cran: ROSE | Projects | Ecosyste.ms: Papers

10.3390/jcm7100322

Derivation and Validation of Machine Learning Approaches to Predict Acute Kidney Injury after Cardiac Surgery
Cited by: 100
Author(s): Hyung Chul Lee, Hyun Kyu Yoon, Karam Nam, Youn Joung Cho, Tae Kyoung Kim, Won Ho Kim, Jae Hyon Bahk
Software Mentions: 12
Published: about 6 years ago

10.1038/s41598-021-85155-z

Validating machine learning approaches for prediction of donor related complication in microsurgical breast reconstruction: a retrospective cohort study
Cited by: 6
Author(s): Yujin Myung, Sungmi Jeon, Chan Yeong Heo, Eun‐Kyu Kim, Eunyoung Kang, Hee-Chul Shin, Eun Joo Yang, Jae Hoon Jeong
Software Mentions: 12
Published: almost 4 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: about 6 years ago

10.1186/s13073-016-0285-0

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins
Cited by: 55
Author(s): Chan Zhou, Samuel R. York, Jennifer Y. Chen, Joshua V. Pondick, Daniel L. Motola, Raymond T. Chung, Alan C. Mullen
Software Mentions: 11
Published: almost 9 years ago

10.1186/s13059-020-02034-y

APEC: an accesson-based method for single-cell chromatin accessibility analysis
Cited by: 11
Author(s): Bin Li, Young Li, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin, Kun Qu
Software Mentions: 10
Published: over 4 years ago

10.1186/s13040-021-00235-0

Data analytics and clinical feature ranking of medical records of patients with sepsis
Cited by: 11
Author(s): Davide Chicco, Luca Oneto
Software Mentions: 10
Published: almost 4 years ago

10.15252/msb.20188339

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks
Cited by: 31
Author(s): Jan‐Philipp Mallm, Murat Iskar, Naveed Ishaque, Lara Klett, Sabrina J. Kugler, Jose M. Muiño, Vladimir B. Teif, Alexandra M Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D. Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Martin Vingron, Stephan Stilgenbauer, Peter Lichter, Marc Zapatka, Daniel Mertens, Karsten Rippe
Software Mentions: 10
Published: over 5 years ago

10.3389/fdata.2020.00015

Improving Diagnosis of Depression With XGBOOST Machine Learning Model and a Large Biomarkers Dutch Dataset (n = 11,081)
Cited by: 42
Author(s): Amita Sharma, W. Verbeke
Software Mentions: 9
Published: over 4 years ago

10.3390/biom10010026

Graph Theory-Based Sequence Descriptors as Remote Homology Predictors
Cited by: 12
Author(s): Guillermı́n Agüero-Chapin, Deborah Galpert Cañizares, Reinaldo Molina Ruiz, Evys Ancede-Gallardo, Gisselle Pérez-Machado, G Riva, Agostinho Antunes
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pone.0196865

Predicting potential drug-drug interactions on topological and semantic similarity features using statistical learning
Cited by: 89
Author(s): Andrej Kastrin, Polonca Ferk, Brane Leskošek
Software Mentions: 8
Published: over 6 years ago

10.1038/s41418-021-00751-w

Bromodomain protein BRDT directs ΔNp63 function and super-enhancer activity in a subset of esophageal squamous cell carcinomas
Cited by: 17
Author(s): Xin Wang, Ana P. Kutschat, Mitsuko Yamada, Evangelos Prokakis, Patricia Böttcher, Koji Tanaka, Yuichiro Doki, Feda H. Hamdan, Steven A. Johnsen
Software Mentions: 7
Published: almost 4 years ago

10.3389/fimmu.2019.00488

The Association Between Vitamin D and Multiple Sclerosis Risk: 1,25(OH)2D3 Induces Super-Enhancers Bound by VDR
Cited by: 24
Author(s): Ming Lu, Bennet J McComish, Kathryn P. Burdon, Bruce Taylor, Heinrich Körner
Software Mentions: 7
Published: almost 6 years ago

10.3390/molecules26113475

Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics Predictions
Cited by: 13
Author(s): Viroj Tachapuripunya, Sittiruk Roytrakul, Pramote Chumnanpuen, Teerasak E-kobon
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0225577

