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

10.3389/fnhum.2021.684950

Electrophysiological and Transcriptomic Features Reveal a Circular Taxonomy of Cortical Neurons
Cited by: 5
Author(s): Alejandro Rodríguez-Collado, Cristina Rueda
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms22041591

Reciprocal Changes in miRNA Expression with Pigmentation and Decreased Proliferation Induced in Mouse B16F1 Melanoma Cells by l-Tyrosine and 5-Bromo-2′-Deoxyuridine
Cited by: 4
Author(s): Hernán Mauricio Rivera, Esther Natalia Muñoz, Daniel Osuna, Mauro Florez, Michael Carvajal, Luis Alberto Gómez
Software Mentions: 4
Published: over 5 years ago

10.1080/21505594.2020.1806665

Tobacco Hornworm (<i>Manduca sexta</i>) caterpillars as a novel host model for the study of fungal virulence and drug efficacy
Cited by: 9
Author(s): Naomi Lyons, Isabel Softley, Andrew Balfour, Carolyn Williamson, Heath O’Brien, Amol Shetty, Vincent M. Bruno, Stephanie Diezmann
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0025851

Examination of Triacylglycerol Biosynthetic Pathways via De Novo Transcriptomic and Proteomic Analyses in an Unsequenced Microalga
Cited by: 200
Author(s): Michael T. Guarnieri, Ambarish Nag, Sharon Smolinski, Al Darzins, Michael Seibert, Philip T. Pienkos
Software Mentions: 4
Published: almost 15 years ago

10.1155/2020/1932948

The SLC Family Are Candidate Diagnostic and Prognostic Biomarkers in Clear Cell Renal Cell Carcinoma
Cited by: 20
Author(s): Weiting Kang, Meng Zhang, Qiang Wang, Dawei Gu, Zhilong Huang, Hanbo Wang, Yuzhu Xiang, Qinghua Xia, Zilian Cui, Xunbo Jin
Software Mentions: 4
Published: over 6 years ago

10.1038/srep13373

Smoking Gun or Circumstantial Evidence? Comparison of Statistical Learning Methods using Functional Annotations for Prioritizing Risk Variants
Cited by: 8
Author(s): Sarah A. Gagliano, Reena Ravji, Michael R. Barnes, Michael E. Weale, Jo Knight
Software Mentions: 4
Published: almost 11 years ago

10.3390/antiox10040618

Differential and Overlapping Effects of Melatonin and Its Metabolites on Keratinocyte Function: Bioinformatics and Metabolic Analyses
Cited by: 4
Author(s): Joanna Stefan, Tae Kang Kim, Fiona Schedel, Zorica Janjetovic, David K. Crossman, Kerstin Steinbrink, Radomir M. Slominski, Jaroslaw W. Żmijewski, Meri K. Tulić, Russel J. Reíter, Konrad Kleszczyński, Andrzej Słomiński
Software Mentions: 4
Published: over 5 years ago

10.1111/eva.13200

Evolution of honey resistance in experimental populations of bacteria depends on the type of honey and has no major side effects for antibiotic susceptibility
Cited by: 5
Author(s): Anna M. Bischofberger, Katia R. Pfrunder‐Cardozo, Michael Baumgärtner, Alex R. Hall
Software Mentions: 4
Published: over 5 years ago

10.1186/s13100-019-0150-y

RepetDB: a unified resource for transposable element references
Cited by: 37
Author(s): Joëlle Amselem, Guillaume Cornut, Nathalie Choisne, Michaël Alaux, Françoise Alfama-Depauw, Véronique Jamilloux, Florian Maumus, Thomas Letellier, Isabelle Luyten, Cyril Pommier, Anne-Françoise Adam-Blondon, Hadi Quesneville
Software Mentions: 4
Published: over 7 years ago

