10.1186/1471-2164-14-728

Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)
Cited by: 80
Author(s): Karl G. Kugler, Gerald Siegwart, Thomas Nußbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus Mayer, Hermann Buerstmayr, Wolfgang Schweiger
Software Mentions: 4
Published: almost 13 years ago

10.1038/s41598-019-44991-w

Identification of a Radiosensitivity Molecular Signature Induced by Enzalutamide in Hormone-sensitive and Hormone-resistant Prostate Cancer Cells
Cited by: 15
Author(s): Maryam Ghashghaei, Tamim Niazi, Adriana Aguilar‐Mahecha, Kathleen Klein, Celia M.T. Greenwood, Mark Basik, Thierry Muanza
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-40992-x

A comparison between the abdominal and femoral adipose tissue proteome of overweight and obese women
Cited by: 18
Author(s): Max Vogel, Ping Wang, Freek G. Bouwman, Nicole Hoebers, Ellen E. Blaak, Johan Renes, E.C.M. Mariman, Gijs H. Goossens
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0226595

Development of a long non-coding RNA signature for prediction of response to neoadjuvant chemoradiotherapy in locally advanced rectal adenocarcinoma
Cited by: 15
Author(s): Lorenzo Ferrando, Gabriella Cirmena, Anna Garuti, Stefano Scabini, Federica Grillo, Luca Mastracci, Edoardo Isnaldi, C. Marrone, Roberta Gonella, Roberto Murialdo, Roberto Fiocca, Emanuele Romairone, Alberto Ballestrero, Gabriele Zoppoli
Software Mentions: 4
Published: over 6 years ago

10.3897/zookeys.1041.63884

Ichthyofauna in the last free-flowing river of the Lower Iguaçu basin: the importance of tributaries for conservation of endemic species
Cited by: 4
Author(s): Suelen Fernanda Ranucci Pini, Maristela Cavicchioli Makrakis, Mayara Pereira Neves, Sérgio Makrakis, Oscar Akio Shibatta, Elaine Antoniassi Luiz Kashiwaqui
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2021.603556

Pharmacological Inhibition and Genetic Knockdown of BCL9 Modulate the Cellular Landscape of Cancer-Associated Fibroblasts in the Tumor-Immune Microenvironment of Colorectal Cancer
Cited by: 5
Author(s): Ming Yang, Wei Zhuang, Mei Feng, Yuanyuan Zhu, Yong Chen, Di Zhu
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-52433-w

Phonological network fluency identifies phonological restructuring through mental search
Cited by: 5
Author(s): Karl David Neergaard, Jin Luo, Chu‐Ren Huang
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-018-34127-x

Bacterial and fungal gut communities of Agrilus mali at different developmental stages and fed different diets
Cited by: 26
Author(s): Zhengqing Zhang, Shuo Jiao, Xiaohui Li, LI Meng-lou
Software Mentions: 4
Published: almost 8 years ago

10.3389/fpls.2012.00202

A High-Throughput Method for Illumina RNA-Seq Library Preparation
Cited by: 134
Author(s): Ravi Kumar, Yasunori Ichihashi, Seisuke Kimura, Daniel H. Chitwood, Lauren R. Headland, Jie Peng, Julin N. Maloof, Neelima Sinha
Software Mentions: 4
Published: over 14 years ago

10.7554/eLife.53459

The histone modification reader ZCWPW1 links histone methylation to PRDM9-induced double-strand break repair
Cited by: 28
Author(s): Tao Huang, Shenli Yuan, Lei Gao, Mengjing Li, Xiaochen Yu, Jianhong Zhan, Yingying Yin, Chao Liu, Chuanxin Zhang, Gang Lü, Wei Li, Jiang Liu, Zi‐Jiang Chen, Hongbin Liu
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0093846

The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non-Coding and Coding RNAs
Cited by: 104
Author(s): Lei Shi, Zhe Zhang, Angela M Yu, Wei Wang, Zhi Wei, Ehtisham Akhter, Kelly Maurer, Patrícia Costa-Reis, Li Song, Michelle Petri, Kathleen E. Sullivan
Software Mentions: 4
Published: over 12 years ago

10.3389/fonc.2020.00627

High Levels of HIST1H2BK in Low-Grade Glioma Predicts Poor Prognosis: A Study Using CGGA and TCGA Data
Cited by: 20
Author(s): Weidong Liu, Zhentao Xu, Jie Zhou, Shuang Xing, Zhiqiang Li, Xu Gao, Shiyu Feng, Yi Xiao
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-11-441

Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties
Cited by: 80
Author(s): Marika Vitikainen, Mikko Arvas, Tiina Pakula, Merja Oja, Merja Penttilä, Markku Saloheimo
Software Mentions: 4
Published: over 16 years ago

10.7717/peerj.7905

Effects of plant growth-promoting rhizobacteria on co-inoculation with <i>Bradyrhizobium</i> in soybean crop: a meta-analysis of studies from 1987 to 2018
Cited by: 51
Author(s): Douglas Mariani Zeffa, Lucas Henrique Fantin, Alessandra Koltun, André Luiz Martinez de Oliveira, Maria Paula Nunes, Marcelo Giovanetti Canteri, Leandro Simões Azeredo Gonçalves
Software Mentions: 4
Published: over 6 years ago

10.3390/genes9120579

Integrated Proteomic and Transcriptomic Analysis of Differential Expression of Chicken Lung Tissue in Response to NDV Infection during Heat Stress
Cited by: 19
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 4
Published: over 7 years ago

10.3389/fonc.2020.01778

Seven-Gene Signature Based on Glycolysis Is Closely Related to the Prognosis and Tumor Immune Infiltration of Patients With Gastric Cancer
Cited by: 36
Author(s): Shanshan Yu, Chuan Hu, Luya Cai, Xuedan Du, Fan Lin, Qiongjie Yu, Lixiao Liu, Cheng Zhang, Xuan Li, Wenfeng Li, Yu Zhan
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-14-675

Efficient and accurate whole genome assembly and methylome profiling of E. coli
Cited by: 40
Author(s): Jason Powers, Victor Weigman, Jenny Shu, John Pufky, Donald Cox, Patrick Hurban
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0169648

The Smc5/6 Complex Restricts HBV when Localized to ND10 without Inducing an Innate Immune Response and Is Counteracted by the HBV X Protein Shortly after Infection
Cited by: 107
Author(s): Congrong Niu, Christine M. Livingston, Li Li, Rudolf K. F. Beran, Stéphane Daffis, Dhivya Ramakrishnan, Dara Burdette, Leanne Peiser, Eduardo Salas, Hilario J. Ramos, Mei Yu, Guofeng Cheng, Michel Strubin, William E. Delaney, Simon P. Fletcher
Software Mentions: 4
Published: over 9 years ago

10.1186/s12889-020-09130-5

Model of genetic and environmental factors associated with type 2 diabetes mellitus in a Chinese Han population
Cited by: 7
Author(s): Zheng Li, Chengyin Ye, Tianyu Zhao, Lei Yang
Software Mentions: 4
Published: about 6 years ago

10.1186/1753-6561-5-S9-S19

Gene-based partial least-squares approaches for detecting rare variant associations with complex traits
Cited by: 8
Author(s): Asuman Türkmen, Shili Lin
Software Mentions: 4
Published: over 14 years ago

10.1371/journal.pone.0226193

Ultra-deep massively parallel sequencing with unique molecular identifier tagging achieves comparable performance to droplet digital PCR for detection and quantification of circulating tumor DNA from lung cancer patients
Cited by: 15
Author(s): Le Son Tran, Hong-Anh Thi Pham, Van Thi Thanh Tran, Thuy Thi Thu Tran, Anh-Thu Huynh Dang, Dinh-Thong Vu Le, Son-Lam Nguyen, Ngoc-Vu Nguyen, Tuan S. Nguyen, Binh Thanh Vo, Hong-Thuy Thi Dao, Nguyen Huu Nguyen, Thuy Tran, Chu Van Nguyen, Phuong Cam Pham, Anh Tuan Dang-Mai, Thien Kim Dinh-Nguyen, Vu Hien Phan, Thanh-Thuy Thi, Kiet Truong Dinh, Han Ngoc, Minh-Duy Phan, Hoa Giang, Hoai-Nghia Nguyen
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-018-2131-4

On the rank-distance median of 3 permutations
Cited by: 4
Author(s): Leonid Chindelevitch, João Paulo Pereira Zanetti, João Meidânis
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms22042006

