bioconductor: GEM | Projects | Ecosyste.ms: Papers

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: almost 9 years ago

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 years ago

10.3390/ijms22115751

Multi-Omics Model Applied to Cancer Genetics
Cited by: 14
Author(s): Francesco Pettini, Anna Visibelli, Vittoria Cicaloni, Daniele Iovinelli, Ottavia Spiga
Software Mentions: 14
Published: over 3 years ago

10.7554/eLife.11613

Epigenomic landscapes of retinal rods and cones
Cited by: 107
Author(s): Alisa Mo, Chongyuan Luo, Fred P. Davis, Eran A. Mukamel, Gilbert L. Henry, Joseph R. Nery, Mark A. Urich, Serge Picard, Ryan Lister, Sean R. Eddy, M Beer, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 11
Published: almost 9 years ago

10.1186/s12864-021-07388-6

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential
Cited by: 3
Author(s): Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez, Edoardo Saccenti
Software Mentions: 10
Published: almost 4 years ago

10.1186/s13059-020-02008-0

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Cited by: 24
Author(s): Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.56980

m6A RNA methylation impacts fate choices during skin morphogenesis
Cited by: 18
Author(s): Linghe Xi, Thomas Carroll, Irina Matos, Ji‐Dung Luo, Lisa Polak, H. Amalia Pasolli, Samie R. Jaffrey, Elaine Fuchs
Software Mentions: 8
Published: over 4 years ago

10.7717/peerj-cs.521

LinkPred: a high performance library for link prediction in complex networks
Cited by: 0
Author(s): Said Kerrache
Software Mentions: 8
Published: over 3 years ago

10.1186/s13072-021-00415-6

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR
Cited by: 1
Author(s): Michael Scherer, Gilles Gasparoni, Souad Rahmouni, Tatiana I. Shashkova, Marion Arnoux, Édouard Louis, Arina Nostaeva, Diana Avalos, Emmanouil T. Dermitzakis, Yurii S. Aulchenko, Thomas Lengauer, Paul Lyons, Michel Georges, Jörn Walter
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pcbi.1006644

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
Cited by: 35
Author(s): Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, Jared T. Broddrick, Karsten Zengler, Jaehyung Kim
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pcbi.1003706

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
Cited by: 54
Author(s): Fredrik Karlsson, Intawat Nookaew, Jens Nielsen
Software Mentions: 7
Published: over 10 years ago

10.1186/s12864-016-3300-3

Assessing characteristics of RNA amplification methods for single cell RNA sequencing
Cited by: 32
Author(s): Hannah Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian–Bing Fan, Stephen Fisher, Jennifer Herstein, Tae Kyung Kim, Jae Mun Kim, Ming-Yi Lin, Rui Li, William J. Mack, Sean McGroty, Joseph Nguyen, Neeraj Salathia, Jamie Shallcross, Tade Souaiaia, Jennifer M. Spaethling, Christopher Walker, Jinhui Wang, Kai Wang, Wei Wang, André Wildberg, Lina Zheng, Robert H. Chow, James Eberwine, James A. Knowles, Kun Zhang, Junhyong Kim
Software Mentions: 7
Published: about 8 years ago

10.3390/jpm11060496

Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models
Cited by: 10
Author(s): Mahdi Jalili, Martin Scharm, Olaf Wolkenhauer, Mehdi Damaghi, Ali Salehzadeh‐Yazdi
Software Mentions: 7
Published: over 3 years ago

10.1186/s13059-019-1730-3

Current status and applications of genome-scale metabolic models
Cited by: 406
Author(s): Changdai Gu, Gi Bae Kim, Won Jun Kim, Hyun Uk Kim, Sang Yup Lee
Software Mentions: 7
Published: over 5 years ago

10.3390/metabo10030088

Analysis and Simulation of Glioblastoma Cell Lines-Derived Extracellular Vesicles Metabolome
Cited by: 25
Author(s): Miroslava Čuperlović-Culf, Nam Huan Khieu, Anuradha Surendra, Melissa Hewitt, Claudie Charlebois, Jagdeep K. Sandhu
Software Mentions: 6
Published: almost 5 years ago

10.1038/sdata.2016.8

Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice
Cited by: 8
Author(s): Xing Tang, Huayang Liu, Arunima Srivastava, Thierry Pécot, Zhong Chen, Qianben Wang, Kun Huang, Maria Teresa Sáenz-Robles, Paul G. Cantalupo, James M. Pipas, Gustavo Leone
Software Mentions: 6
Published: almost 9 years ago

