10.3390/ijms20225621

APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival
Cited by: 45
Author(s): Mariko Asaoka, Takashi Ishikawa, Kazuaki Takabe, Santosh K. Patnaik
Software Mentions: 11
Published: almost 7 years ago

10.1017/S003329171800315X

A machine learning ensemble to predict treatment outcomes following an Internet intervention for depression
Cited by: 37
Author(s): Rahel Pearson, Derek Pisner, Björn Meyer, Jason Shumake, Christopher G. Beevers
Software Mentions: 11
Published: almost 8 years ago

10.1186/s12859-017-1579-y

metaX: a flexible and comprehensive software for processing metabolomics data
Cited by: 402
Author(s): Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
Software Mentions: 11
Published: over 9 years ago

10.1186/s12859-020-03846-2

ARPIR: automatic RNA-Seq pipelines with interactive report
Cited by: 10
Author(s): Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini, Maria Paola Martelli
Software Mentions: 11
Published: almost 6 years ago

10.3389/fgene.2021.609174

METTL14 Acts as a Potential Regulator of Tumor Immune and Progression in Clear Cell Renal Cell Carcinoma
Cited by: 11
Author(s): Tianbo Xu, Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 11
Published: over 5 years ago

10.3389/fgene.2021.625145

Identification of Tumor Microenvironment-Related Prognostic Biomarkers for Ovarian Serous Cancer 3-Year Mortality Using Targeted Maximum Likelihood Estimation: A TCGA Data Mining Study
Cited by: 2
Author(s): Lu Wang, Xiaoru Sun, Chuandi Jin, Yue Fan, Fuzhong Xue
Software Mentions: 11
Published: over 5 years ago

10.3389/fphys.2020.00845

Dynamic Courtship Signals and Mate Preferences in Sepia plangon
Cited by: 5
Author(s): Alejandra López Galán, Wen-Sung Chung, N. Justin Marshall
Software Mentions: 11
Published: about 6 years ago

10.3390/ijms22147269

Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula
Cited by: 3
Author(s): Jean-Stéphane Venisse, Eele Õunapuu-Pikas, Maxime Dupont, Aurélie Gousset-Dupont, Mouadh Saadaoui, Mohamed Faize, Song Chen, Su Chen, Gilles Pétel, Boris Fumanal, Patricia Roeckel‐Drevet, Arne Sellin, Philippe Label
Software Mentions: 11
Published: about 5 years ago

10.1038/srep44348

Major shifts at the range edge of marine forests: the combined effects of climate changes and limited dispersal
Cited by: 70
Author(s): Jorge Assis, Estíbaliz Berecibar, Bruno Claro, Filipe Alberto, Daniel C. Reed, Peter T. Raimondi, Ester Á. Serrão
Software Mentions: 11
Published: over 9 years ago

10.1038/srep26929

High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing
Cited by: 43
Author(s): Fábio Pértille, Carlos Guerrero-Bosagna, Vinícius da Silva, Clarissa Boschiero, José de Ribamar da Silva Nunes, Mônica Corrêa Ledur, Per Jensen, Luiz Lehmann Coutinho
Software Mentions: 11
Published: over 10 years ago

10.12688/wellcomeopenres.16430.2

Polysomal mRNA Association and Gene Expression in Trypanosoma brucei
Cited by: 0
Author(s): Michele Tinti, Anna Kelner-Mirôn, Lizzie J. Marriott, Michael A. J. Ferguson
Software Mentions: 11
Published: about 5 years ago

10.3389/fonc.2021.614052

MRI Radiomics Signature as a Potential Biomarker for Predicting KRAS Status in Locally Advanced Rectal Cancer Patients
Cited by: 9
Author(s): Zhiyuan Zhang, Lijun Shen, Yan Wang, Jiazhou Wang, Hui Zhang, Xuesen Fan, Juefeng Wan
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-021-93411-5

Epidemiological overview of multidimensional chromosomal and genome toxicity of cannabis exposure in congenital anomalies and cancer development
Cited by: 33
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 11
Published: about 5 years ago