Transcriptome Analysis Reveals HgCl2 Induces Apoptotic Cell Death in Human Lung Carcinoma H1299 Cells through Caspase-3-Independent Pathway
Cited by: 2
Author(s): Mi Jin Kim, Jin‐Hong Park, Jin-Ho Kim, Jiyoung Kim, Mi-Jin An, Geun-Seup Shin, Hyun-Min Lee, Chulhong Kim, Jung-Woong Kim
Software Mentions: 4
Published: over 5 years ago

10.1155/2013/270362

A Case Report and Genetic Characterization of a Massive Acinic Cell Carcinoma of the Parotid with Delayed Distant Metastases
Cited by: 5
Author(s): Anthony C. Nichols, Michelle Chan-Seng-Yue, John Yoo, Sumit Agrawal, Maud H.W. Starmans, Daryl Waggott, Nicholas J. Harding, Samuel Dowthwaite, David A. Palma, Kevin Fung, Bret Wehrli, Danielle MacNeil, Philippe Lambin, Eric Winquist, James Koropatnick, Joe S. Mymryk, Paul C. Boutros, John W. Barrett
Software Mentions: 4
Published: over 13 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

10.1155/2017/8932583

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos
Cited by: 9
Author(s): Wenqing Jean Lee, Satadal Chatterjee, Sook Peng Yap, Siew Lan Lim, Xing Xing, Petra Kraus, Wenjie Sun, Xiaoming Hu, V. Sivakamasundari, Hsiao Yun Chan, Prasanna R. Kolatkar, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0256343

Antimalarial drug resistance in the Central and Adamawa regions of Cameroon: Prevalence of mutations in P. falciparum crt, Pfmdr1, Pfdhfr and Pfdhps genes
Cited by: 10
Author(s): Aline Gaelle Bouopda Tuedom, Elangwe Milo Sarah-Matio, Carole Else Eboumbou Moukoko, Brice Lionel Feufack-Donfack, Christelle Ngou Maffo, Albert N. Bayibéki, Hermann Parfait Awono-Ambene, Lawrence Ayong, Antoine Berry, Luc Abate, Isabelle Morlais, Sandrine E. Nsango
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0225382

Biomarker discovery in inflammatory bowel diseases using network-based feature selection
Cited by: 17
Author(s): Mostafa M. Abbas, John Matta, Thanh Le, Halima Bensmail, Tayo Obafemi-Ajayi, Vasant Honavar, Yasser EL-Manzalawy
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0193958

Grass pollen production and group V allergen content of agriculturally relevant species and cultivars
Cited by: 20
Author(s): Stephan Jung, Nicole Estrella, Michael W. Pfaffl, Stephan Hartmann, Ellinor Handelshauser, Annette Menzel
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-020-03888-6

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data
Cited by: 1
Author(s): Noel‐Marie Plonski, Emily Johnson, Madeline Frederick, Heather Mercer, Gail Fraizer, Richard S. Meindl, Gemma Casadesús, Helen Piontkivska
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms9081673

Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types
Cited by: 2
Author(s): Andrea K. Borsodi, Márton Mucsi, Gergely Krett, Attila Szabó, Tamás Felföldi, Tibor Szili‐Kovács
Software Mentions: 4
Published: about 5 years ago

10.3389/fpsyg.2021.705668

Spoken Word Segmentation in First and Second Language: When ERP and Behavioral Measures Diverge
Cited by: 2
Author(s): Annie C. Gilbert, Jasmine G. Lee, Kristina Coulter, Max Wolpert, Shanna Kousaie, Vincent L. Gracco, Denise Klein, Debra Titone, Natalie A. Phillips, Shari R. Baum
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0213930

Consistent declines in wing lengths of Calidridine sandpipers suggest a rapid morphometric response to environmental change
Cited by: 15
Author(s): Alexandra M. Anderson, Christian Friis, Cheri L. Gratto‐Trevor, R. I. Guy Morrison, Paul A. Smith, Erica Nol
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2020.01628

Networking and Specificity-Changing DNA Methyltransferases in Helicobacter pylori
Cited by: 9
Author(s): Hirokazu Yano, Zobaidul Alam, Emiko Rimbara, Tomoko Shibata, Masaki Fukuyo, Yoshikazu Furuta, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0219293

Health status of honey bee colonies (Apis mellifera) and disease-related risk factors for colony losses in Austria
Cited by: 51
Author(s): Linde Morawetz, Hemma Köglberger, Antonia Griesbacher, Irmgard Derakhshifar, Karl Crailsheim, Robert Brodschneider, Rudolf Moosbeckhofer
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0181192

Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity
Cited by: 23
Author(s): Ulrika Lind, Michael Järvå, Magnus Alm Rosenblad, Piero Pingitore, Emil Karlsson, Anna-Lisa Wrange, Emelie Kamdal, Kristina Sundell, Carl André, Per R. Jonsson, Jonathan N. Havenhand, Leif A. Eriksson, Kristina Hedfalk, Anders Blomberg
Software Mentions: 4
Published: about 9 years ago

10.1155/2020/8886914

An Integrative Analysis Reveals the Potential Mechanism between Herbal Medicine Yinchen and Immunoregulation in Hepatocellular Carcinoma
Cited by: 3
Author(s): Zhuomao Mo, Zhirui Cao, Ling Yu, Yongdan Wang, Pan Li, You-Wu Lin, Shijun Zhang
Software Mentions: 4
Published: over 5 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

10.3389/fmicb.2017.01808

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses
Cited by: 36
Author(s): François Thomas, Philippe Bordron, Damien Eveillard, Gurvan Michel
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-020-60623-0

First evidence of production of the lantibiotic nisin P
Cited by: 29
Author(s): Enriqueta García-Gutiérrez, Paula M. O’Connor, Gerhard Saalbach, Calum J. Walsh, James W. Hegarty, Caitriona M. Guinane, Melinda J. Mayer, Arjan Narbad, Paul D. Cotter
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2021.705511

Screening and Validation of the Hypoxia-Related Signature of Evaluating Tumor Immune Microenvironment and Predicting Prognosis in Gastric Cancer
Cited by: 27
Author(s): Jun‐Peng Pei, Chundong Zhang, Maimaititusun Yusupu, Dong‐Qiu Dai
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.61531

HAT cofactor TRRAP modulates microtubule dynamics via SP1 signaling to prevent neurodegeneration
Cited by: 6
Author(s): Alicia Tapias, David Rodríguez Lázaro, Bo-Kun Yin, Seyed Mohammad Mahdi Rasa, Anna Krepelova, Erika Kelmer Sacramento, Paulius Grigaravičius, Philipp Koch, Joanna Kirkpatrick, Alessandro Ori, Francesco Neri, Zhaoqi Wang
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.7138

Could do better! A high school market survey of fish labelling in Sydney, Australia, using DNA barcodes
Cited by: 12
Author(s): Andrew Mitchell, Anna Rothbart, Greta J. Frankham, Rebecca N. Johnson, Linda E. Neaves
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0186118

Finding the signal in the noise: Could social media be utilized for early hospital notification of multiple casualty events?
Cited by: 10
Author(s): Rachael A. Callcut, Sara Moore, Glenn K. Wakam, Alan Hubbard, Mitchell J. Cohen
Software Mentions: 4
Published: almost 9 years ago

10.1111/mmi.12977

<scp>K</scp>dm<scp>A</scp>, a histone<scp>H</scp>3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in<scp><i>A</i></scp><i>spergillus nidulans</i>
Cited by: 41
Author(s): Agnieszka Gacek‐Matthews, Luke M. Noble, Clemens Gruber, Harald Berger, Michael Sulyok, Ana T. Marcos, Joseph Strauss, Alex Andrianopoulos
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pntd.0001274

Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host
Cited by: 88
Author(s): Sophia J. Parker-Manuel, Alasdair Ivens, G. Dillon, R. A. Wilson
Software Mentions: 4
Published: almost 15 years ago

10.1186/s13059-019-1785-1

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center
Cited by: 21
Author(s): Matthew J. Ellington, Eva Heinz, Alexander M. Wailan, Matthew J. Dorman, Marcus C. de Goffau, Amy K. Cain, Sonal P. Henson, Nicholas Gleadall, Christine J. Boinett, Gordon Dougan, Nicholas M. Brown, Neil Woodford, Julian Parkhill, M. Estée Török, Sharon J. Peacock, Nicholas R. Thomson
Software Mentions: 4
Published: almost 7 years ago

10.1111/mmi.14417

BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy data
Cited by: 23
Author(s): Renske van Raaphorst, Morten Kjos, Jan‐Willem Veening
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0150094

Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens
Cited by: 8
Author(s): Jigna Shah, Prerak Desai, Ying Zhang, Sarah K. Scharber, Joshua A. Baller, Zheng Xing, Carol J. Cardona
Software Mentions: 4
Published: over 10 years ago