10.3390/vaccines9070731

Sero-Monitoring of Horses Demonstrates the Equivac® HeV Hendra Virus Vaccine to Be Highly Effective in Inducing Neutralising Antibody Titres
Cited by: 8
Author(s): Kim Halpin, Kerryne Graham, Peter A. Durr
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0134168

Comparative Proteomics of Activated THP-1 Cells Infected with Mycobacterium tuberculosis Identifies Putative Clearance Biomarkers for Tuberculosis Treatment
Cited by: 19
Author(s): Benjawan Kaewseekhao, Vivek Naranbhai, Sittiruk Roytrakul, Wises Namwat, Atchara Paemanee, Viraphong Lulitanond, Angkana Chaiprasert, Kiatichai Faksri
Software Mentions: 4
Published: about 11 years ago

10.1186/s13059-018-1406-4

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
Cited by: 159
Author(s): Koen Van den Berge, Fanny Perraudeau, Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms21239211

Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2]
Cited by: 10
Author(s): Isabel Marques, Isabel Fernandes, Pedro Henrique Chorão David, Octávio S. Paulo, Luís F. Goulão, Ana S. Fortunato, Fernando C. Lidon, Fábio M. DaMatta, José C. Ramalho, Ana I. Ribeiro‐Barros
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.38190

A kinematic synergy for terrestrial locomotion shared by mammals and birds
Cited by: 26
Author(s): Giovanna Catavitello, Yuri P. Ivanenko, Francesco Lacquaniti
Software Mentions: 4
Published: almost 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

10.3390/ijms21197069

Human Fibroblasts In Vitro Exposed to 2.45 GHz Continuous and Pulsed Wave Signals: Evaluation of Biological Effects with a Multimethodological Approach
Cited by: 7
Author(s): Elisa Regalbuto, Anna Anselmo, Stefania De Sanctis, Valeria Franchini, Florigio Lista, Monica Benvenuto, Roberto Bei, Laura Masuelli, G. D’Inzeo, Alessandra Paffi, Eugenio Trodella, Antonella Sgura
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms21186946

Proteomic and Transcriptomic Patterns during Lipid Remodeling in Nannochloropsis gaditana
Cited by: 13
Author(s): Chris J. Hulatt, Irina Smolina, Adam Dowle, Martina Kopp, Ghana Kalerammana Vasanth, Galice Hoarau, René H. Wijffels, Viswanath Kiron
Software Mentions: 4
Published: almost 6 years ago

10.1002/ece3.6118

A comparison of wetland characteristics between Agricultural Conservation Easement Program and public lands wetlands in West Virginia, USA
Cited by: 4
Author(s): Katharine E. Lewis, Christopher T. Rota, James T. Anderson
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-019-0430-6

Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms
Cited by: 18
Author(s): Boxiang Liu, Melissa A. Calton, Nathan S. Abell, Gillie Benchorin, Michael J. Gloudemans, Ming Chen, Jane Hu, Xin Li, Brunilda Balliu, Dean Bok, Stephen B. Montgomery, Douglas Vollrath
Software Mentions: 4
Published: about 7 years ago

10.18632/aging.103254

Alterations in glycolytic/cholesterogenic gene expression in hepatocellular carcinoma
Cited by: 13
Author(s): Jianwen Jiang, Qiuxian Zheng, Weiwei Zhu, Xinhua Chen, Haifeng Lü, Deying Chen, Hua Zhang, Min Shao, Lin Zhou, Shusen Zheng
Software Mentions: 4
Published: about 6 years ago

10.1186/s12885-015-1530-4

Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors
Cited by: 77
Author(s): Tomasz Wrzesiński, Małgorzata Szeląg, Wojciech A Cieślikowski, Agnieszka Ida, Rachel Giles, Elżbieta Zodro, Joanna Szumska, Joanna Poźniak, Zbigniew Kwias, Hans A.R. Bluyssen, Joanna Wesoły
Software Mentions: 4
Published: about 11 years ago