10.1128/mBio.02699-19

The Toxoplasma gondii Cyst Wall Interactome
Cited by: 24
Author(s): Vincent Tu, Tadakimi Tomita, Tatsuki Sugi, Joshua Mayoral, Bing Han, Rama R. Yakubu, Tere Williams, Aline Luciano Horta, Yanfen Ma, Louis M. Weiss
Software Mentions: 11
Published: over 6 years ago

10.3389/fmolb.2021.684050

Characterization of Hypoxia-Related Molecular Subtypes in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy and Targeted Therapy via Multi-Omics Analysis
Cited by: 10
Author(s): Weimin Zhong, Hongbin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-021-94656-w

A global assessment of surveillance methods for dominant malaria vectors
Cited by: 4
Author(s): Bram van de Straat, Tanya L. Russell, Kyran M. Staunton, Marianne Sinka, Thomas R. Burkot
Software Mentions: 11
Published: about 5 years ago

10.3389/fpsyg.2019.01529

Social Support and Emotional Intelligence as Protective Resources for Well-Being in Moroccan Adolescents
Cited by: 33
Author(s): Esther López-Zafra, Manuel M. Ramos‐Álvarez, Karima El Ghoudani, Octavio Luque-Reca, José María Augusto Landa, Benaissa Zarhbouch, Smail Alaoui, Daniel Cortés-Denia, Manuel Pulido-Martos
Software Mentions: 11
Published: about 7 years ago

10.1107/S1600577518016570

Automated data collection and real-time data analysis suite for serial synchrotron crystallography
Cited by: 34
Author(s): Shibom Basu, Jakub Wojciech Kaminski, Ezequiel Panepucci, Chia‐Ying Huang, Rangana Warshamanage, Meitian Wang, Justyna Aleksandra Wojdyla
Software Mentions: 11
Published: almost 8 years ago

10.1186/s42523-020-00066-0

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary
Cited by: 16
Author(s): Rebecca J. Stevick, Anton F. Post, Marta Gómez-Chiarri
Software Mentions: 11
Published: over 5 years ago

10.1186/s12859-018-2105-6

Building protein-protein interaction networks for Leishmania species through protein structural information
Cited by: 17
Author(s): Crhisllane Rafaele dos Santos Vasconcelos, Túlio de Lima Campos, Antônio Mauro Rezende
Software Mentions: 11
Published: over 8 years ago

10.1111/tpj.14784

Segmental duplications are hot spots of copy number variants affecting barley gene content
Cited by: 4
Author(s): Gianluca Bretani, Laura Rossini, Chiara Ferrandi, Joanne Russell, Robbie Waugh, Benjamin Kilian, Paolo Bagnaresi, Luigi Cattivelli, Agostino Fricano
Software Mentions: 11
Published: over 6 years ago

10.1098/rspb.2021.0616

Juvenile ecology drives adult morphology in two insect orders
Cited by: 4
Author(s): Peter T. Rühr, Thomas van de Kamp, Tomáš Faragó, Jörg U. Hammel, Fabian Wilde, Elena Borisova, Carina Edel, Melina Frenzel, Tilo Baumbach, Alexander Blanke
Software Mentions: 11
Published: over 5 years ago

10.1016/j.mex.2018.07.003

A practical method to control spatiotemporal confounding in environmental impact studies
Cited by: 4
Author(s): Rezvan Hatami
Software Mentions: 11
Published: almost 9 years ago

10.12688/f1000research.26771.2

HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas
Cited by: 1
Author(s): Tim O. Nieuwenhuis, Marc K. Halushka
Software Mentions: 11
Published: over 5 years ago

10.1111/jcmm.16552

Identification of autophagy‐related genes signature predicts chemotherapeutic and immunotherapeutic efficiency in bladder cancer (BLCA)
Cited by: 8
Author(s): Rui Cao, Bo Ma, Gang Wang, Yaoyi Xiong, Ye Tian, Lushun Yuan
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-021-94324-z

Modest changes in Spi1 dosage reveal the potential for altered microglial function as seen in Alzheimer’s disease
Cited by: 17
Author(s): Ruth Jones, Robert Andrews, Peter Holmans, Matthew Hill, Philip R. Taylor
Software Mentions: 11
Published: about 5 years ago