10.1186/s40168-019-0776-5

Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities
Cited by: 55
Author(s): Eslam O. Osman, David J. Suggett, Christian R. Voolstra, D. Tye Pettay, Dave R. Clark, Claudia Pogoreutz, Eugenia M. Sampayo, Mark E. Warner, David J. Smith
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0192383

Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen
Cited by: 40
Author(s): Claire Brice, Francisco A. Cubillos, Sylvie Dequin, Carole Camarasa, Claudio Martı́nez
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms21093129

Bisphenol A Exposure in utero Disrupts Hypothalamic Gene Expression Particularly Genes Suspected in Autism Spectrum Disorders and Neuron and Hormone Signaling
Cited by: 18
Author(s): Anne De Piante Henriksen, Alejandro Andrade, Erin P. Harris, Emilie F. Rissman, Jennifer T. Wolstenholme
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-016-1014-0

The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum
Cited by: 83
Author(s): Evelien M. Bunnik, Gayani Batugedara, Anita Saraf, Jacques Prudhomme, Laurence Florens, Karine G. Le Roch
Software Mentions: 4
Published: about 10 years ago

10.1186/s12874-016-0254-8

Least absolute shrinkage and selection operator type methods for the identification of serum biomarkers of overweight and obesity: simulation and application
Cited by: 119
Author(s): Monica M. Vasquez, Chengcheng Hu, Denise J. Roe, Zhao Chen, Marilyn Halonen, Stefano Guerra
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pcbi.1003376

Current Practice in Software Development for Computational Neuroscience and How to Improve It
Cited by: 27
Author(s): Marc‐Oliver Gewaltig, Robert C. Cannon
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0248759

Impact of elevated air temperature and drought on pollen characteristics of major agricultural grass species
Cited by: 6
Author(s): Stephan Jung, Nicole Estrella, Michael W. Pfaffl, Stephan Hartmann, Franziska Ewald, Annette Menzel
Software Mentions: 4
Published: over 5 years ago

10.1186/s12880-019-0355-z

Computed tomography-based predictive nomogram for differentiating primary progressive pulmonary tuberculosis from community-acquired pneumonia in children
Cited by: 21
Author(s): Bei Wang, Min Li, He Ma, Fangfang Han, Yan Wang, Shunying Zhao, Zhimin Liu, Tao Yu, Jie Tian, Di Dong, Yun Peng
Software Mentions: 4
Published: about 7 years ago

10.1186/s13148-020-00990-7

DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome
Cited by: 25
Author(s): Laila C. Schenkel, Erfan Aref‐Eshghi, Kathleen Rooney, Jennifer Kerkhof, Michael A. Levy, Haley McConkey, R. Curtis Rogers, Katy Phelan, Sara M. Sarasua, Lavanya Jain, Rini Pauly, Luigi Boccuto, Barbara R. DuPont, Gerarda Cappuccio, Nicola Brunetti‐Pierri, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 4
Published: over 5 years ago

10.1186/s12880-021-00564-w

CT-based radiomics combined with signs: a valuable tool to help radiologist discriminate COVID-19 and influenza pneumonia
Cited by: 14
Author(s): Yurong Huang, Zhenguang Zhang, Siyun Liu, Xiang Li, Yaewon Yang, Jiyao Ma, Zhipeng Li, Jialong Zhou, Yuanming Jiang, Bo He
Software Mentions: 4
Published: over 5 years ago

10.3389/fcimb.2018.00187

Staphylococcus aureus CC30 Lineage and Absence of sed,j,r-Harboring Plasmid Predict Embolism in Infective Endocarditis
Cited by: 3
Author(s): Jean-Philippe Rasigade, Amélie Leclère, François Alla, Adrien Tessier, Michèle Bes, Catherine Lechiche, Véronique Vernet-Garnier, Cédric Laouénan, François Vandenesch, Catherine Leport
Software Mentions: 4
Published: about 8 years ago

10.1186/s40462-019-0176-2

Mesoscale movement and recursion behaviors of Namibian black rhinos
Cited by: 10
Author(s): Dana Paige Seidel, Wayne L. Linklater, Werner Kilian, Pierre du Preez, Wayne M. Getz
Software Mentions: 4
Published: almost 7 years ago