Designing machine learning workflows with an application to topological data analysis
Cited by: 4
Author(s): Eric Cawi, Patricio S. La Rosa, Arye Nehorai
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-019-50686-z

Antimicrobial Resistance Prediction for Gram-Negative Bacteria via Game Theory-Based Feature Evaluation
Cited by: 22
Author(s): Abu Sayed Chowdhury, Douglas R. Call, Shira L. Broschat
Software Mentions: 7
Published: about 5 years ago

10.1186/s13059-015-0688-z

Ultra-large alignments using phylogeny-aware profiles
Cited by: 109
Author(s): Nam Nguyen, Siavash Mirarab, Karthik Kumar, Tandy Warnow
Software Mentions: 7
Published: over 9 years ago

10.1016/j.stem.2018.06.014

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells
Cited by: 137
Author(s): Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, André F. Rendeiro, Elena Perenthaler, Christoph Bock, Ian Chambers
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2021.673530

Profiling of 3D Genome Organization in Nasopharyngeal Cancer Needle Biopsy Patient Samples by a Modified Hi-C Approach
Cited by: 3
Author(s): Sambhavi Animesh, Ruchi Choudhary, Bertrand Jern Han Wong, Charlotte Tze Jia Koh, Xin Yi Ng, J. S. H. Tay, Wan-Qin Chong, Jian Han, Leilei Chen, Boon Cher Goh, Melissa J. Fullwood
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-021-02339-6

Functional mapping of androgen receptor enhancer activity
Cited by: 15
Author(s): Chia Chi Flora Huang, Shreyas Lingadahalli, Tunç Morova, Doğancan Özturan, Eugene Hu, Ivan Pak Lok Yu, Simon Linder, Marlous Hoogstraat, Suzan Stelloo, Funda Sar, Henk van der Poel, Umut Berkay Altıntaş, Mohammadali Saffarzadeh, Stéphane Le Bihan, Brian McConeghy, Bengul Gokbayrak, Felix Y. Feng, Martin Gleave, Andries M. Bergman, Colin C. Collins, Faraz Hach, Wilbert Zwart, Eldon Emberly, Nathan A. Lack
Software Mentions: 6
Published: over 3 years ago

10.1038/s41597-020-0458-y

Epigenomic profiling of neuroblastoma cell lines
Cited by: 23
Author(s): Kristen Upton, Apexa Modi, Khushbu Patel, Nathan M. Kendsersky, Karina L. Conkrite, Robyn T. Sussman, Gregory P. Way, Rebecca N. Adams, Gregory I. Sacks, Paolo Fortina, Sharon J. Diskin, John M. Maris, Jo Lynne Rokita
Software Mentions: 6
Published: over 4 years ago

10.15252/msb.202110272

RNA polymerase II clusters form in line with surface condensation on regulatory chromatin
Cited by: 32
Author(s): Agnieszka Pancholi, Tim Klingberg, Weichun Zhang, Roshan Prizak, Irina Mamontova, Amra Noa, Marcel Sobucki, Andrei Yu Kobitski, G. Ulrich Nienhaus, Vasily Zaburdaev, Lennart Hilbert
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-019-38979-9

Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers
Cited by: 10
Author(s): Aziz Khan, Xuegong Zhang
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1008516

Ligand dependent gene regulation by transient ERα clustered enhancers
Cited by: 17
Author(s): Bharath Saravanan, Deepanshu Soota, Zubairul Islam, Sudeshna Majumdar, Rajat Mann, Sweety Meel, Umer Farooq, Kaivalya Walavalkar, Srimonta Gayen, Anurag Kumar Singh, Sridhar Hannenhalli, Dimple Notani
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12859-017-1594-z

Identification of long non-coding transcripts with feature selection: a comparative study
Cited by: 20
Author(s): Giovanna Maria Ventola, Teresa Maria Rosaria Noviello, Salvatore D’Aniello, Antonietta Spagnuolo, Michele Ceccarelli, Luigi Cerulo
Software Mentions: 6
Published: almost 8 years ago

10.1186/s13072-019-0297-2

MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells
Cited by: 9
Author(s): Temesgen Fufa, Laura L. Baxter, Julia C. Wedel, Derek Gildea, Stacie K. Loftus, William J. Pavan
Software Mentions: 6
Published: over 5 years ago