10.3390/nu12020302

The Role of Glycemic Index and Glycemic Load in the Development of Real-Time Postprandial Glycemic Response Prediction Models for Patients with Gestational Diabetes
Cited by: 14
Author(s): Evgenii Pustozerov, Aleksandra Tkachuk, Elena Vasukova, А. В. Дронова, Ekaterina S. Shilova, Anna D. Anopova, Faina Piven, Tatiana Pervunina, Elena Vasilieva, Elena Grineva, Polina Popova
Software Mentions: 11
Published: over 6 years ago

10.1186/s13059-020-1926-6

Eleven grand challenges in single-cell data science
Cited by: 646
Author(s): David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan‐Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M Keizer, Indu Khatri, Szymon M. Kiełbasa, Jan Korbel, Alexey M Kozlov, Tzu Hao Kuo, Boudewijn P. F. Lelieveldt, Ion Măndoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Łukasz Rączkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alexander Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
Software Mentions: 11
Published: over 6 years ago

10.1186/s12935-020-01393-7

Small nucleolar RNAs signature (SNORS) identified clinical outcome and prognosis of bladder cancer (BLCA)
Cited by: 5
Author(s): Rui Cao, Bo Ma, Lushun Yuan, Gang Wang, Ye Tian
Software Mentions: 11
Published: about 6 years ago

10.1098/rsos.150632

Kinship as a frequency dependent strategy
Cited by: 15
Author(s): Ting Ji, Xiu-Deng Zheng, Qiao-Qiao He, Jiajia Wu, Ruth Mace, Yi Tao
Software Mentions: 11
Published: over 10 years ago

10.1038/s41598-019-44765-4

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression
Cited by: 35
Author(s): Ingrid Tarr, Emma McCann, Beben Benyamin, Timothy J. Peters, Natalie A. Twine, Katharine Y. Zhang, Qiongyi Zhao, Zong Hong Zhang, Dominic B. Rowe, Garth A. Nicholson, Denis C. Bauer, Susan J. Clark, Ian P. Blair, Kelly L. Williams
Software Mentions: 11
Published: over 7 years ago

10.1242/jeb.210302

Time-critical influences of gestational diet in a seahorse model of male pregnancy
Cited by: 7
Author(s): Francisco Otero‐Ferrer, Freddy Lättekivi, James Ord, Ene Reimann, Sulev Kõks, Marisol Izquierdo, William V. Holt, Alireza Fazeli
Software Mentions: 11
Published: almost 8 years ago

10.1186/s13058-021-01451-6

Transcriptome and genome evolution during HER2-amplified breast neoplasia
Cited by: 3
Author(s): Peipei Lu, Joseph W. Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert B. West
Software Mentions: 11
Published: about 5 years ago

10.1038/s41408-019-0199-3

Deciphering the chronology of copy number alterations in Multiple Myeloma
Cited by: 35
Author(s): Anıl Aktaş Samur, Stéphane Minvielle, Masood A. Shammas, Mariateresa Fulciniti, Florence Magrangeas, Paul G. Richardson, Philippe Moreau, Michel Attal, Kenneth C. Anderson, Giovanni Parmigiani, Hervé Avet‐Loiseau, Nikhil C. Munshi, Mehmet K. Samur
Software Mentions: 11
Published: over 7 years ago

10.3389/fonc.2021.672928

Glioma-Associated Stromal Cells Stimulate Glioma Malignancy by Regulating the Tumor Immune Microenvironment
Cited by: 13
Author(s): Xiangming Cai, Feng Yuan, Junhao Zhu, Jin Yang, Chao Tang, Zixiang Cong, Chiyuan Ma
Software Mentions: 11
Published: over 5 years ago

10.1155/2016/7972351

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments
Cited by: 11
Author(s): Francesco Russo, Dario Righelli, Claudia Angelini
Software Mentions: 11
Published: almost 11 years ago

10.1534/g3.120.401612

A Reference Genome Sequence for Giant Sequoia
Cited by: 53
Author(s): Alison Dawn Scott, Aleksey V. Zimin, Daniela Puiu, Rachael E. Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily E. Burns, Jill L. Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
Software Mentions: 11
Published: almost 6 years ago