10.1128/mBio.01959-21

Multifactorial Role of Mitochondria in Echinocandin Tolerance Revealed by Transcriptome Analysis of Drug-Tolerant Cells
Cited by: 13
Author(s): Rocio Garcia-Rubio, Cristina Jiménez‐Ortigosa, Lucius DeGregorio, Christopher Quinteros, Erika Shor, David S. Perlin
Software Mentions: 4
Published: almost 5 years ago

10.1089/hum.2020.213

Genetic Rescue of X-Linked Retinoschisis Mouse (<i>Rs1</i>^−/y) Retina Induces Quiescence of the Retinal Microglial Inflammatory State Following AAV8-<i>RS1</i> Gene Transfer and Identifies Gene Networks Underlying Retinal Recovery
Cited by: 16
Author(s): Camasamudram Vijayasarathy, Yong Zeng, Matthew Brooks, Robert N Fariss, Paul A. Sieving
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0221694

Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages
Cited by: 15
Author(s): Robert Danczak, Michael D. Johnston, Chris Kenah, Michael T. Slattery, Michael J. Wilkins
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0239026

Impact of COVID-19 epidemic curtailment strategies in selected Indian states: An analysis by reproduction number and doubling time with incidence modelling
Cited by: 14
Author(s): Arun Mitra, Abhijit Pakhare, Adrija Roy, Ankur Joshi
Software Mentions: 4
Published: almost 6 years ago

10.1186/s10020-020-00266-z

The transcriptome-wide association search for genes and genetic variants which associate with BMI and gestational weight gain in women with type 1 diabetes
Cited by: 2
Author(s): Agnieszka H. Ludwig-Słomczyńska, Michał Seweryn, Przemysław Kapusta, Ewelina Pitera, Urszula Mantaj, Katarzyna Cyganek, Paweł Gutaj, Łucja Dobrucka, Ewa Wender-Ożegowska, Maciej Małecki, Paweł Wołkow
Software Mentions: 4
Published: over 5 years ago

10.1080/21655979.2020.1864912

Analysis of Collagen type X alpha 1 (COL10A1) expression and prognostic significance in gastric cancer based on bioinformatics
Cited by: 33
Author(s): Shuai Chen, Wei Yi, Hanyang Liu, Yu Gong, Yan Zhou, Haojun Yang, Liming Tang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-016-0963-3

Leveraging protein quaternary structure to identify oncogenic driver mutations
Cited by: 8
Author(s): Gregory A. Ryslik, Yu‐Wei Cheng, Yorgo Modis, Hongyu Zhao
Software Mentions: 4
Published: over 10 years ago

10.1016/j.immuni.2021.05.016

A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression
Cited by: 22
Author(s): Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela María Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1003246

dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
Cited by: 13
Author(s): Dongjun Chung, Dan Park, Kevin S. Myers, Jeffrey A. Grass, Patricia J. Kiley, Robert Landick, Sündüz Keleş
Software Mentions: 4
Published: almost 13 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

10.3389/fcell.2021.671806

Knockdown of Splicing Complex Protein PCBP2 Reduces Extravillous Trophoblast Differentiation Through Transcript Switching
Cited by: 6
Author(s): Danai Georgiadou, Souad Boussata, Remco Keijser, Dianta Janssen, Gijs B. Afink, Marie van Dijk
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-54782-y

Investigating the energy crisis in Alzheimer disease using transcriptome study
Cited by: 21
Author(s): S. Akila Parvathy Dharshini, Y-h. Taguchi, M. Michael Gromiha
Software Mentions: 4
Published: over 6 years ago

10.3390/cells10061291

Innate and Adaptive Immune Genes Associated with MERS-CoV Infection in Dromedaries
Cited by: 6
Author(s): Sara Lado, Jean P. Elbers, Martin Plášil, Tom Loney, Pia Weidinger, Jeremy V. Camp, Jolanta Kolodziejek, Ján Futas, Dafalla A. Kannan, Pablo Orozco‐terWengel, Petr Hořín, Norbert Nowotny, Pamela A. Burger
Software Mentions: 4
Published: about 5 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

10.1371/journal.pone.0194056

Genetic structure of wild pea (Pisum sativum subsp. elatius) populations in the northern part of the Fertile Crescent reflects moderate cross-pollination and strong effect of geographic but not environmental distance
Cited by: 59
Author(s): Petr Smýkal, Oldřich Trněný, Jan Brus, Pavel Hanáček, Abhishek Rathore, Rani Das Roma, Vilém Pechanec, Martin Duchoslav, Debjyoti Bhattacharyya, Michael Bariotakis, Stergios Pirintsos, Jens Berger, Cengiz Toker
Software Mentions: 4
Published: over 8 years ago