10.1093/aobpla/ply013

Patterns of alternative splicing vary between species during heat stress
Cited by: 25
Author(s): Sumetha Kannan, Gillian Halter, Tanya Renner, Elizabeth R. Waters
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0179901

Microarray analyses of otospheres derived from the cochlea in the inner ear identify putative transcription factors that regulate the characteristics of otospheres
Cited by: 2
Author(s): Takehiro Iki, Michihiro Tanaka, Shin‐ichiro Kitajiri, Tomoko Kita, Yoshihisa Kawasaki, Akifumi Mizukoshi, Wataru Fujibuchi, Takayuki Nakagawa, Tatsutoshi Nakahata, Juichi Ito, Koichi Omori, Megumu K. Saito
Software Mentions: 4
Published: about 9 years ago

10.1002/advs.201902312

CRISPR/Cas Systems in Genome Editing: Methodologies and Tools for sgRNA Design, Off‐Target Evaluation, and Strategies to Mitigate Off‐Target Effects
Cited by: 136
Author(s): Hakim Manghwar, Bo Li, Xiao Ding, Amjad Hussain, Keith Lindsey, Xianlong Zhang, Shuangxia Jin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008286

Breaking the circularity in circular analyses: Simulations and formal treatment of the flattened average approach
Cited by: 8
Author(s): Howard Bowman, Joseph Brooks, Omid Hajilou, Alexia Zoumpoulaki, Vladimir Litvak
Software Mentions: 4
Published: over 5 years ago

10.1093/bioinformatics/btaa202

HiChIP-Peaks: a HiChIP peak calling algorithm
Cited by: 10
Author(s): Chenfu Shi, Magnus Rattray, Gisela Orozco
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.02929

Transcriptional Landscape of a blaKPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10
Cited by: 11
Author(s): Agnès B Jousset, Isabelle Rosinski‐Chupin, Julie Takissian, Philippe Glaser, Rémy A. Bonnin, Thierry Naas
Software Mentions: 4
Published: over 7 years ago

10.1038/s42003-021-02524-0

Pulmonary immune cell trafficking promotes host defense against alcohol-associated Klebsiella pneumonia
Cited by: 10
Author(s): Derrick R. Samuelson, Min Gu, Judd E. Shellito, Patricia E. Molina, Christopher M. Taylor, Meng Luo, David A. Welsh
Software Mentions: 4
Published: almost 5 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

10.1111/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

10.1111/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

10.3389/fmicb.2019.02371

The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions
Cited by: 10
Author(s): Eoghan M. Smyth, Suhana Chattopadhyay, Kelsey R. Babik, Molly C. Reid, Jessica Chopyk, Leena Malayil, Prachi Kulkarni, Lauren E. Hittle, Pamela I. Clark, Amy R. Sapkota, Emmanuel F. Mongodin
Software Mentions: 4
Published: almost 7 years ago

10.1128/AEM.01336-19

Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction
Cited by: 11
Author(s): Maria Fernanda Campa, Stephen M. Techtmann, Mallory P. Ladd, Jun Yan, Megan Patterson, Amanda Garcia de Matos Amaral, Kimberly E. Carter, Nikea Ulrich, Christopher J. Grant, Robert L. Hettich, Regina Lamendella, Terry C. Hazen
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-019-6088-0

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Cited by: 10
Author(s): Jonas Ibn-Salem, Miguel A. Andrade‐Navarro
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12885-021-08207-7

Five long non-coding RNAs establish a prognostic nomogram and construct a competing endogenous RNA network in the progression of non-small cell lung cancer
Cited by: 8
Author(s): Yongjun Yu, Kewei Ren
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.29750

cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool
Cited by: 29
Author(s): Vladimir Camarena, David W. Sant, Tyler C. Huff, Sushmita Mustafi, Ryan K Muir, Allegra T. Aron, Christopher J. Chang, Adam R. Renslo, Paula V. Monje, Gaofeng Wang
Software Mentions: 4
Published: over 8 years ago