10.1016/j.cell.2018.08.067

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
Cited by: 396
Author(s): James Kinchen, Hannah H. Chen, Kaushal Parikh, Agne Antanaviciute, Marta Jagielowicz, David Fawkner-Corbett, Neil Ashley, Laura Cubitt, Esther Mellado-Gomez, Moustafa Attar, Eshita Sharma, Quin F. Wills, Rory Bowden, Felix Clemens Richter, David Ahern, Kamal D. Puri, Jill Hénault, François G. Gervais, Hashem Koohy, Alison Simmons
Software Mentions: 11
Published: about 8 years ago

10.3389/fcvm.2021.624714

Identification of Potential Biomarkers and Immune Infiltration Characteristics in Idiopathic Pulmonary Arterial Hypertension Using Bioinformatics Analysis
Cited by: 21
Author(s): Haowei Zeng, Xiaoqin Liu, Yushun Zhang
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0156825

Inundation and Fire Shape the Structure of Riparian Forests in the Pantanal, Brazil
Cited by: 32
Author(s): Wellinton de Sá Arruda, Jens Oldeland, Antônio Conceição Paranhos Filho, Arnildo Pott, Nicolay Leme da Cunha, Iria Hiromi Ishii, Geraldo Alves Damasceno
Software Mentions: 11
Published: over 10 years ago

10.1371/journal.pone.0238026

Funding sources and breast cancer research frame
Cited by: 3
Author(s): Wonkwang Jo
Software Mentions: 11
Published: about 6 years ago

10.1038/srep42192

Application of Machine-Learning Models to Predict Tacrolimus Stable Dose in Renal Transplant Recipients
Cited by: 86
Author(s): Jie Tang, Rong Liu, Yueli Zhang, Mou-Ze Liu, HU Yong-fang, Minghai Shao, Lan Zhu, Hua‐Wen Xin, Feng Gao, Wenjun Shang, Xiang‐Gao Meng, Lirong Zhang, Yingzi Ming, Wei Zhang
Software Mentions: 11
Published: over 9 years ago

10.1080/0886022X.2021.1960563

Derivation and validation of a model to predict acute kidney injury following cardiac surgery in patients with normal renal function
Cited by: 8
Author(s): Penghua Hu, Zhiming Mo, Yuanhan Chen, Yanhua Wu, Li Song, Li Zhang, Zhilian Li, Lei Fu, Huaban Liang, Yiming Tao, Shuangxin Liu, Zhiming Ye, Xinling Liang
Software Mentions: 11
Published: almost 6 years ago

10.1038/s41598-020-59494-2

Unstable crop yields reveal opportunities for site-specific adaptations to climate variability
Cited by: 30
Author(s): Rafael A. Martinez-Feria, Bruno Basso
Software Mentions: 11
Published: over 6 years ago

10.1186/cc13993

Relationship between acid–base status and inflammation in the critically ill
Cited by: 38
Author(s): Fernando Godinho Zampieri, John A. Kellum, Marcelo Park, Otávio T. Ranzani, Hermes Vieira Barbeiro, Heraldo Possolo de Souza, Luiz Monteiro da Cruz Neto, Fabiano Pinheiro da Silva
Software Mentions: 11
Published: almost 13 years ago

10.3389/fpsyg.2021.638659

Syllable Complexity and Morphological Synthesis: A Well-Motivated Positive Complexity Correlation Across Subdomains
Cited by: 2
Author(s): Shelece Easterday, Matthew Stave, Marc Allassonnière-Tang, Frank Seifart
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-021-82043-4

PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
Cited by: 10
Author(s): Pablo Acera Mateos, Renzo F. Balboa, Simon Easteal, Eduardo Eyras, Hardip R. Patel
Software Mentions: 11
Published: over 5 years ago

10.3390/foods10010143

Intramuscular Fat Prediction Using Color and Image Analysis of Bísaro Pork Breed
Cited by: 7
Author(s): Alfredo Teixeira, Severiano Silva, Marianne Hasse, José Almeida, Luís G. Dias
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0169662