10.18632/oncotarget.20949

Overcoming resistance to single-agent therapy for oncogenic <i>BRAF</i> gene fusions <i>via</i> combinatorial targeting of MAPK and PI3K/mTOR signaling pathways
Cited by: 35
Author(s): Payal Jain, Amanda Silva, Harry Han, Shih Shan Lang, Yuankun Zhu, Katie Boucher, Tiffany Smith, Aesha Vakil, Patrick Diviney, Namrata Choudhari, Pichai Raman, Christine Busch, Timothy Delaney, Xiaodong Yang, Aleksandra Olow, Sabine Mueller, Daphne A. Haas‐Kogan, Elizabeth Fox, Phillip B. Storm, Adam Resnick, Angela J. Waanders
Software Mentions: 4
Published: almost 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

10.3389/fgene.2020.00253

Integrated Analysis to Evaluate the Prognostic Value of Signature mRNAs in Glioblastoma Multiforme
Cited by: 11
Author(s): Jian Yang, Long Wang, Zhou Xu, Liquan Wu, Baohui Liu, Junmin Wang, Daofeng Tian, Xiaoxing Xiong, Qianxue Chen
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0085097

Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity
Cited by: 7
Author(s): Leah C. Blasiak, Alex W. Schmidt, Honoré Andriamiarinoro, Temesgen Belayneh Mulaw, Rado Rasolomampianina, Wendy L. Applequist, Chris Birkinshaw, Félicitée Rejo-Fienena, Porter P. Lowry, Thomas M. Schmidt, Russell T. Hill
Software Mentions: 4
Published: over 12 years ago

10.1007/s11105-017-1032-4

Drought-Tolerant Brassica rapa Shows Rapid Expression of Gene Networks for General Stress Responses and Programmed Cell Death Under Simulated Drought Stress
Cited by: 25
Author(s): Yi Guo, Birgit Samans, Sheng Chen, Kidist B. Kibret, Sarah Hatzig, Neil C. Turner, Matthew N. Nelson, Wallace Cowling, Rod J. Snowdon
Software Mentions: 4
Published: about 9 years ago

10.1186/s12859-017-1816-4

mmquant: how to count multi-mapping reads?
Cited by: 29
Author(s): Matthias Zytnicki
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13073-016-0355-3

Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease
Cited by: 191
Author(s): Minghui Wang, Panos Roussos, Andrew McKenzie, Xianxiao Zhou, Yuji Kajiwara, Kristen J. Brennand, Gabriele C. DeLuca, John F. Crary, Patrizia Casaccia, Joseph D. Buxbaum, Michelle E. Ehrlich, Sam Gandy, Alison M. Goate, Pavel Katsel, Eric E. Schadt, Vahram Haroutunian, Bin Zhang
Software Mentions: 4
Published: almost 10 years ago

10.3389/fpsyg.2021.663035

Psychometric Evaluation of the Chinese Recovering Quality of Life (ReQoL) Outcome Measure and Assessment of Health-Related Quality of Life During the COVID-19 Pandemic
Cited by: 5
Author(s): Richard Huan Xu, Anju Devianee Keetharuth, Lingling Wang, Asy Cheung, Eliza Lai-Yi Wong
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0041370

Identification of Catalytic Residues Using a Novel Feature that Integrates the Microenvironment and Geometrical Location Properties of Residues
Cited by: 12
Author(s): Lei Han, Yongjun Zhang, Jiangning Song, Ming S. Liu, Ziding Zhang
Software Mentions: 4
Published: about 14 years ago

10.1186/1471-2288-11-77

Logistic random effects regression models: a comparison of statistical packages for binary and ordinal outcomes
Cited by: 99
Author(s): Baoyue Li, Hester F. Lingsma, Ewout W. Steyerberg, Emmanuel Lesaffre
Software Mentions: 4
Published: about 15 years ago

10.18632/oncotarget.22130

Systematic analysis of the expression profile of non-coding RNAs involved in ischemia/reperfusion-induced acute kidney injury in mice using RNA sequencing
Cited by: 25
Author(s): Jun Zhou, Hongtao Chen, Yu Fan
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2156-13-24

Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap software system
Cited by: 4
Author(s): Ross E. Curtis, Anuj Goyal, Eric P. Xing
Software Mentions: 4
Published: over 14 years ago

10.1371/journal.pone.0253037

A meta-analysis of transcriptomic profiles of Huntington’s disease patients
Cited by: 14
Author(s): Manuel Seefelder, Stefan Kochanek
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2105-15-198

CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data
Cited by: 35
Author(s): Delphine Naquin, Yves d’Aubenton-Carafa, Claude Thermes, Maud Silvain
Software Mentions: 4
Published: about 12 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0240037

Changes in root-associated fungal communities in Triticum aestivum ssp. spelta L. and Triticum aestivum ssp. vulgare L. under drought stress and in various soil processing
Cited by: 12
Author(s): Sylwia Salamon, Katarzyna Mikołajczak, Lidia Błaszczyk, Karolina Ratajczak, H. Sulewska
Software Mentions: 4
Published: almost 6 years ago

10.1172/jci.insight.151621

Combinatorial transcription factor profiles predict mature and functional human islet α and β cells
Cited by: 21
Author(s): Shristi Shrestha, Diane Saunders, John T. Walker, Joan Camunas-Soler, Xiao-Qing Dai, Rachana Haliyur, Radhika Aramandla, Greg Poffenberger, Nripesh Prasad, Rita Bottino, Roland Stein, Jean‐Philippe Cartailler, Stephen C. J. Parker, Patrick E. MacDonald, Shawn Levy, Alvin C. Powers, Marcela Briššová
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpsyg.2017.00795

Improving Assessment of the Spectrum of Reward-Related Eating: The RED-13
Cited by: 31
Author(s): Ashley E. Mason, Uku Vainik, Michael Acree, A. Janet Tomiyama, Alain Dagher, Elissa S. Epel, Frederick M. Hecht
Software Mentions: 3
Published: about 9 years ago

10.1186/s13024-018-0274-4

Long-read sequencing across the C9orf72 ‘GGGGCC’ repeat expansion: implications for clinical use and genetic discovery efforts in human disease
Cited by: 90
Author(s): Mark T. W. Ebbert, Stefan L. Farrugia, Jonathon P. Sens, Karen Jansen-West, Tania F. Gendron, Mercedes Prudencio, Ian McLaughlin, Brett Bowman, Matthew G. Seetin, Mariely DeJesus-Hernandez, Jazmyne L. Jackson, Patricia E. Brown, Dennis W. Dickson, Marka van Blitterswijk, Rosa Rademakers, Leonard Petrucelli, John Denis Fryer
Software Mentions: 3
Published: almost 8 years ago

10.1042/BSR20210055

Early B-cell factors involve in the tumorigenesis and predict the overall survival of gastric cancer
Cited by: 3
Author(s): Qing Wang, Jiahong Liang, Xianyu Hu, Shen Gu, Qingdong Xu, Yan Jiang
Software Mentions: 3
Published: about 5 years ago

10.1002/1878-0261.12734

The MSP‐RON axis stimulates cancer cell growth in models of triple negative breast cancer
Cited by: 10
Author(s): Rhona Millar, Anna Kilbey, Sarah-Jane Remak, Tesa Severson, Sandeep Dhayade, Emma Sandilands, Kyla Foster, David M. Bryant, Karen Blyth, Seth B. Coffelt
Software Mentions: 3
Published: about 6 years ago

10.1002/ece3.3542

Precopulatory but not postcopulatory male reproductive traits diverge in response to mating system manipulation in<i>Drosophila melanogaster</i>
Cited by: 15
Author(s): Kristina U. Wensing, Mareike Koppik, Claudia Fricke
Software Mentions: 3
Published: almost 9 years ago

10.15252/emmm.201708274

Identification of potential therapeutic targets in prostate cancer through a cross‐species approach
Cited by: 30
Author(s): Sarah Jurmeister, Antonio Ramos-Montoya, Carmen Sandi, Nelma Pértega‐Gomes, Karan Wadhwa, Alastair Lamb, Mark J. Dunning, Jan Attig, Jason S. Carroll, Lee G.D. Fryer, Sérgio Luís Felisbino, David E. Neal
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0229192

Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota
Cited by: 16
Author(s): Lucas R Koester, Daniel Poole, Nick V. L. Serão, Stephan Schmitz‐Esser
Software Mentions: 3
Published: about 6 years ago