10.1038/s42003-021-02089-y

Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases
Cited by: 10
Author(s): Kei Fukuda, Chikako Shimura, Hisashi Miura, Akie Tanigawa, Takehiro Suzuki, Naoshi Dohmae, Ichiro Hiratani, Yoichi Shinkai
Software Mentions: 4
Published: over 5 years ago

10.1002/mbo3.1200

Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution‐derived hydrogen
Cited by: 2
Author(s): Mario Toubes-Rodrigo, Sanja Potgieter‐Vermaak, Robin Sen, Edda Sigurdís Oddsdóttir, David R. Elliott, Simon J. Cook
Software Mentions: 4
Published: about 5 years ago

10.1186/s12885-021-08796-3

Pan-cancer evaluation of gene expression and somatic alteration data for cancer prognosis prediction
Cited by: 3
Author(s): Xingyu Zheng, Christopher I. Amos, H. Robert Frost
Software Mentions: 4
Published: almost 5 years ago

10.1038/s42003-021-01912-w

CRISPR activation screen in mice identifies novel membrane proteins enhancing pulmonary metastatic colonisation
Cited by: 10
Author(s): Louise van der Weyden, Victoria Harle, Gemma Turner, Victoria Offord, Vivek Iyer, Alastair P. Droop, A Swiaţkowska, Roy Rabbie, Andrew D. Campbell, Owen J. Sansom, Mercedes Pardo, Jyoti Choudhary, Ingrid Ferreira, Mark Tullett, Mark J. Arends, Anneliese O. Speak, David J. Adams
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.55526

Delineating the early transcriptional specification of the mammalian trachea and esophagus
Cited by: 27
Author(s): Akela Kuwahara, Ace E. Lewis, Coohleen Coombes, Fang-Shiuan Leung, Michelle Percharde, Jeffrey O. Bush
Software Mentions: 4
Published: about 6 years ago

10.1002/mbo3.964

Microbial composition of enigmatic bird parasites: <i>Wolbachia</i> and <i>Spiroplasma</i> are the most important bacterial associates of quill mites (Acariformes: Syringophilidae)
Cited by: 7
Author(s): Eliza Głowska, Zuzanna Karolina Filutowska, Mirosława Dabert, Michael Gerth
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2020.595910

A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data
Cited by: 17
Author(s): Xiaochen Yin, Tomer Altman, Erica Rutherford, Kiana West, Yonggan Wu, Jinlyung Choi, Paul L. Beck, Gilaad G. Kaplan, Karim Dabbagh, Todd Z. DeSantis, Shoko Iwai
Software Mentions: 4
Published: over 5 years ago

10.1002/mbo3.1022

Geographical separation and physiology drive differentiation of microbial communities of two discrete populations of the bat Leptonycteris yerbabuenae
Cited by: 10
Author(s): Osiris Gaona, Daniel Cerqueda‐García, Andrés Moya, Ximena Neri‐Barrios, Luisa I. Falcón
Software Mentions: 4
Published: over 6 years ago

10.3390/ijerph17207671

Significant Associations between AXIN1 rs1805105, rs12921862, rs370681 Haplotypes and Variant Genotypes of AXIN2 rs2240308 with Risk of Congenital Heart Defects
Cited by: 0
Author(s): George Andrei Crauciuc, Mihaela Iancu, Peter Olah, Florin Tripon, Mădălina Anciuc, Liliana Gozar, Rodica Togănel, Claudia Bănescu
Software Mentions: 4
Published: almost 6 years ago

10.1099/mgen.0.000338

Coinfinder: detecting significant associations and dissociations in pangenomes
Cited by: 33
Author(s): Fiona Whelan, Martin Rusilowicz, James O. McInerney
Software Mentions: 4
Published: over 6 years ago