10.1186/1471-2105-8-254

Progressive multiple sequence alignments from triplets
Cited by: 22
Author(s): Matthias Kruspe, Peter F. Stadler
Software Mentions: 5
Published: over 17 years ago

10.1186/1471-2105-12-S9-S4

Fast and accurate methods for phylogenomic analyses
Cited by: 34
Author(s): Jimmy C. Yang, Tandy Warnow
Software Mentions: 5
Published: about 13 years ago

10.3390/ijms19020593

Luminal lncRNAs Regulation by ERα-Controlled Enhancers in a Ligand-Independent Manner in Breast Cancer Cells
Cited by: 13
Author(s): Valentina Miano, Giulio Ferrero, Valentina Rosti, Eleonora Manitta, Jamal Elhasnaoui, Giulia Basile, Michele De Bortoli
Software Mentions: 5
Published: almost 7 years ago

10.3390/cancers13174317

Comprehensively Exploring the Mutational Landscape and Patterns of Genomic Evolution in Hypermutated Cancers
Cited by: 2
Author(s): Peng-Chan Lin, Yu-Min Yeh, Hui‐Ping Hsu, Ren‐Hao Chan, Bo Lin, Po-Chuan Chen, Chien-Chang Pan, Keng-Fu Hsu, Jenn-Ren Hsiao, Yan‐Shen Shan, Meng-Ru Shen
Software Mentions: 5
Published: over 3 years ago

10.1128/mBio.01457-20

Kaposi’s Sarcoma-Associated Herpesvirus Drives a Super-Enhancer-Mediated Survival Gene Expression Program in Primary Effusion Lymphoma
Cited by: 13
Author(s): Mark Manzano, Thomas Guenther, Honglyoul Ju, John Nicholas, Elizabeth T. Bartom, Adam Grundhoff, Eva Gottwein
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-021-02376-1

A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks
Cited by: 15
Author(s): Chongze Yuan, Haojie Chen, Shiqi Tu, Hsin Yi Huang, Yunjian Pan, Xiuqi Gui, Muyu Kuang, Xuxia Shen, Qiang Zheng, Yang Zhang, Chao Cheng, Hui Hong, Xiaoting Tao, Yizhou Peng, Xingxin Yao, Fei-Long Meng, Hongbin Ji, Zongshu Shao, Yihua Sun
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.34077

Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver
Cited by: 51
Author(s): Bryan J. Matthews, David J. Waxman
Software Mentions: 5
Published: over 6 years ago

10.1002/1878-0261.12726

Characterization of super‐enhancer‐associated functional lncRNAs acting as ceRNAs in ESCC
Cited by: 22
Author(s): Qiuyu Wang, Peng Liu, Chen Yang, Lian‐Di Liao, Jiaxin Chen, Meng Li, Yanyu Li, Fengcui Qian, Yuexin Zhang, Fan Wang, Chunquan Li, De–Chen Lin, Li‐Yan Xu, En‐Min Li
Software Mentions: 5
Published: over 4 years ago

10.7150/thno.47830

LncRNA DSCAM-AS1 interacts with YBX1 to promote cancer progression by forming a positive feedback loop that activates FOXA1 transcription network
Cited by: 68
Author(s): Yin Zhang, Yong-Xin Huang, Dan-Lan Wang, Bing Yang, Haiyan Yan, Lehang Lin, Yun Li, Jie Chen, Lisha Xie, Yongsheng Huang, Jian-You Liao, Kaishun Hu, Jun He, Phei Er Saw, Xiaoding Xu, Yin Ding
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13072-018-0252-7

Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia
Cited by: 14
Author(s): Sara Wernig-Zorc, Mukesh Yadav, Pradeep Kumar Kopparapu, Mats Bemark, Hallgerður Lind Kristjánsdóttir, Per‐Ola Andersson, Chandrasekhar Kanduri, Meena Kanduri
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-019-3180-z

DEEPSEN: a convolutional neural network based method for super-enhancer prediction
Cited by: 13
Author(s): Hongda Bu, Jiaqi Hao, Yanglan Gan, Shuigeng Zhou, Jihong Guan
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.64370