10.1186/gb-2005-6-9-r76

Cited by: 122
Author(s): Stephen Henderson, David B. Guiliano, Nadège Presneau, Sean R. McLean, Richard Frow, Sonja Vujovic, John Anderson, Neil J. Sebire, Jeremy Whelan, Nick Athanasou, Adrienne M. Flanagan, Chris Boshoff
Software Mentions: 6
Published: almost 20 years ago

10.1093/gigascience/gix049

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Cited by: 114
Author(s): Sarah S.T. Mak, Shyam Gopalakrishnan, Christian Carøe, Chunyu Geng, Shanlin Liu, Mikkel‐Holger S. Sinding, Lukas F. K. Kuderna, Wenwei Zhang, Shujin Fu, Filipe Garrett Vieira, Mietje Germonpré, Hervé Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Pontén, Tomás Marquès-Bonet, Guojie Zhang, Hui Jiang, M. Thomas P. Gilbert
Software Mentions: 6
Published: over 7 years ago

10.1038/s41398-020-0710-4

Large epigenome-wide association study of childhood ADHD identifies peripheral DNA methylation associated with disease and polygenic risk burden
Cited by: 49
Author(s): Michael A. Mooney, Peter Ryabinin, Beth Wilmot, Priya Bhatt, Jonathan Mill, Joel T. Nigg
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12859-020-3403-3

Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes
Cited by: 1
Author(s): Vasudha Sharma, Sharmistha Majumdar
Software Mentions: 6
Published: almost 5 years ago

10.3389/fcell.2020.592348

Limited Mitochondrial Activity Coupled With Strong Expression of CD34, CD90 and EPCR Determines the Functional Fitness of ex vivo Expanded Human Hematopoietic Stem Cells
Cited by: 7
Author(s): Luena Papa, Mansour Djedaini, Tiphaine Martin, Mahtab Zangui, Kristin G. Beaumont, Robert Sebra, Ramon Parsons, Christoph Schaniel, Ronald Hoffman
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-016-0991-z

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains
Cited by: 29
Author(s): Joshua Starmer, Terry Magnuson
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.51243

Global genome diversity of the Leishmania donovani complex
Cited by: 77
Author(s): Susanne U. Franssen, Caroline Durrant, Olivia Stark, Bettina A. Moser, Tim Downing, Hideo Imamura, Jean Claude Dujardin, Mandy Sanders, Isabel Maurício, Michael A. Miles, Lionel F. Schnur, Charles L. Jaffe, Abedelmajeed Nasereddin, Henk D. F. H. Schallig, Matthew Yeo, Tapan Bhattacharyya, Mohammad Zahangir Alam, Matthew Berriman, Thierry Wirth, Gabriele Schönian, James A. Cotton
Software Mentions: 5
Published: over 4 years ago

10.3390/metabo9020022

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview
Cited by: 65
Author(s): Partho Sen, Matej Orešič
Software Mentions: 5
Published: almost 6 years ago

10.1186/1748-7188-8-25

Data compression for sequencing data
Cited by: 84
Author(s): Sebastian Deorowicz, Szymon Grabowski
Software Mentions: 5
Published: almost 12 years ago

10.1038/s41598-017-15629-6

Innate Cell-Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional and RNA-seq Study
Cited by: 30
Author(s): Elena Chaves-Pozo, Yulema Valero, Anna Esteve‐Codina, Jèssica Gómez-Garrido, Marc Dabad, Tyler Alioto, José Meseguer, M. Ángeles Esteban, Alberto Cuesta
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0097277

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads
Cited by: 6
Author(s): Andrea Manconi, Alessandro Orro, Elias Manca, Giuliano Armano, Luciano Milanesi
Software Mentions: 5
Published: over 10 years ago

10.3390/genes12010048

Probably Correct: Rescuing Repeats with Short and Long Reads
Cited by: 3
Author(s): Monika Čechová
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13068-020-01838-1

Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production
Cited by: 16
Author(s): Nhung Pham, Maarten J.M.F. Reijnders, María Suárez-Diez, Bart Nijsse, Jan Springer, Gerrit Eggink, Peter J. Schaap
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pcbi.1002638

