, Miho Ota, Yurie Oka, Namiko Nishida, Hayato Tabu, Noriko Sato, Takashi Hanakawa
Software Mentions: 1
Published: almost 9 years ago

10.3390/ijms21218069

Intra-Individual Behavioural Variability: A Trait under Genetic Control
Cited by: 12
Author(s): Rie Henriksen, Andrey Höglund, Jesper Fogelholm, Robin N. Abbey-Lee, Martin Johnsson, Niels Jeroen Dingemanse, Dominic Wright
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms22126505

Screen Key Genes Associated with Distraction-Induced Osteogenesis of Stem Cells Using Bioinformatics Methods
Cited by: 2
Author(s): Jishizhan Chen, Jia Hua, Wenhui Song
Software Mentions: 1
Published: about 5 years ago