10.1099/mgen.0.000266

Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors
Cited by: 18
Author(s): Eva Heinz, Richard Brindle, Andrina Morgan-McCalla, Keisha Peters, Nicholas R. Thomson
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.11948

Quantifying bite force in coexisting tayassuids and feral suids: a comparison between morphometric functional proxies and in vivo measurements
Cited by: 1
Author(s): Fernando Lencastre Sicuro, Luiz Flamarion B. Oliveira, Carla Deonísia Hendges, Carlos Fonseca
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2020.612840

Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data
Cited by: 3
Author(s): Phillipe Loher, Nestoras Karathanasis
Software Mentions: 4
Published: over 5 years ago

10.1186/s12885-021-08201-z

Predictive nomogram for postoperative pancreatic fistula following pancreaticoduodenectomy: a retrospective study
Cited by: 8
Author(s): Jian Shen, Feng Guo, Yan Sun, Jingyuan Zhao, Jin Hu, Zunxiang Ke, Yushun Zhang, Xin Jin, Heshui Wu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12885-020-07712-5

Construction of a nine DNA repair-related gene prognostic classifier to predict prognosis in patients with endometrial carcinoma
Cited by: 7
Author(s): Jinhui Liu, Pinping Jiang, Xucheng Chen, Yujie Shen, Guoliang Cui, Ziyan Ma, Shaojie Zhao, Yan Zhang
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.47138

Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila
Cited by: 94
Author(s): Evan Witt, Sigi Benjamin, Nicolas Svetec, Li Zhao
Software Mentions: 4
Published: almost 7 years ago

10.1099/mgen.0.000484

Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
Cited by: 14
Author(s): Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ray, Nicholas M. Thomson, Sheikh Jarju, Brenda Kwambana-Adams, Arss Secka, Justin O’Grady, Martín Antonio, Mark J. Pallen
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.01551

Concerted Metabolic Shifts Give New Insights Into the Syntrophic Mechanism Between Propionate-Fermenting Pelotomaculum thermopropionicum and Hydrogenotrophic Methanocella conradii
Cited by: 22
Author(s): Pengfei Liu, Yahai Lu
Software Mentions: 4
Published: about 8 years ago

10.3389/fgene.2021.736423

Comprehensive Analysis of Splicing Factor and Alternative Splicing Event to Construct Subtype-Specific Prognosis-Predicting Models for Breast Cancer
Cited by: 4
Author(s): He Zhang, Baoai Han, Xingxing Han, Yuying Zhu, Hui Liu, Zhiyong Wang, Yanfen Cui, Ran Tian, Zicong Gao, Ruinan Tian, Sixin Ren, Xiaoyan Zuo, Jianfei Tian, Fei Zhang, Ruifang Niu
Software Mentions: 4
Published: almost 5 years ago

10.1186/1472-6920-13-70

Teaching and learning the Hodgkin-Huxley model based on software developed in NEURON’s programming language hoc
Cited by: 6
Author(s): Oscar E Hernández, Eduardo Zurek
Software Mentions: 4
Published: about 13 years ago

10.3389/fcimb.2021.723481

Dual RNASeq Reveals NTHi-Macrophage Transcriptomic Changes During Intracellular Persistence
Cited by: 6
Author(s): Jodie Ackland, Ashley Heinson, David W. Cleary, Myron Christodoulides, Tom Wilkinson, Karl J. Staples
Software Mentions: 4
Published: almost 5 years ago

10.1007/s00248-021-01719-6

Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding
Cited by: 8
Author(s): Camila Duarte Ritter, Dominik Forster, Josué A. R. Azevedo, Alexandre Antonelli, R. Henrik Nilsson, Martha E. Trujillo, Micah Dunthorn
Software Mentions: 4
Published: over 5 years ago