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
Cited by: 255
Author(s): Yuchun Guo, Shaun Mahony, David K. Gifford
Software Mentions: 5
Published: over 12 years ago

10.1155/2016/7983236

A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data
Cited by: 32
Author(s): Jennifer D. Hintzsche, William A. Robinson, Aik Choon Tan
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pgen.1009784

R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements
Cited by: 1
Author(s): D. S. Ellis, Félix Reyes-Martín, María Rodríguez-López, Cristina Cotobal, Xi‐Ming Sun, Quentin Saintain, Daniel C. Jeffares, Samuel Marguerat, Juan Jiménez, Jürg Bähler
Software Mentions: 5
Published: over 3 years ago

10.1186/s13742-016-0134-5

Genome sequence of the olive tree, Olea europaea
Cited by: 158
Author(s): Fernando Cruz, Irene Julca, Jèssica Gómez-Garrido, Damian Loska, Marina Marcet‐Houben, Emilio Cano, Beatriz Galán, Leonor Frías, Paolo Ribeca, Sophia Derdak, Marta Gut, Manuel Sánchez-Fernández, José Luis Garcı́a, Pablo Vargas, Tyler Alioto, Toni Gabaldón
Software Mentions: 5
Published: over 8 years ago

10.1093/bioinformatics/btt016

Grape RNA-Seq analysis pipeline environment
Cited by: 28
Author(s): David G. Knowles, Maik Röder, Angelika Merkel, Roderic Guigó
Software Mentions: 5
Published: almost 12 years ago

10.1186/1471-2164-15-472

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
Cited by: 43
Author(s): Rebecca Worsley Hunt, Anthony Mathelier, Luis del Peso, Wyeth W. Wasserman
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pcbi.1007764

StanDep: Capturing transcriptomic variability improves context-specific metabolic models
Cited by: 19
Author(s): Chintan Joshi, Song‐Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O’Rourke, Nathan E. Lewis
Software Mentions: 5
Published: over 4 years ago

10.1186/gb-2014-15-8-r70

DNA copy number evolution in Drosophila cell lines
Cited by: 94
Author(s): Hangnoh Lee, C. Joel McManus, Dong-Yeon Cho, Matthew L. Eaton, Fioranna Renda, Maria Patrizia Somma, Lucy Cherbas, Gemma E. May, Sara Powell, Dayu Zhang, Lijun Zhan, Alissa Resch, Justen Andrews, S Celniker, Peter Cherbas, Teresa M. Przytycka, Maurizio Gatti, Brian Oliver, Brenton R. Graveley, David M. MacAlpine
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2019.00770

Maternal Smoking During Pregnancy Induces Persistent Epigenetic Changes Into Adolescence, Independent of Postnatal Smoke Exposure and Is Associated With Cardiometabolic Risk
Cited by: 65
Author(s): Sebastian Rauschert, Phillip E. Melton, Graham C. Burdge, Jeffrey M. Craig, Keith M. Godfrey, Joanna D. Holbrook, Karen A. Lillycrop, Trevor A. Mori, Lawrence J. Beilin, Wendy H. Oddy, Craig E. Pennell, Rae‐Chi Huang
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pmed.1003229

Maternal dysglycaemia, changes in the infant’s epigenome modified with a diet and physical activity intervention in pregnancy: Secondary analysis of a randomised control trial
Cited by: 52
Author(s): Elie Antoun, Negusse Tadesse Kitaba, Philip Titcombe, Kathryn V. Dalrymple, Emma Garratt, Sheila J. Barton, Robert Murray, Paul Seed, Joanna D. Holbrook, Michael S. Kobor, David T.S. Lin, Julia L. MacIsaac, Graham C. Burdge, Sara L. White, Lucilla Poston, Keith M. Godfrey, Karen A. Lillycrop
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2105-16-S17-S10

SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data
Cited by: 3
Author(s): Chong Chu, Li X, Yufeng Wu
Software Mentions: 4
Published: about 9 years ago

10.3389/fbioe.2015.00028

G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods
Cited by: 8
Author(s): Andrea Manconi, Elias Manca, Marco Moscatelli, Matteo Gnocchi, Alessandro Orro, Giuliano Armano, Luciano Milanesi
Software Mentions: 4
Published: almost 10 years ago