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
Cited by: 171
Author(s): John Vollmers, Sandra Wiegand, Anne‐Kristin Kaster
Software Mentions: 11
Published: over 9 years ago

10.18632/aging.203242

Glycolysis- and immune-related novel prognostic biomarkers of Ewing's sarcoma: glucuronic acid epimerase and triosephosphate isomerase 1
Cited by: 9
Author(s): Jie Jiang, Xinli Zhan, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Liyi Chen, Shengsheng Huang, Xuhua Sun, Ming Yi, Zide Zhang, Yuanlin Yao, Chong Liu
Software Mentions: 11
Published: about 5 years ago

10.3390/ijms19030742

Effect of Presence and Concentration of Plasticizers, Vegetable Oils, and Surfactants on the Properties of Sodium-Alginate-Based Edible Coatings
Cited by: 48
Author(s): Tugce Sentürk Parreidt, Michael Schott, Markus Schmid, Kajetan Müller
Software Mentions: 11
Published: over 8 years ago

10.3389/fvets.2017.00002

Using Machine Learning to Predict Swine Movements within a Regional Program to Improve Control of Infectious Diseases in the US
Cited by: 28
Author(s): Pablo Valdes–Donoso, Kimberly VanderWaal, Lovell S. Jarvis, Spencer Wayne, Andres Pérez
Software Mentions: 11
Published: over 9 years ago

10.3390/cancers12123800

Dynamics of Fecal Microbiota with and without Invasive Cervical Cancer and Its Application in Early Diagnosis
Cited by: 14
Author(s): Gi-Ung Kang, Da-Ryung Jung, Yoon Hee Lee, Se Young Jeon, Hyung Soo Han, Gun Oh Chong, Jae‐Ho Shin
Software Mentions: 11
Published: almost 6 years ago

10.1186/s42523-020-00029-5

Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef
Cited by: 19
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pcbi.1003929

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
Cited by: 18
Author(s): Hai Fang
Software Mentions: 11
Published: almost 12 years ago

10.7717/peerj.1981

DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
Cited by: 6
Author(s): Christophe D. Chabbert, Lars M. Steinmetz, Bernd Klaus
Software Mentions: 11
Published: over 10 years ago

10.1177/1176934320956575

Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins
Cited by: 10
Author(s): Xiaoyan Gu, Adrian C. Brennan, Wenbin Wei, Guang-Qin Guo, Keith Lindsey
Software Mentions: 11
Published: almost 7 years ago

10.3389/fonc.2021.709077

Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis
Cited by: 57
Author(s): Anji Ju, Jintian Tang, Shuohua Chen, Yan Fu, Yongzhang Luo
Software Mentions: 11
Published: about 5 years ago

10.3390/ani11040961

Grumpy Dogs Are Smart Learners—The Association between Dog–Owner Relationship and Dogs’ Performance in a Social Learning Task
Cited by: 8
Author(s): Péter Pongrácz, Gabriella Rieger, Kata Vékony
Software Mentions: 11
Published: over 5 years ago

10.18632/oncotarget.22928

Comparing the genomes of cutaneous melanoma tumors to commercially available cell lines
Cited by: 10
Author(s): Stephen A. Luebker, Weiwei Zhang, Scott A. Koepsell
Software Mentions: 11
Published: almost 9 years ago

10.7717/peerj.4395

COREMIC: a web-tool to search for a niche associated CORE MICrobiome
Cited by: 17
Author(s): Richard R. Rodrigues, Nyle C. Rodgers, Xiaowei Wu, Mark A. Williams
Software Mentions: 11
Published: over 8 years ago

10.1155/2021/6616908

Interpreting the Molecular Mechanisms of Yinchenhao Decoction on Hepatocellular Carcinoma through Absorbed Components Based on Network Pharmacology
Cited by: 5
Author(s): Jijia Sun, Tao Han, Tao Yang, Yunhui Chen, Jihan Huang
Software Mentions: 11
Published: over 5 years ago

