cran: SAM | Projects | Ecosyste.ms: Papers

10.1007/s10577-020-09643-0

CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites
Cited by: 4
Author(s): Michi Miura, Honglin Chen
Software Mentions: 4
Published: about 4 years ago

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification
Cited by: 9
Author(s): Lőrinc Sándor Pongor, Roberto Vera, Balázs Ligeti
Software Mentions: 4
Published: over 10 years ago

10.7717/peerj.5551

BioWorkbench: a high-performance framework for managing and analyzing bioinformatics experiments
Cited by: 11
Author(s): Maria Luiza Mondelli, Thiago Tavares Magalhães, Guilherme Loss, Michael Wilde, Ian Foster, Marta Mattoso, Daniel S. Katz, Hélio J. C. Barbosa, Ana Tereza Ribeiro de Vasconcelos, Kary Ocaña, Luiz M. R. Gadelha
Software Mentions: 4
Published: about 6 years ago

10.15252/embj.2018100003

A common molecular logic determines embryonic stem cell self‐renewal and reprogramming
Cited by: 31
Author(s): Sara‐Jane Dunn, Meng Amy Li, Elena Carbognin, Austin Smith, Graziano Martello
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0181463

DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing
Cited by: 49
Author(s): Byunghan Lee, Taesup Moon, Sungroh Yoon, Tsachy Weissman
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0033575

Genetic Dissection of Acute Ethanol Responsive Gene Networks in Prefrontal Cortex: Functional and Mechanistic Implications
Cited by: 78
Author(s): Aaron R. Wolen, Charles Phillips, Michael A. Langston, Alex H. Putman, Paul J. Vorster, Nathan A. Bruce, Timothy P. York, Robert W. Williams, Michael F. Miles
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0110134

Integrated Exon Level Expression Analysis of Driver Genes Explain Their Role in Colorectal Cancer
Cited by: 20
Author(s): Mohammad Azhar Aziz, Sathish Periyasamy, Zeyad Yousef, Ibrahim AlAbdulkarim, Majed Al Otaibi, Abdulaziz Alfahed, Glowi Alasiri
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2229-14-169

RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications
Cited by: 190
Author(s): Lei Wang, Chenlong Cao, Qibin Ma, Qiaoying Zeng, Haifeng Wang, Zhihao Cheng, Genfeng Zhu, Ji Qi, Hong Mā, Hai Nian, Yingxiang Wang
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0001344

Adipose Gene Expression Prior to Weight Loss Can Differentiate and Weakly Predict Dietary Responders
Cited by: 48
Author(s): David M. Mutch, Ramzi Temanni, Corneliu Hénégar, Florence Combes, Véronique Pelloux, Claus Holst, Thorkild I A Sørensen, Arne Astrup, J. Alfredo Martínez, Wim H. M. Saris, Nathalie Viguerie, Dominique Langin, Jean-Daniel Zucker, Karine Clément
Software Mentions: 4
Published: almost 17 years ago

10.1371/journal.pone.0166721

A Genetic Algorithm for Diploid Genome Reconstruction Using Paired-End Sequencing
Cited by: 3
Author(s): Chuan-Kang Ting, Chun-Shin Lin, Ming-Tsai Chan, Jeremy J.W. Chen, Sheng-Yu Chuang, Yao‐Ting Huang
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0215465

FDG PET based prediction of response in head and neck cancer treatment: Assessment of new quantitative imaging features
Cited by: 18
Author(s): Reinhard Beichel, Ethan Ulrich, Brian J. Smith, Christian Bauer, Bruce P. Brown, Thomas L. Casavant, John Sunderland, Michael M. Graham, John M. Buatti
Software Mentions: 4
Published: over 5 years ago

10.3390/cells8121566

Stromal Cell Signature Associated with Response to Neoadjuvant Chemotherapy in Locally Advanced Breast Cancer
Cited by: 20
Author(s): Maria Lúcia Hirata Katayama, René Aloísio da Costa Vieira, Victor Piana de Andrade, Rosimeire Aparecida Roela, Luciana Lima, Lígia Maria Kerr, Adriano Polpo de Campos, Carlos Alberto Pereira, Pedro Adolpho de Menezes Pacheco Serio, Giselly Encinas, Simone Maistro, Matheus de Almeida Leite Petroni, Maria Mitzi Brentani, Maria Aparecida Azevedo Koike Folgueira
Software Mentions: 4
Published: almost 5 years ago

10.1186/1752-0509-4-121

Gene set analysis exploiting the topology of a pathway
Cited by: 62
Author(s): M. Sofia Massa, Monica Chiogna, Chiara Romualdi
Software Mentions: 4
Published: about 14 years ago

10.1186/1753-6561-3-S4-S9

Microarray data mining using Bioconductor packages
Cited by: 8
Author(s): Haisheng Nie, Pieter Neerincx, Jan van der Poel, Francesco Ferrari, Silvio Bicciato, Jack A. M. Leunissen, Martien A. M. Groenen
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pone.0240474