10.1186/1756-8935-7-26

Protection of CpG islands against de novo DNA methylation during oogenesis is associated with the recognition site of E2f1 and E2f2
Cited by: 23
Author(s): Heba Saadeh, Reiner Schulz
Software Mentions: 4
Published: about 10 years ago

10.3390/ijms19010245

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review
Cited by: 106
Author(s): Arun Sudhagar, Gokhlesh Kumar, Mansour El-Matbouli
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.12081

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
Cited by: 141
Author(s): Álvaro Martínez Barrio, Sangeet Lamichhaney, Guangyi Fan, Nima Rafati, Mats E. Pettersson, He Zhang, Jacques Dainat, Diana Ekman, Marc P. Höppner, Patric Jern, Marcel Martin, Björn Nystedt, Xin Liu, Wenbin Chen, Xinming Liang, Chengcheng Shi, Yuanyuan Fu, Kailong Ma, Xiaowei Zhan, Chungang Feng, Ulla Gustafson, Carl-Johan Rubin, Markus Sällman Almén, Martina Blass, Michèle Casini, Arild Folkvord, Linda Laikre, Nils Ryman, Simon Ming‐Yuen Lee, Xun Xu, Leif Andersson
Software Mentions: 4
Published: over 8 years ago

10.3390/s20133726

Movable Platform-Based Topology Detection for a Geographic Routing Wireless Sensor Network
Cited by: 1
Author(s): Runzhi Li, Jian Wang, Jiongyi Chen
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.54462

The evolutionary history and genomics of European blackcap migration
Cited by: 39
Author(s): Kira E. Delmore, Juan Carlos Illera, Javier Pérez‐Tris, Gernot Segelbacher, Juan Sebastian Lugo Ramos, Gillian Durieux, Jun Ishigohoka, Miriam Liedvogel
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0221760

Population size estimation for quality control of ChIP-Seq datasets
Cited by: 4
Author(s): Semyon Kolmykov, Yury V. Kondrakhin, Ivan S. Yevshin, Ruslan N. Sharipov, Anna S. Ryabova, Fedor A. Kolpakov
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giaa007

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines
Cited by: 79
Author(s): Stephen J. Bush, Dona Foster, David W Eyre, Emily L. Clark, Nicola De Maio, Liam P. Shaw, Nicole Stoesser, Tim Peto, Derrick W. Crook, A Sarah Walker
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13040-017-0149-1

Genetically improved BarraCUDA
Cited by: 7
Author(s): William B. Langdon, Brian Y.H. Lam
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-020-03729-6

Theoretical characterisation of strand cross-correlation in ChIP-seq
Cited by: 2
Author(s): Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pcbi.1003246

dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
Cited by: 13
Author(s): Dongjun Chung, Dan Park, Kevin S. Myers, Jeffrey A. Grass, Patricia J. Kiley, Robert Landick, Sündüz Keleş
Software Mentions: 4
Published: about 11 years ago

10.7717/peerj-cs.357

Survey on graph embeddings and their applications to machine learning problems on graphs
Cited by: 48
Author(s): Ilya Makarov, Dmitrii Kiselev, Nikita Nikitinsky, Lovro Šubelj
Software Mentions: 4
Published: almost 4 years ago

10.1002/bit.26380

Metabolic modeling to identify engineering targets forKomagataella phaffii: The effect of biomass composition on gene target identification
Cited by: 13
Author(s): Ayca Cankorur-Cetinkaya, Duygu Dikicioglu, Stephen G. Oliver
Software Mentions: 4
Published: over 7 years ago

10.1099/mgen.0.000393

Evaluation of methods for detecting human reads in microbial sequencing datasets
Cited by: 10
Author(s): Stephen J. Bush, Thomas R. Connor, Tim Peto, Derrick W. Crook, A Sarah Walker
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-021-02289-z

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
Cited by: 55
Author(s): David B Bernstein, Snorre Sulheim, Eivind Almaas, Daniel Segrè
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13072-021-00386-8

Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing
Cited by: 20
Author(s): Bradley P. Balaton, Oriol Fornés, Wyeth W. Wasserman, Carolyn J. Brown
Software Mentions: 3
Published: almost 4 years ago