SATB2 induction of a neural crest mesenchyme-like program drives melanoma invasion and drug resistance
Cited by: 8
Author(s): Maurizio Fazio, Ellen van Rooijen, Michelle Dang, Glenn van de Hoek, Julien Ablain, Jeffrey K. Mito, Song Yang, Andrew Thomas, Jonathan Michael, Tania Fabo, Rodsy Modhurima, Patrizia Pessina, Charles Kaufman, Yi Zhou, Richard M. White, Leonard I. Zon
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0125795

Predicting Human Genetic Interactions from Cancer Genome Evolution
Cited by: 18
Author(s): Xiaowen Lu, Wout Megchelenbrink, Richard A. Notebaart, Martijn A. Huynen
Software Mentions: 4
Published: over 9 years ago

10.1093/bioinformatics/btab263

Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited
Cited by: 1
Author(s): Wei Wang, Ahmad Hejasebazzi, Julia Zheng, Kevin J. Liu
Software Mentions: 4
Published: over 3 years ago

10.1186/s13071-018-3182-0

Monthly variation in the probability of presence of adult Culicoides populations in nine European countries and the implications for targeted surveillance
Cited by: 17
Author(s): Ana Carolina Cuéllar, Lene Jung Kjær, Andreas Baum, Anders Stockmarr, Henrik Skovgård, Søren Achim Nielsen, Matilda Andersson, Anders Lindström, Jan Chirico, Renke Lühken, S. Steinke, Ellen Kiel, Jörn Gethmann, Franz Josef Conraths, Magdalena Larska, Marcin Smreczak, Anna Orłowska, Inger Sofie Hamnes, Ståle Sviland, Petter Hopp, Katharina Brugger, Franz Rubel, Thomas Balenghien, Claire Garros, Ignace Rakotoarivony, Xavier Allène, Jonathan Lhoir, David Chavernac, Jean-Claude Delécolle, Bruno Mathieu, Delphine Delécolle, Marie-Laure Setier-Rio, Roger Venail, Bethsabée Scheid, Miguel Ángel Miranda Chueca, Carlos Barceló, Javier Lucientes, Rolando Estrada, Alexander Mathis, Wesley Tack, René Bødker
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0238076

Deletion of Mediator 1 suppresses TGFβ signaling leading to changes in epidermal lineages and regeneration
Cited by: 3
Author(s): Yuko Oda, Thai Nguyen, Akiko Hata, Mark B. Meyer, J. Wesley Pike, Daniel Bikle
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-017-1698-5

NaviSE: superenhancer navigator integrating epigenomics signal algebra
Cited by: 5
Author(s): Alex M. Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta, Marcos J. Araúzo-Bravo
Software Mentions: 4
Published: over 7 years ago

10.1186/s13059-021-02485-x

Mapping the evolving landscape of super-enhancers during cell differentiation
Cited by: 16
Author(s): Yan Kai, Bin E. Li, Min Zhu, Grace Y Li, Fei Chen, Yingli Han, Hye Young Ji, Stuart H. Orkin, Wenqing Cai, Jialiang Huang, Guo‐Cheng Yuan
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-017-00176-x

Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
Cited by: 28
Author(s): Feinan Wu, Jie Yao
Software Mentions: 3
Published: almost 8 years ago

10.3389/fcell.2021.682561

Genome-Wide Histone H3K27 Acetylation Profiling Identified Genes Correlated With Prognosis in Papillary Thyroid Carcinoma
Cited by: 7
Author(s): Luyao Zhang, Dan Xiong, Qian Liu, Yiling Luo, Yuhan Tian, Xi Xiao, Ye Sang, Yihao Liu, Shubin Hong, Shuang Yu, Jie Li, Weiming Lv, Yanbing Li, Zhonghui Tang, Rengyun Liu, Qian Zhong, Hang Xiao
Software Mentions: 3
Published: over 3 years ago

10.1186/gb-2008-9-10-r147

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
Cited by: 24
Author(s): Avinash V. Varadarajan, Robert K. Bradley, Ian Holmes
Software Mentions: 3
Published: almost 17 years ago

10.3390/genes10050348

Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver
Cited by: 6
Author(s): Yu Luan, Lu Zhang, Mingyang Hu, Yongming Xu, Ye Hou, Xinyun Li, Zhao Song, Yi‐Fang Zhao, Changchun Li
Software Mentions: 3
Published: over 5 years ago