10.18632/oncotarget.21378

Progesterone receptor isoforms, agonists and antagonists differentially reprogram estrogen signaling
Cited by: 48
Author(s): Hari Singhal, Mark E. Greene, Allison L. Zarnke, Muriel Lainé, Rose Al Abosy, Yung-Fu Chang, Anna Dembo, Kelly Q. Schoenfelt, Raga Vadhi, Xintao Qiu, Prakash K. Rao, Bindu Santhamma, Hareesh B. Nair, Klaus Nickisch, Henry W. Long, Lev Becker, Myles Brown, Geoffrey L. Greene
Software Mentions: 4
Published: almost 9 years ago

10.1111/1751-7915.13393

Black soldier fly larvae (<i>Hermetia illucens</i>) strengthen the metabolic function of food waste biodegradation by gut microbiome
Cited by: 107
Author(s): Cheng-Liang Jiang, Wei-Zheng Jin, Xin-Hua Tao, Qian Zhang, Jun Zhu, Shiyun Feng, Xinhua Xu, Hongyi Li, Zehua Wang, Zhijian Zhang
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pcbi.1000392

Fast Statistical Alignment
Cited by: 303
Author(s): Robert K. Bradley, Anjeanette Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian Holmes, Lior Pachter
Software Mentions: 4
Published: about 17 years ago

10.1371/journal.ppat.1007226

Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles
Cited by: 79
Author(s): Steffen Hahnel, Stefan Zdraljevic, Briana Rodriguez, Yuehui Zhao, Patrick T. McGrath, Erik C. Andersen
Software Mentions: 4
Published: almost 8 years ago

10.1155/2014/346074

MAVTgsa: An R Package for Gene Set (Enrichment) Analysis
Cited by: 5
Author(s): Chih-Yi Chien, Ching‐Wei Chang, Chen‐An Tsai, James J. Chen
Software Mentions: 4
Published: over 12 years ago

10.3389/fmicb.2021.617151

Rapid Changes in the Phytoplankton Community of a Subtropical, Shallow, Hypereutrophic Lake During the Rainy Season
Cited by: 19
Author(s): Osiris Díaz-Torres, José de Anda, Ofelia Yadira Lugo-Melchor, Adriana Pacheco, Danielle A. Orozco-Nunnelly, Harvey Shear, Carolina Senés‐Guerrero, Misael Sebastian Gradilla‐Hernández
Software Mentions: 4
Published: over 5 years ago

10.1186/s12885-020-07331-0

LINC00649 underexpression is an adverse prognostic marker in acute myeloid leukemia
Cited by: 11
Author(s): Chao Guo, Ya-yue Gao, Qianqian Ju, Chunxia Zhang, Ming Gong, Zhenling Li
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-018-2139-9

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
Cited by: 141
Author(s): MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary T. Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X. Shirley Liu, Henry W. Long
Software Mentions: 4
Published: over 8 years ago

10.1016/j.gpb.2018.11.002

Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates
Cited by: 8
Author(s): Valentina Galata, Cédric Christian Laczny, Christina Backes, Georg Hemmrich-Stanisak, Susanne Schmolke, André Franke, Eckart Meese, Mathias Herrmann, Lutz von Müller, Achim Plum, Rolf Müller, Cord Stähler, Andreas E. Posch
Software Mentions: 4
Published: over 7 years ago

10.1093/bioinformatics/btw580

DAPAR &amp; ProStaR: software to perform statistical analyses in quantitative discovery proteomics
Cited by: 212
Author(s): Samuel Wieczorek, Florence Combes, Cosmin Lazar, Quentin Giai Gianetto, Laurent Guy, Alexia Dorffer, Anne-Marie Hesse, Yohann Couté, Myriam Ferro, Christophe Bruley, Thomas Bürger
Software Mentions: 4
Published: almost 10 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

10.1186/s12885-020-07194-5

A panel of DNA methylation signature from peripheral blood may predict colorectal cancer susceptibility
Cited by: 12
Author(s): Justina Ucheojor Onwuka, Dapeng Li, Yupeng Liu, Hao Huang, Jing Xu, Ying Liu, Yuanyuan Zhang, Yong Zhao
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.7191