10.1002/ece3.2281

Examining variation in the leaf mass per area of dominant species across two contrasting tropical gradients in light of community assembly
Cited by: 24
Author(s): Margot Neyret, Lisa Patrick Bentley, Imma Oliveras, Beatriz Schwantes Marimon, Edmar Almeida de Oliveira, Fabio B. Passos, Rosa Castro Ccoscco, Josias dos Santos, Simone Matias Reis, Paulo S. Morandi, Gloria Rayme Paucar, A. Robles Caceres, Yolvi Valdez Tejeira, Yovana Yllanes Choque, Norma Salinas, Alexander Shenkin, Gregory P. Asner, Sandra Dı́az, Brian J. Enquist, Yadvinder Malhi
Software Mentions: 3
Published: over 8 years ago

10.1093/ajcn/nqaa193

Effect of maternal preconceptional and pregnancy micronutrient interventions on children’s DNA methylation: Findings from the EMPHASIS study
Cited by: 17
Author(s): Ayden Saffari, Smeeta Shrestha, Prachand Issarapu, Sara Sajjadi, Modupeh Betts, Sirazul A. Sahariah, Ashutosh Singh Tomar, Philip James, Akshay Dedaniya, Dilip Kumar Yadav, Kalyanaraman Kumaran, Andrew M. Prentice, Karen A. Lillycrop, Caroline Fall, Giriraj Ratan Chandak, Matt J. Silver
Software Mentions: 3
Published: about 4 years ago

10.3389/fbioe.2020.01008

Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery
Cited by: 39
Author(s): Marina Julio Pinheiro, Nemailla Bonturi, Isma Belouah, Everson Alves Miranda, Petri‐Jaan Lahtvee
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-016-1161-z

Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment
Cited by: 37
Author(s): Hong Pan, Joanna D. Holbrook, Neerja Karnani, Chee Keong Kwoh
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-018-4508-1

CoVaCS: a consensus variant calling system
Cited by: 22
Author(s): Matteo Chiara, Silvia Gioiosa, Giovanni Chillemi, Mattia D’Antonio, Tiziano Flati, Ernesto Picardi, Federico Zambelli, David S. Horner, Graziano Pesole, Tiziana Castrignanò
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-5805-z

Corrupted DNA-binding specificity and ectopic transcription underpin dominant neomorphic mutations in KLF/SP transcription factors
Cited by: 19
Author(s): Melissa Ilsley, Stephen Huang, Graham Magor, Michael J. Landsberg, Kevin R. Gillinder, Andrew C. Perkins
Software Mentions: 3
Published: over 5 years ago

10.1016/j.isci.2021.102722

Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning
Cited by: 8
Author(s): Xiangyu Li, Woonghee Kim, Kajetan Juszczak, Muhammad Arif, Yusuke Sato, Haruki Kume, Seishi Ogawa, Hasan Türkez, Jan Borén, Jens Nielsen, Mathias Uhlén, Cheng Cheng Zhang, Adil Mardinoğlu
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-15-S1-S10

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units
Cited by: 4
Author(s): Andrea Manconi, Alessandro Orro, Elias Manca, Giuliano Armano, Luciano Milanesi
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0065632

SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner
Cited by: 111
Author(s): Ruibang Luo, Thomas K. F. Wong, Jian-Qiao Zhu, Chi-Man Liu, Xinhua Zhu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Shaoliang Peng, Chang Yu, Yingrui Li, Ruiqiang Li, Tak Wah Lam
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0243332

Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data
Cited by: 0
Author(s): Ruslan N. Sharipov, Yury V. Kondrakhin, Anna S. Ryabova, Ivan S. Yevshin, Fedor A. Kolpakov
Software Mentions: 3
Published: about 4 years ago

10.26508/lsa.202000654

A dichotomy of gene regulatory associations during the activated B-cell to plasmablast transition
Cited by: 4
Author(s): Mario Cocco, Matthew A. Care, Amel Saadi, Muna Al-Maskari, Gina M. Doody, Reuben Tooze
Software Mentions: 3
Published: over 4 years ago

10.3390/s19183976

SAR and Optical Data Comparison for Detecting Co-Seismic Slip and Induced Phenomena during the 2018 Mw 7.5 Sulawesi Earthquake
Cited by: 9
Author(s): Marco Polcari, Cristiano Tolomei, Christian Bignami, Salvatore Stramondo
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-3006-6

Genome-wide recruitment profiling of transcription factor Crz1 in response to high pH stress
Cited by: 24
Author(s): Alicia Roque, Silvia Petrezsélyová, Albert Serra-Cardona, Joaquı́n Ariño
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0122011