10.3390/s21041199

Hand Motion Capture from a 3D Leap Motion Controller for a Musculoskeletal Dynamic Simulation
Cited by: 9
Author(s): Robin Fonk, Sean Schneeweiss, Ulrich Simon, Lucas Engelhardt
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1006745

GRHL3 binding and enhancers rearrange as epidermal keratinocytes transition between functional states
Cited by: 39
Author(s): Rachel Herndon Klein, Ziguang Lin, Amelia Soto Hopkin, William Gordon, Lam C. Tsoi, Yun Liang, Jóhann E. Guðjónsson, Bogi Andersen
Software Mentions: 3
Published: over 7 years ago

10.1038/s41389-020-00285-9

Triptolide targets super-enhancer networks in pancreatic cancer cells and cancer-associated fibroblasts
Cited by: 32
Author(s): Pawan Noel, Shaimaa Hussein, Serina Ng, Corina E. Antal, Wei Lin, Emily Rodela, Priscilla Delgado, Sanna Naveed, Michael Downes, Yin Lin, Ronald M. Evans, Daniel D. Von Hoff, Haiyong Han
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.43821

HDAC3 restrains CD8-lineage genes to maintain a bi-potential state in CD4+CD8+ thymocytes for CD4-lineage commitment
Cited by: 23
Author(s): Rachael Laura Philips, Jeong Heon Lee, Krutika S. Gaonkar, Pritha Chanana, Ji Young Chung, Sinibaldo Romero Arocha, Aaron Schwab, Tamás Ördög, Virginia Smith Shapiro
Software Mentions: 3
Published: almost 6 years ago

10.1093/bioinformatics/btz082

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability
Cited by: 7
Author(s): Jia‐Ming Chang, Evan Floden, Javier Herrero, Olivier Gascuel, Paolo Di Tommaso, Cédric Notredame
Software Mentions: 3
Published: almost 6 years ago

10.3389/fneur.2021.638267

Machine Learning-Enabled 30-Day Readmission Model for Stroke Patients
Cited by: 13
Author(s): Negar Darabi, Niyousha Hosseinichimeh, Anthony Noto, Ramin Zand, Vida Abedi
Software Mentions: 3
Published: over 3 years ago

10.3390/molecules26123671

K-Nearest Neighbor and Random Forest-Based Prediction of Putative Tyrosinase Inhibitory Peptides of Abalone Haliotis diversicolor
Cited by: 6
Author(s): Sasikarn Kongsompong, Teerasak E-kobon, Pramote Chumnanpuen
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.590672

Integrative Epigenomic Analysis of Transcriptional Regulation of Human CircRNAs
Cited by: 3
Author(s): Xuecang Li, Zhidong Tang, Li Peng, Yanyu Li, Fengcui Qian, Jian Zhao, Ling-Wen Ding, Xiaojuan Du, Meng Li, Jian Zhang, Xuefeng Bai, Jiang Zhu, Chenchen Feng, Qiuyu Wang, Jian Pan, Chunquan Li
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41419-020-02963-3

EZH2 reduction is an essential mechanoresponse for the maintenance of super-enhancer polarization against compressive stress in human periodontal ligament stem cells
Cited by: 9
Author(s): Qian Li, Xiwen Sun, Yunyi Tang, Yanan Qu, Yanheng Zhou, Yu Zhang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12943-020-01301-7

Targeting CDK7 suppresses super enhancer-linked inflammatory genes and alleviates CAR T cell-induced cytokine release syndrome
Cited by: 12
Author(s): Wei Ye, Chong Li, Huifang Bian, Wei Qian, Kaizhou Jin, Tianmin Xu, Xiaomao Guo, Lu Xia, Fengtao Su
Software Mentions: 3
Published: almost 4 years ago

10.1038/s42003-021-02209-8

Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes
Cited by: 4
Author(s): Hong Wang, Aiping Duan, Jing Zhang, Qi Wang, Yufei Xing, Zhaohui S. Qin, Zhihong Liu, Jingping Yang
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-14-20

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure
Cited by: 4
Author(s): Yasin Bakış, Hasan H. Otu, Nivart Taşçı, Cem Meydan, Neş’e Bilgin, Sırrı Yüzbaşıoğlu, Osman Uğur Sezerman
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12859-019-2646-3