The effects of high versus low talker variability and individual aptitude on phonetic training of Mandarin lexical tones
Cited by: 17
Author(s): Henry Y. Dong, Meghan Clayards, Helen Brown, Elizabeth Wonnacott
Software Mentions: 4
Published: about 7 years ago

10.1016/j.isci.2021.102751

The effects of aging on molecular modulators of human embryo implantation
Cited by: 6
Author(s): Panagiotis Ntostis, Grace Swanson, Georgia Kokkali, David Iles, John Huntriss, Agni Pantou, Maria Tzetis, Konstantinos Pantos, Helen M. Picton, Stephen A. Krawetz, D. H. Miller
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-020-03551-0

ARTDeco: automatic readthrough transcription detection
Cited by: 15
Author(s): Samuel J. Roth, Sven Heinz, Christopher Benner
Software Mentions: 4
Published: about 6 years ago

10.3389/fimmu.2017.01351

Critical Role of Plasmacytoid Dendritic Cells in Regulating Gene Expression and Innate Immune Responses to Human Rhinovirus-16
Cited by: 11
Author(s): Xi Yang, Niamh M. Troy, Denise Anderson, Olga M. Pena, Jason P. Lynch, Simon Phipps, Anthony Bosco, John W. Upham
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

10.26508/lsa.201900535

The molecular clock protein Bmal1 regulates cell differentiation in mouse embryonic stem cells
Cited by: 12
Author(s): Amador Gallardo, Ana Rodríguez Molina, Helena G Asenjo, Jordi Martorell-Marugán, Rosa Montes, Verónica Ramos-Mejía, Antonio Sánchez–Pozo, Pedro Carmona-Sáez, Lourdes López-Onieva, David Landeira
Software Mentions: 4
Published: over 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

10.1186/s12864-019-6427-1

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences
Cited by: 44
Author(s): Narayan Nicole, Thomas Weinmaier, Emilio J Laserna-Mendieta, Marcus J. Claesson, Fergus Shanahan, Karim Dabbagh, Shoko Iwai, Todd Z. DeSantis
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0253009

miR-361-5p as a promising qRT-PCR internal control for tumor and normal breast tissues
Cited by: 4
Author(s): Sogol Ghanbari, Adel Salimi, Saeid Rahmani, Nahid Nafissi, Ali Sharifi‐Zarchi, Seyed Javad Mowla
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-020-03591-6

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities
Cited by: 1
Author(s): Yulia Kondratenko, Anton Korobeynikov, Alla Lapidus
Software Mentions: 4
Published: about 6 years ago

10.1111/jcmm.16696

Establishment and experimental validation of an immune miRNA signature for assessing prognosis and immune landscape of patients with colorectal cancer
Cited by: 28
Author(s): Zaoqu Liu, Taoyuan Lu, Yanli Wang, Dechao Jiao, Zhaonan Li, Libo Wang, Long Liu, Chunguang Guo, Yanan Zhao, Xinwei Han
Software Mentions: 4
Published: about 5 years ago

10.1007/s11306-020-1646-7

Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry
Cited by: 13
Author(s): Tim U. H. Baumeister, Marine Vallet, Filip Kaftan, Laure Guillou, Aleš Svatoš, Georg Pohnert
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.63852

Psychosocial experiences modulate asthma-associated genes through gene-environment interactions
Cited by: 10
Author(s): Justyna Resztak, Allison K. Farrell, Henriette Mair-Meijers, Adnan Alazizi, Xiaoquan Wen, Derek E. Wildman, Samuele Zilioli, Richard B. Slatcher, Roger Piqué-Regi, Francesca Luca
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.3334

<i>pathVar:</i>a new method for pathway-based interpretation of gene expression variability
Cited by: 6
Author(s): Laurence de Torrenté, Stephanie M. Zimmerman, Deanne Taylor, Yu Hasegawa, Christine A. Wells, Jessica C. Mar
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.33084