The Transcriptome of Equine Peripheral Blood Mononuclear Cells
Cited by: 17
Author(s): Alicja Pacholewska, Michaela Drögemüller, Jolanta Klukowska‐Rötzler, Simone Lanz, Eman Hamza, Emmanouil T. Dermitzakis, Eliane Marti, V. Gerber, Tosso Leeb, Vidhya Jagannathan
Software Mentions: 3
Published: almost 10 years ago

10.1101/2021.08.13.21261910

Gene-environment interaction analysis incorporating sex, cardiometabolic diseases, and multiple deprivation index reveals novel genetic associations with COVID-19 severity
Cited by: 0
Author(s): Kenneth Westerman, Joanna Lin, Magda Sevilla-Gonzalez, Beza Tadess, Alisa K. Manning, Casey Marchek
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-016-3404-9

ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data
Cited by: 25
Author(s): Bernardo Rodríguez-Martín, Emilio Palumbo, Santiago Marco-Sola, Thasso Griebel, Paolo Ribeca, Graciela Alonso, Alberto Rastrojo, Begoña Aguado, Roderic Guigó, Sarah Djebali
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0086869

CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
Cited by: 46
Author(s): Yong-Chao Liu, Bernt Popp, Bertil Schmidt
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0104567

Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants
Cited by: 30
Author(s): Liliana Greger, Jing Su, Johan Rung, Pedro G. Ferreira, Tuuli Lappalainen, Emmanouil T. Dermitzakis, Alvis Brāzma
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1007071

Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease
Cited by: 20
Author(s): Christopher A. Odhams, Deborah S. Cunninghame Graham, Timothy J. Vyse
Software Mentions: 3
Published: about 7 years ago

10.1186/s13059-019-1863-4

Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data
Cited by: 72
Author(s): Fenglin Liu, Yuanyuan Zhang, Lei Zhang, Ziyi Li, Fang Qiao, Ranran Gao
Software Mentions: 3
Published: about 5 years ago

10.1186/1752-0509-7-102

Antibacterial mechanisms identified through structural systems pharmacology
Cited by: 23
Author(s): Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson
Software Mentions: 3
Published: about 11 years ago

10.1186/1752-0509-8-79

A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database
Cited by: 42
Author(s): Daniel Weaver, Ingrid M. Keseler, Amanda Mackie, Ian T. Paulsen, Peter D. Karp
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pcbi.1006541

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
Cited by: 208
Author(s): Hao Wang, Simonas Marcišauskas, Benjamín J. Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Ågren, Jens Nielsen, Eduard J. Kerkhoven
Software Mentions: 3
Published: about 6 years ago

10.1186/s12918-016-0271-6

Systems biology of the structural proteome
Cited by: 47
Author(s): Elizabeth Brunk, Nathan Mih, Jonathan M. Monk, Zhen Zhang, Edward J. O’Brien, Spencer Bliven, Ke Chen, Roger L. Chang, Philip E. Bourne, Bernhard Ø. Palsson
Software Mentions: 3
Published: almost 9 years ago

10.3389/fphys.2015.00413

Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine
Cited by: 96
Author(s): Cheng Cheng Zhang, Qiang Hua
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13059-017-1269-0

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics
Cited by: 128
Author(s): Joshua D. Welch, Alexander J. Hartemink, Jan F. Prins
Software Mentions: 3
Published: over 7 years ago

10.1186/s13007-019-0489-6

EnRoot: a narrow-diameter, inexpensive and partially 3D-printable minirhizotron for imaging fine root production
Cited by: 15
Author(s): Marie Arnaud, Andy J. Baird, Paul J. Morris, Angela Harris, Jonny Huck
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1003501

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
Cited by: 75
Author(s): Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2018.02559

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient
Cited by: 33
Author(s): Xin Fang, Jonathan M. Monk, Sergey Nurk, Margarita Akseshina, Quanyin Zhu, Christopher Gemmell, Connor Gianetto-Hill, Nelly Leung, Richard Szubin, Jon G. Sanders, Paul L. Beck, Weizhong Li, William J. Sandborn, Scott D. Gray-Owen, Rob Knight, Emma Allen‐Vercoe, Bernhard Ø. Palsson, Larry Smarr
Software Mentions: 3
Published: about 6 years ago