10.3389/fmicb.2021.633659

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast
Cited by: 14
Author(s): Maria Luis de Vilar Correia Brito Bôto, Catarina Magalhães, Rafaela Perdigão, Diogo A. M. Alexandrino, Joana P. Fernandes, Ana M. Bernabéu, Sandra Ramos, Maria F. Carvalho, Miguel Semedo, Julie LaRoche, C. Marisa R. Almeida, Ana P. Mucha
Software Mentions: 11
Published: over 5 years ago

10.3390/ijms21124217

Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide
Cited by: 6
Author(s): Łukasz Paukszto, Anita Mikołajczyk, J Jastrzebski, Marta Majewska, Kamil Dobrzyń, Marta Kieżun, Tadeusz Kamiński
Software Mentions: 11
Published: over 6 years ago

10.1186/s13059-019-1716-1

A practical guide to methods controlling false discoveries in computational biology
Cited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: over 7 years ago

10.1371/journal.pone.0234503

Nest boxes buffer the effects of climate on breeding performance in an African urban raptor
Cited by: 17
Author(s): Petra Sumasgutner, Andrew R. Jenkins, Arjun Amar, Res Altwegg
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pcbi.1007665

CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data
Cited by: 8
Author(s): Thilde Terkelsen, Anders Krogh, Elena Papaleo
Software Mentions: 11
Published: over 6 years ago

10.3390/ijms221910302

The Impact of m1A Methylation Modification Patterns on Tumor Immune Microenvironment and Prognosis in Oral Squamous Cell Carcinoma
Cited by: 17
Author(s): Li Gao, Ru Chen, Masahiro Sugimoto, Masanobu Mizuta, Yo Kishimoto, Koichi Omori
Software Mentions: 11
Published: about 5 years ago

10.1371/journal.pone.0245127

Adaptation and validation of a German version of the Strengths Use and Deficit Correction (SUDCO) questionnaire
Cited by: 2
Author(s): Timo Lorenz, Kathrin Heinitz, Clemens Beer, Marianne van Woerkom
Software Mentions: 11
Published: over 5 years ago

10.1186/1471-2164-9-419

Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: Comparison of rat and mouse
Cited by: 74
Author(s): Paul C. Boutros, Rui Yan, Ivy D. Moffat, Raimo Pohjanvirta, Allan B. Okey
Software Mentions: 11
Published: almost 19 years ago

10.3389/fnins.2020.00919

HYGRIP: Full-Stack Characterization of Neurobehavioral Signals (fNIRS, EEG, EMG, Force, and Breathing) During a Bimanual Grip Force Control Task
Cited by: 10
Author(s): Pablo Ortega, Tong Zhao, A. Aldo Faisal
Software Mentions: 11
Published: almost 6 years ago

10.1186/s12918-018-0662-y

Integrating node embeddings and biological annotations for genes to predict disease-gene associations
Cited by: 27
Author(s): Sezin Kircali Ata, Le Ou-Yang, Yuan Fang, Chee-Keong Kwoh, Min Wu, Xiaoli Li
Software Mentions: 11
Published: almost 8 years ago

10.1371/journal.pone.0180791

A validation of 11 body-condition indices in a giant snake species that exhibits positive allometry
Cited by: 29
Author(s): Bryan G. Falk, Ray W. Snow, Robert N. Reed
Software Mentions: 11
Published: about 9 years ago

10.3389/fonc.2021.640150

Construction of Competitive Endogenous RNA Network and Verification of 3-Key LncRNA Signature Associated With Distant Metastasis and Poor Prognosis in Patients With Clear Cell Renal Cell Carcinoma
Cited by: 19
Author(s): Yang Su, Tianxiang Zhang, Jiapeng Tang, Li Zhang, Song Fan, Jun Zhou, Chaozhao Liang
Software Mentions: 11
Published: over 5 years ago

10.1002/cam4.2983

Comprehensive insights on pivotal prognostic signature involved in clear cell renal cell carcinoma microenvironment using the ESTIMATE algorithm
Cited by: 30
Author(s): Jun Luo, Yi Xie, Yuxiao Zheng, Chenji Wang, Feng Qi, Jiateng Hu, Yixiang Xu
Software Mentions: 11
Published: over 6 years ago