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
Cited by: 23
Author(s): Michelle C. Ward, Siming Zhao, Kaixuan Luo, Bryan J. Pavlovic, Mehdi Karimi, Matthew Stephens, Yoav Gilad
Software Mentions: 4
Published: over 8 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

10.3389/fgene.2020.608325

Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation
Cited by: 1
Author(s): Xiaoli Ma, Mei Shang, Baofeng Su, Anne A. Wiley, Max R. Bangs, Veronica Alston, Rhoda Mae C. Simora, Mai Thi Thanh Nguyen, Nathan J. C. Backenstose, Anthony G. Moss, Dương Thúy Yên, Xiaozhu Wang, Rex A. Dunham
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0252026

Differential association between inflammatory cytokines and multiorgan dysfunction in COVID-19 patients with obesity
Cited by: 8
Author(s): Marie-Agnès Dragon-Durey, Xiaoyi Chen, Amos Kirilovsky, Nadine Benhamouda, Carine El Sissy, Jules Russick, Etienne Charpentier, Yannick Binois, Florence Marliot, Maxime Meylan, Clémence Granier, Hélène Péré, Antonin Saldmann, Bastien Rance, Anne Sophie Jannot, Stéphanie Baron, M. Chebbi, Antoine Fayol, Nathalie Josseaume, Claire Rives‐Lange, Pierre‐Louis Tharaux, Bernard Cholley, Jean‐Luc Diehl, Jean‐Benoît Arlet, Michel Azizi, Alexandre Karras, Sébastien Czernichow, David Smadja, Jean‐Sébastien Hulot, Isabelle Cremer, Éric Tartour, Élie Mousseaux, Franck Pagès
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0237715

Teosinte (Zea mays ssp parviglumis) growth and transcriptomic response to weed stress identifies similarities and differences between varieties and with modern maize varieties
Cited by: 4
Author(s): Stephanie A. Bruggeman, David P. Horvath, Anne Fennell, Jose L. Gonzalez-Hernandez, Sharon A. Clay
Software Mentions: 4
Published: almost 6 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

10.7554/eLife.52621

FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences
Cited by: 78
Author(s): Raeann Goering, Laura I. Hudish, Bryan B. Guzman, Nisha Raj, Gary J. Bassell, Holger A. Russ, Daniel Domínguez, J. Matthew Taliaferro
Software Mentions: 4
Published: about 6 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

10.7554/eLife.56720

CARD14E138A signalling in keratinocytes induces TNF-dependent skin and systemic inflammation
Cited by: 14
Author(s): Joan Manils, Louise V. Webb, Ashleigh Howes, Julia Janzen, Stefan Boeing, Anne M. Bowcock, Steven C. Ley
Software Mentions: 4
Published: about 6 years ago

10.1097/MD.0000000000024949

Tumor microenvironment immune subtypes for classification of novel clear cell renal cell carcinoma profiles with prognostic and therapeutic implications
Cited by: 5
Author(s): Qiang Wang, Jinding Hu, Weiting Kang, Jin Wang, Yuzhu Xiang, Min Fu, Hui Gao, Zhilong Huang
Software Mentions: 4
Published: over 5 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

10.1128/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

10.1186/s12859-020-3366-4

A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells
Cited by: 4
Author(s): Bin Liu, Patrick Lindner, Adan Chari Jirmo, Ulrich A. Maus, Thomas Illig, David S. DeLuca
Software Mentions: 4
Published: over 6 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

10.3390/ani11051372

Choice of Commercial DNA Extraction Method Does Not Affect 16S Sequencing Outcomes in Cloacal Swabs
Cited by: 0
Author(s): Emily Van Syoc, Natália Carrillo Gaeta, Erika Ganda
Software Mentions: 4
Published: over 5 years ago