10.3390/biom11040490

Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines
Cited by: 9
Author(s): Ewelina Węglarz-Tomczak, Thierry D.G.A. Mondeel, Diewertje G. E. Piebes, Hans V. Westerhoff
Software Mentions: 3
Published: over 3 years ago

10.3389/fninf.2015.00030

The GAAIN Entity Mapper: An Active-Learning System for Medical Data Mapping
Cited by: 4
Author(s): Naveen Ashish, Peehoo Dewan, Arthur W. Toga
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0148321

ePIANNO: ePIgenomics ANNOtation tool
Cited by: 4
Author(s): Chia-Hsin Liu, Bing-Ching Ho, Chun Ling Chen, Yun‐chien Chang, Yi Chiung Hsu, Yu Cheng Li, Shin Sheng Yuan, Yi Huan Huang, Chi Chen Chang, Ker Chau Li, Hsuan Yu Chen
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2105-16-S7-S10

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)
Cited by: 14
Author(s): Ruibang Luo, Jeanno Cheung, Edward Wu, Heng Wang, S. C. Chan, Wai-Chun Law, Guangzhu He, Chang Yu, Chi-Man Liu, Dazong Zhou, Yingrui Li, Ruiqiang Li, Jun Wang, Xinhua Zhu, Shaoliang Peng, Tak Wah Lam
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2016.00024

Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells
Cited by: 98
Author(s): Valentina Boeva
Software Mentions: 3
Published: almost 9 years ago

10.3389/fonc.2021.736113

Efficacy and Safety of First-Line Chemotherapies for Patients With Advanced Biliary Tract Carcinoma: A Systematic Review and Network Meta-Analysis
Cited by: 5
Author(s): Yanfeng Jiang, Zhiming Zeng, Jie Zeng, Cuizhen Liu, Jinfeng Qiu, Ye Li, Jing Tang, Ning Mo, Lili Du, Jie Ma
Software Mentions: 3
Published: about 3 years ago

10.3390/ijerph17186616

What Role Can Process Mining Play in Recurrent Clinical Guidelines Issues? A Position Paper
Cited by: 12
Author(s): Roberto Gatta, Mauro Vallati, Carlos Fernández-Llatas, Antonio Martínez-Millana, Stefania Orini, Lucia Sacchi, Jacopo Lenkowicz, Mar Marcos, Jorge Muñoz-Gama, Michel A. Cuendet, Berardino De Bari, Luis Marco-Ruiz, Alessandro Stefanini, Zoe Valero-Ramón, Olivier Michielin, Tomas Lapinskas, Antanas Montvila, Niels Martin, Erica Tavazzi, Maurizio Castellano
Software Mentions: 3
Published: over 4 years ago

10.1186/1472-6947-12-128

A study of diverse clinical decision support rule authoring environments and requirements for integration
Cited by: 18
Author(s): Li Zhou, Neelima Karipineni, Janet Lewis, Saverio M. Maviglia, Amanda Fairbanks, Tonya Hongsermeier, Blackford Middleton, Roberto A. Rocha
Software Mentions: 2
Published: about 12 years ago

10.1186/s12859-021-04097-5

A flexible ChIP-sequencing simulation toolkit
Cited by: 4
Author(s): An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren, Melissa Gymrek
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-018-2094-5

Fast and efficient short read mapping based on a succinct hash index
Cited by: 16
Author(s): Haowen Zhang, Yuandong Chan, Kaichao Fan, Bertil Schmidt, Weiguo Liu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13072-017-0165-x

Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning
Cited by: 17
Author(s): Gabriel Gutiérrez, Gonzalo Millán-Zambrano, Daniel A. Medina, Antonio Jordán-Pla, Jose E. Pérez-Ortı́n, Xenia Peñate, Sebastián Chávez
Software Mentions: 2
Published: about 7 years ago

10.1186/s12859-016-0957-1

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection
Cited by: 4
Author(s): Qi Zhang, Xin Zeng, Samuel G. Younkin, Trupti Kawli, M Snyder, Sündüz Keleş
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2164-15-633

Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
Cited by: 4
Author(s): Verónica Lloréns‐Rico, Luís Serrano, María Lluch‐Senar
Software Mentions: 2
Published: over 10 years ago

10.1186/s12859-019-2849-7

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets
Cited by: 76
Author(s): Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres, Philipp Rescheneder
Software Mentions: 2
Published: over 5 years ago

Projects: bioconductor: GEM

Papers Mentioning GEM 317