A new class of constitutively active super-enhancers is associated with fast recovery of 3D chromatin loops
Cited by: 12
Author(s): Jayoung Ryu, Hyunwoong Kim, Dongchan Yang, Andrew Lee, Inkyung Jung
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1006474

Comparative Transcriptomic and Epigenomic Analyses Reveal New Regulators of Murine Brown Adipogenesis
Cited by: 42
Author(s): Reinhard Brunmeir, Jingyi Wu, Peng Xu, Sun-Yee Kim, Sylvain Julien, Qiongyi Zhang, Wei Xie, Feng Xu
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0235343

Super-enhancer acquisition drives oncogene expression in triple negative breast cancer
Cited by: 15
Author(s): Ryan Raisner, Russell Bainer, Peter M. Haverty, Kelli L. Benedetti, Karen E. Gascoigne
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-88172-0

Machine learning and deep learning to predict mortality in patients with spontaneous coronary artery dissection
Cited by: 29
Author(s): Chayakrit Krittanawong, Hafeez Ul Hassan Virk, Anirudh Kumar, Mehmet Aydar, Zhen Wang, Matthew Stewart, Jonathan L. Halperin
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0088901

QuickProbs—A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors
Cited by: 13
Author(s): Adam Gudyś, Sebastian Deorowicz
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-12-456

Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach
Cited by: 4
Author(s): Luz B. Gilbert, Lee Chae, Takao Kasuga, John W. Taylor
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-016-3101-8

Scaling statistical multiple sequence alignment to large datasets
Cited by: 13
Author(s): Michael Nute, Tandy Warnow
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-020-73558-3

Survival prediction of patients with sepsis from age, sex, and septic episode number alone
Cited by: 19
Author(s): Davide Chicco, Giuseppe Jurman
Software Mentions: 2
Published: about 4 years ago

10.1038/s41419-021-04176-8

USP7 facilitates SMAD3 autoregulation to repress cancer progression in p53-deficient lung cancer
Cited by: 10
Author(s): Yu Huang, An Chieh Cheng, Hui Chi Tang, Guo Cheng Huang, Ling Cai, Ta Hsien Lin, Kou Juey Wu, Ping Hui Tseng, Greg G. Wang, Wei Yi Chen
Software Mentions: 2
Published: about 3 years ago

10.1111/jcmm.16583

Krϋppel‐like factor 15 suppresses renal glomerular mesangial cell proliferation via enhancing P53 SUMO1 conjugation
Cited by: 2
Author(s): Lingling Wu, Li Ou, Fengge Zhu, Xu Wang, Pu Chen, Guangyan Cai, Xiangmei Chen, Quan Hong
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-02257-3

Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions
Cited by: 68
Author(s): Fan Cao, Yiwen Fang, Hong Kee Tan, Yufen Goh, Jocelyn Yeen Hui Choy, Bryan T. H. Koh, Jiong Hao Tan, Nicolas Bertin, Aroul Ramadass, Ewan Hunter, Jayne Green, Matthew Salter, Alexandre Akoulitchev, Wilson Wang, Wee Joo Chng, Daniel G. Tenen
Software Mentions: 2
Published: over 7 years ago

10.3390/diagnostics9040210

Ultrasound and Clinical Preoperative Characteristics for Discrimination Between Ovarian Metastatic Colorectal Cancer and Primary Ovarian Cancer: A Case-Control Study
Cited by: 8
Author(s): Maciej Stukan, Juan Luis Alcázar, Jacek Gębicki, E. Epstein, Marcin Liro, A Sufliarska, Sebastian Szubert, S. Guerriero, Elena Ioana Braicu, Mariusz Szajewski, Małgorzata Pietrzak-Stukan, D. Fischerová
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.8764

PigLeg: prediction of swine phenotype using machine learning
Cited by: 15
Author(s): Siroj Bakoev, Lyubov Getmantseva, Maria Kolosova, Olga Kostyunina, Duane R. Chartier, Tatiana V. Tatarinova
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0253256