10.1038/s41598-018-20825-z

Mosquito community influences West Nile virus seroprevalence in wild birds: implications for the risk of spillover into human populations
Cited by: 30
Author(s): Josué Martínez‐de la Puente, Martina Ferraguti, Santiago Ruíz, David Roiz, Francisco Rubio Llorente, Elisa Pérez‐Ramírez, Miguel Ángel Jiménez‐Clavero, Ramón C. Soriguer, Jordi Figuerola
Software Mentions: 11
Published: over 8 years ago

10.3389/fphys.2021.714195

Development and Validation of a Prediction Model for Elevated Arterial Stiffness in Chinese Patients With Diabetes Using Machine Learning
Cited by: 5
Author(s): Qingqing Li, Wenhui Xie, Liping Li, Lijing Wang, Qinyi You, Lu Chen, Jing Li, Yilang Ke, Jun Fang, Libin Liu, Huashan Hong
Software Mentions: 11
Published: about 5 years ago

10.1042/BSR20210527

Construction of a prognostic model for non-small-cell lung cancer based on ferroptosis-related genes
Cited by: 10
Author(s): Ke Han, Jukun Wang, Kun Qian, Teng Zhao, Xingsheng Liu, Yi Zhang
Software Mentions: 11
Published: over 5 years ago

10.18632/aging.203257

Characterization of ferroptosis signature to evaluate the predict prognosis and immunotherapy in glioblastoma
Cited by: 14
Author(s): Xiaopeng Zhu, Yuxiang Zhou, Yangqian Ou, Zebo Cheng, Deqing Han, Zhou Chu, Sian Pan
Software Mentions: 10
Published: about 5 years ago

10.1186/s12917-018-1331-5

A large-scale study of a poultry trading network in Bangladesh: implications for control and surveillance of avian influenza viruses
Cited by: 32
Author(s): Natalie Moyen, Graba Ahmed, Suman Das Gupta, Tenzin Tenzin, Rasheda Khan, Tooba Khan, Nitish Debnath, Mat Yamage, Dirk U. Pfeiffer, Guillaume Fournié
Software Mentions: 10
Published: over 8 years ago

10.1111/eva.13209

Mixed‐stock analysis using Rapture genotyping to evaluate stock‐specific exploitation of a walleye population despite weak genetic structure
Cited by: 17
Author(s): Peter T. Euclide, Tom MacDougall, Jason M. Robinson, Matthew D. Faust, Chris C. Wilson, Kuan‐Yu Chen, Elizabeth A. Marschall, Wesley A. Larson, Stuart A. Ludsin
Software Mentions: 10
Published: over 5 years ago

10.3389/fcell.2021.731790

Identification and Validation of a Nine-Gene Amino Acid Metabolism-Related Risk Signature in HCC
Cited by: 34
Author(s): Yajuan Zhao, Junli Zhang, Shuhan Wang, Qianqian Jiang, Ke Xu
Software Mentions: 10
Published: about 5 years ago

10.1371/journal.pone.0216723

A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to Mexico
Cited by: 10
Author(s): Juliano Palacios‐Abrantes, Andrés M. Cisneros‐Montemayor, Miguel Á. Cisneros-Mata, Laura Rodríguez, Francisco Arreguı́n-Sánchez, Verónica Aguilar, Santiago Domínguez-Sánchez, Stuart Fulton, Raquel López-Sagástegui, Héctor Reyes‐Bonilla, Rocío Rivera-Campos, Silvia Salas, Nuno Simões, William W. L. Cheung
Software Mentions: 10
Published: over 7 years ago

10.1186/s13059-018-1466-5

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data
Cited by: 40
Author(s): Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
Software Mentions: 10
Published: about 8 years ago

10.1186/s13059-016-0999-8

Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia
Cited by: 64
Author(s): Syed Haider, Alan McIntyre, Ruud G.P.M. van Stiphout, Laura Winchester, Simon Wigfield, Adrian L. Harris, Francesca M. Buffa
Software Mentions: 10
Published: over 10 years ago

10.1371/journal.pone.0131435

Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes
Cited by: 30
Author(s): Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores‐Villela, Matthew K. Fujita
Software Mentions: 10
Published: over 11 years ago

10.1007/s10456-020-09743-9

Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Cited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: about 6 years ago