The impact of timetable on student’s absences and performance
Cited by: 6
Author(s): Souad Larabi Marie-Sainte, Roohi Jan, Ali Al-Matouq, Sara Alabduhadi
Software Mentions: 2
Published: over 3 years ago

10.3389/fonc.2019.01281

A Diagnostic Panel of DNA Methylation Biomarkers for Lung Adenocarcinoma
Cited by: 30
Author(s): Nan Shen, Jie Du, Hui Zhou, Nan Chen, Yi Pan, Jörg D. Hoheisel, Zonghui Jiang, Ling Xiao, Yue Tao, Xi Mo
Software Mentions: 2
Published: about 5 years ago

10.3389/fphar.2021.648805

Predicting Drug-Induced Liver Injury Using Machine Learning on a Diverse Set of Predictors
Cited by: 4
Author(s): Temidayo Adeluwa, Brett A. McGregor, Kai Guo, Junguk Hur
Software Mentions: 2
Published: over 3 years ago

10.1155/2014/237243

Network-Based Analysis of Software Change Propagation
Cited by: 7
Author(s): Rongcun Wang, Rubing Huang, Binbin Qu
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0163056

Rapid On-Site Evaluation Does Not Improve Endoscopic Ultrasound-Guided Fine Needle Aspiration Adequacy in Pancreatic Masses: A Meta-Analysis and Systematic Review
Cited by: 63
Author(s): Fanyang Kong, Jianwei Zhu, Xiangyu Kong, Tao Sun, Xuan Deng, Yiqi Du, Zhao‐Shen Li
Software Mentions: 2
Published: about 8 years ago

10.1093/bioinformatics/bts578

Adding unaligned sequences into an existing alignment using MAFFT and LAST
Cited by: 184
Author(s): Kazutaka Katoh, Martin C. Frith
Software Mentions: 2
Published: about 12 years ago

10.1016/j.mex.2020.101165

High-performance method for identification of super enhancers from ChIP-Seq data with configurable cloud virtual machines
Cited by: 5
Author(s): Н. Н. Орлова, Olga V. Bogatova, А. В. Орлов
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0033104

Treelength Optimization for Phylogeny Estimation
Cited by: 5
Author(s): Kevin Liu, Tandy Warnow
Software Mentions: 2
Published: almost 13 years ago

10.3390/ijms22094852

Testing EGFR with Idylla on Cytological Specimens of Lung Cancer: A Review
Cited by: 16
Author(s): Alessandro Caputo, Angela D’Ardia, Francesco Sabbatino, Caterina Picariello, Chiara Ciaparrone, Pio Zeppa, Antonio D’Antonio
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-6-66

Cited by: 152
Author(s): Alap R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern
Software Mentions: 1
Published: almost 20 years ago

10.1186/s12859-019-3207-5

SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution
Cited by: 3
Author(s): Esaie Kuitche, Safa Jammali, Aïda Ouangraoua
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-6-273

Ancestral sequence alignment under optimal conditions
Cited by: 11
Author(s): Alexander K. Hudek, Daniel G. Brown
Software Mentions: 1
Published: about 19 years ago

10.1186/1471-2105-6-108

Cited by: 112
Author(s): Erik L. L. Sonnhammer, Volker Hollich
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2105-10-S1-S11

Simultaneous phylogeny reconstruction and multiple sequence alignment
Cited by: 17
Author(s): Jijun Tang, Yue Feng
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-8-S5-S9

Automatic extraction of reliable regions from multiple sequence alignments
Cited by: 8
Author(s): Timo Lassmann, Erik L. L. Sonnhammer
Software Mentions: 1
Published: over 17 years ago

10.1186/1741-7007-10-47

Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi
Cited by: 175
Author(s): Salvador Capella-Gutiérrez, Marina Marcet‐Houben, Toni Gabaldón
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2407-14-8

Lymph node fine needle Cytology in the staging and follow-up of Cutaneous Lymphomas
Cited by: 30
Author(s): Elena Vigliar, Immacolata Cozzolino, Marco Picardi, Andrea Peluso, Laura Virginia Sosa Fernandez, A Vetrani, Gerardo Botti, Fabrizio Pane, Carmine Selleri, Pio Zeppa
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-017-4117-4

Evolving DNA methylation and gene expression markers of B-cell chronic lymphocytic leukemia are present in pre-diagnostic blood samples more than 10 years prior to diagnosis
Cited by: 14
Author(s): Panagiotis Georgiadis, Irene Liampa, Dennie G. A. J. Hebels, Julian Krauskopf, Aristotelis Chatziioannou, Ioannis Valavanis, Theo M. C. M. de Kok, Jos Kleinjans, Ingvar A. Bergdahl, Beatrice Melin, Florentin Spaeth, Domenico Palli, Roel Vermeulen, Jelle Vlaanderen, Marc Chadeau‐Hyam, Paolo Víneis, Soterios A. Kyrtopoulos
Software Mentions: 1
Published: over 7 years ago

10.1186/s12890-019-0927-2

Bronchoscopic management of peripheral pulmonary lesions: robotic approach paves the way to the future
Cited by: 4
Author(s): Michele Mondoni, Giovanni Sotgiu
Software Mentions: 1
Published: over 5 years ago

10.1186/s13040-021-00260-z

Machine learning and statistical approaches for classification of risk of coronary artery disease using plasma cytokines
Cited by: 4
Author(s): Seema Singh Saharan, Pankaj Nagar, Kate Townsend Creasy, Eveline Oestreicher Stock, James Feng, Mary J. Malloy, John P. Kane
Software Mentions: 1
Published: over 3 years ago

10.1155/2020/9842768

Diagnostic Value of Rapid On-Site Evaluation for CT-Guided Percutaneous Fine Needle Aspiration in the Diagnosis of Pulmonary Occupying Lesions
Cited by: 8
Author(s): Tianfeng Peng, Tao Ren, Hansheng Wang, Zhe-Xiang Feng, Meifang Wang
Software Mentions: 1
Published: about 4 years ago

10.1155/2019/5049248

The Utility of Rapid On-Site Evaluation during Bronchoscopic Biopsy: A 2-Year Respiratory Endoscopy Central Experience
Cited by: 6
Author(s): Hansheng Wang, Na Wei, Yijun Tang, Yunyun Wang, Guangheng Luo, Tao Ren, Xiong Cai, Hongbo Li, Meifang Wang, Xin Qian
Software Mentions: 1
Published: about 5 years ago

10.1186/s13058-019-1132-1

BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells
Cited by: 15
Author(s): Xiaowen Zhang, Yao Wang, Huai-Chin Chiang, Yung-Hsu Hsieh, Chang Lu, Ben Ho Park, Ismail Jatoi, Victor X. Jin, Yanfen Hu, Rong Li
Software Mentions: 1
Published: over 5 years ago

10.1097/MD.0000000000021168

Diagnostic value of rapid on-site evaluation in interventional pulmonology
Cited by: 0
Author(s): Xiangwen Weng, Lijia Zhi, Xing An, Mei-Xin Xu, Hua Zhang, Kunlan Long, Peiyang Gao
Software Mentions: 1
Published: over 4 years ago

10.1264/jsme2.ME14061

Application of Locked Nucleic Acid (LNA) Oligonucleotide–PCR Clamping Technique to Selectively PCR Amplify the SSU rRNA Genes of Bacteria in Investigating the Plant-Associated Community Structures
Cited by: 29
Author(s): Makoto Ikenaga, Masao Sakai
Software Mentions: 1
Published: almost 11 years ago

10.1264/jsme2.ME18071

Improvements in Bacterial Primers to Enhance Selective SSU rRNA Gene Amplification of Plant-associated Bacteria by Applying the LNA Oligonucleotide-PCR Clamping Technique
Cited by: 12
Author(s): Makoto Ikenaga, Shohei Katsuragi, Yoshihiro Handa, Hiroshi Katsumata, Naoya Chishaki, Tomohiro Kawauchi, Masao Sakai
Software Mentions: 1
Published: almost 7 years ago

10.3390/molecules23051057

Targeting General Transcriptional Machinery as a Therapeutic Strategy for Adult T-Cell Leukemia
Cited by: 7
Author(s): Regina Wan Ju Wong, Takashi Ishida, Takaomi Sanda
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.1002220

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage
Cited by: 282
Author(s): Marina Marcet‐Houben, Toni Gabaldón
Software Mentions: 1
Published: over 9 years ago

Projects: cran: ROSE

Papers Mentioning ROSE 131