10.1186/s12935-019-0890-2

Comprehensive bioinformatics analysis reveals potential lncRNA biomarkers for overall survival in patients with hepatocellular carcinoma: an on-line individual risk calculator based on TCGA cohort
Cited by: 19
Author(s): Zhiqiao Zhang, Yanling Ouyang, Yiyan Huang, Peng Wang, Jing Li, Tingshan He, Qingbo Liu
Software Mentions: 10
Published: about 7 years ago

10.1093/molbev/msaa218

Few Fixed Variants between Trophic Specialist Pupfish Species Reveal Candidate<i>Cis</i>-Regulatory Alleles Underlying Rapid Craniofacial Divergence
Cited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 10
Published: about 6 years ago

10.1172/jci.insight.145854

Cell-autonomous retinoic acid receptor signaling has stage-specific effects on mouse enteric nervous system
Cited by: 6
Author(s): Tao Gao, Elizabeth C. Wright-Jin, Rajarshi Sengupta, Jessica B. Anderson, Robert O. Heuckeroth
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pbio.3001053

Identification of 3′ UTR motifs required for mRNA localization to myelin sheaths in vivo
Cited by: 13
Author(s): Katie M. Yergert, Caleb A. Doll, Rebecca O’Rouke, Jacob H. Hines, Bruce Appel
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pone.0247535

Tools for mapping multi-scale settlement patterns of building footprints: An introduction to the R package foot
Cited by: 21
Author(s): Warren C. Jochem, Andrew J. Tatem
Software Mentions: 10
Published: over 5 years ago

10.1002/ece3.7563

The interaction of resource use and gene flow on the phenotypic divergence of benthic and pelagic morphs of Icelandic Arctic charr (<i>Salvelinus alpinus</i>)
Cited by: 10
Author(s): Matthew K. Brachmann, Kevin J. Parsons, Skúli Skúlason, Moira M. Ferguson
Software Mentions: 10
Published: over 5 years ago

10.1007/s00228-020-03052-2

Potentially inappropriate prescribing in older hospitalized Dutch patients according to the STOPP/START criteria v2: a longitudinal study
Cited by: 9
Author(s): Birgit A. Damoiseaux-Volman, Stephanie Medlock, Kimmy Raven, Danielle Sent, Johannes A. Romijn, Nathalie van der Velde, Ameen Abu‐Hanna
Software Mentions: 10
Published: almost 6 years ago

10.1038/s41598-020-72369-w

Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology
Cited by: 10
Author(s): Natacha Nikolic, Iratxe Montes, Maxime Lalire, Alexis Puech, Nathalie Bodin, Sophie Arnaud‐Haond, Sven E. Kerwath, Emmanuel Corse, Philippe Gaspar, Stéphanie Hollanda, Jérôme Bourjea, Wendy West, Sylvain Bonhommeau
Software Mentions: 10
Published: about 6 years ago

10.3389/fmicb.2018.01598

Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility
Cited by: 60
Author(s): Kristopher D. Parker, Shannon E. Albeke, Jason P. Gigley, Allan M. Goldstein, Naomi Ward
Software Mentions: 10
Published: about 8 years ago

10.1186/s13148-019-0795-x

DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis
Cited by: 50
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 10
Published: almost 7 years ago

10.1186/s12859-017-1770-1

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction
Cited by: 24
Author(s): Carlos Guzmán, Iván D’Orso
Software Mentions: 10
Published: about 9 years ago

10.1371/journal.pone.0233242

Determining soil particle-size distribution from infrared spectra using machine learning predictions: Methodology and modeling
Cited by: 4
Author(s): Élizabeth Parent, Léon‐Étienne Parent, Léon E. Parent
Software Mentions: 10
Published: about 5 years ago

10.3389/fpls.2020.587426

Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces
Cited by: 13
Author(s): Victor Allan, Mani Vetriventhan, R. Senthil, S. Geetha, Santosh Deshpande, Abhishek Rathore, Vinod Kumar, Prabhat Kumar Singh, Surender Reddymalla, V. C. R. Azevedo
Software Mentions: 10
Published: almost 6 years ago