Were domestic camelids present on the prehispanic South American agricultural frontier? An ancient DNA study
Cited by: 7
Author(s): Cinthia Carolina Abbona, Gustavo Adolfo, Jeff Johnson, Tracy Kim, Adolfo Gil, Steve Wolverton
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0023581

Strategy to Find Molecular Signatures in a Small Series of Rare Cancers: Validation for Radiation-Induced Breast and Thyroid Tumors
Cited by: 16
Author(s): Nicolas Ugolin, Catherine Ory, Emilie Lefèvre, Nora Benhabilès, Paul Hofman, Martin Schlumberger, Sylvie Chevillard
Software Mentions: 4
Published: over 13 years ago

10.1099/mgen.0.000039

Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case
Cited by: 9
Author(s): Steven T. Pullan, Talima Pearson, Jennie Latham, Joanne Mason, Barry Atkinson, Nigel Silman, Chung K. Marston, Jason W. Sahl, Dawn N. Birdsell, Alex R. Hoffmaster, Paul Keim, Richard Vipond
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0255952

Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study design
Cited by: 1
Author(s): Aslı Devrim-Lanpir, Havvanur Yoldaş İlktaç, Katharina Wirnitzer, Lee Hill, Thomas Rosemann, Beat Knechtle
Software Mentions: 4
Published: about 3 years ago

10.7717/peerj.7156

Spread of the non-native anemone Anemonia alicemartinae Häussermann & Försterra, 2001 along the Humboldt-current large marine ecosystem: an ecological niche model approach
Cited by: 7
Author(s): Javier Pinochet, Reinaldo Rivera, Paula E. Neill, Antonio Brante, Cristián E. Hernández
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22041837

Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer
Cited by: 5
Author(s): Diamanto Skopelitou, Benchun Miao, Aayushi Srivastava, Abhishek Kumar, Magdalena Kuswick, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.830

The effect of listening to music on human transcriptome
Cited by: 32
Author(s): Chakravarthi Kanduri, Pirre Raijas, Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 3
Published: over 9 years ago

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: about 13 years ago

10.1016/j.dib.2020.105297

Transcriptomic data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S treated with novobiocin
Cited by: 4
Author(s): Natalia Gogoleva, Tatiana A. Konnova, Alexander S. Balkin, А. О. Плотников, Alexander A. Kamnev
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.8275

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
Cited by: 9
Author(s): Daniel Liu
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms22179246

Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus
Cited by: 8
Author(s): Nesma Shalby, Ibrahim A. A. Mohamed, Jie Xiong, Kaining Hu, Yuting Yang, Elsayed Nishawy, Bin Yi, Jing Wen, Chaozhi Ma, Tingdong Fu, Jinxing Tu
Software Mentions: 3
Published: about 3 years ago

10.1093/dnares/dst017

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data
Cited by: 69
Author(s): Hideki Nagasaki, Takako Mochizuki, Yuichi Kodama, Satoshi Saruhashi, Shota Morizaki, Hideaki Sugawara, Hajime Ohyanagi, Nori Kurata, Kousaku Okubo, Toshihisa Takagi, Eli Kaminuma, Yasukazu Nakamura
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0239627

Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel
Cited by: 5
Author(s): Gabriel Schneebauer, Constantin Lindemann, Victoria Drechsel, Lasse Marohn, Klaus Wysujack, Elena Santidrian, Ron P. Dirks, Reinhold Hanel, Bernd Pelster
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0238907

A new advanced in silico drug discovery method for novel coronavirus (SARS-CoV-2) with tensor decomposition-based unsupervised feature extraction
Cited by: 33
Author(s): Y-h. Taguchi, Turki Turki
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0201851

Small RNAs detected in exosomes derived from the MH7A synovial fibroblast cell line with TNF-α stimulation
Cited by: 19
Author(s): Yosuke Takamura, Wataru Aoki, Atsushi Satomura, Seiji Shibasaki
Software Mentions: 3
Published: over 6 years ago

10.3390/metabo11090627

Comparative Untargeted Metabolomic Profiling of Induced Mitochondrial Fusion in Pancreatic Cancer
Cited by: 0
Author(s): Nathalie Nguyen, Meifang Yu, Vinit Y. Reddy, Ariana Carolina Acevedo-Diaz, Enzo C. Mesarick, Joseph Abi Jaoude, Min Yuan, John M. Asara, Cullen M. Taniguchi
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-019-43141-6

CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement
Cited by: 62
Author(s): Joshua K. Young, Gina Zastrow-Hayes, Stéphane Deschamps, Sergei Svitashev, Mindaugas Zaremba, Ananta Acharya, Sushmitha Paulraj, Brooke D. Peterson-Burch, Chris Schwartz, Vesna Djukanovic, Brian Lenderts, Lanie Feigenbutz, Limin Wang, Clara M. Alarcon, Virginijus Šikšnys, Gregory D. May, N. Doane Chilcoat, Sandeep Kumar
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-017-04786-3

sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Cited by: 25
Author(s): Julie Bronsard, Gaëtan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2016.01528

Invasive Shrub Mapping in an Urban Environment from Hyperspectral and LiDAR-Derived Attributes
Cited by: 29
Author(s): Curtis M. Chance, Nicholas C. Coops, Andrew Plowright, Thoreau Rory Tooke, Andreas Christen, Neal W. Aven
Software Mentions: 3
Published: about 8 years ago

10.3389/fphar.2019.01690

SAMbinder: A Web Server for Predicting S-Adenosyl-L-Methionine Binding Residues of a Protein From Its Amino Acid Sequence
Cited by: 3
Author(s): Piyush Agrawal, Gaurav Mishra, Gajendra P. S. Raghava
Software Mentions: 3
Published: almost 5 years ago

10.1111/tpj.12307

Resistance gene enrichment sequencing (<scp>R</scp>en<scp>S</scp>eq) enables reannotation of the <scp>NB</scp>‐<scp>LRR</scp> gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Cited by: 327
Author(s): Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga Śliwka, Leighton Pritchard, Graham J. Etherington, Dan MacLean, Peter J. A. Cock, Richard M. Leggett, Glenn J. Bryan, Linda Cardle, Ingo Hein, Jonathan D. G. Jones
Software Mentions: 3
Published: about 11 years ago

10.1002/prot.25697

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
Cited by: 142
Author(s): Jie Hou, Tai Tsun Wu, Renzhi Cao, Jianlin Cheng
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.ppat.1009175

Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response
Cited by: 5
Author(s): Qi Wang, Nadia Shakoor, Adam Boyher, Kira M. Veley, Jeffrey C. Berry, Todd C. Mockler, Rebecca Bart
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-23641-7

Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol
Cited by: 43
Author(s): Joseph A. Russell, Brittany Campos, Jennifer Stone, Erik M. Blosser, Nathan D. Burkett‐Cadena, Jonathan L. Jacobs
Software Mentions: 3
Published: over 6 years ago

10.1111/tpj.14468

An ‘ <scp>eFP</scp> ‐Seq Browser’ for visualizing and exploring <scp>RNA</scp> sequencing data
Cited by: 31
Author(s): Alexander Sullivan, Priyank Purohit, Nowlan H. Freese, Asher Pasha, Eddi Esteban, Jamie Waese, Alison Wu, Michelle Chen, Chih Ying Chin, Richard Song, Sneha Ramesh Watharkar, Agnes P. Chan, Vivek Krishnakumar, Matthew Vaughn, Chris Town, Ann E. Loraine, Nicholas J. Provart
Software Mentions: 3
Published: about 5 years ago

10.1093/jxb/erx349

Transfer of a starch phenotype from wild wheat to bread wheat by deletion of a locus controlling B-type starch granule content
Cited by: 21
Author(s): Tansy Chia, Nikolai M Adamski, Benedetta Saccomanno, Andrew J. Greenland, Alastair Nash, Cristóbal Uauy, Kay Trafford
Software Mentions: 3
Published: about 7 years ago

10.3389/fpsyt.2021.685656

Metabolic Profiling Indicates Diversity in the Metabolic Physiologies Associated With Maternal Postpartum Depressive Symptoms
Cited by: 4
Author(s): Emma Bränn, Christina J. Malavaki, Emma Fransson, Maria-Konstantina Ioannidi, Hanna Henriksson, Fotios C. Papadopoulos, George P. Chrousos, Maria I. Klapa, Alkistis Skalkidou
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1005096

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework
Cited by: 10
Author(s): Qi Zheng, Elizabeth A. Grice
Software Mentions: 3
Published: about 8 years ago

10.1186/1472-6807-11-16

Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: Possible misannotation of this tubercle bacilli-hemolysin
Cited by: 27
Author(s): Nelson E. Arenas, Luz Mary Salazar, Carlos Y. Soto, Carolina Vizcaíno, Manuel Elkín Patarroyo, Arley Gómez
Software Mentions: 3
Published: over 13 years ago

10.1029/2020MS002138

Clouds and Convective Self‐Aggregation in a Multimodel Ensemble of Radiative‐Convective Equilibrium Simulations
Cited by: 69
Author(s): Allison A. Wing, Catherine L. Stauffer, Tobias Becker, Kevin A. Reed, Min‐Seop Ahn, Nathan Arnold, Sandrine Bony, Mark Branson, G. H. Bryan, Jean‐Pierre Chaboureau, Stephan R. de Roode, Gayatri Kulkarni, Cathy Hohenegger, I‐Kuan Hu, Fredrik Jansson, Todd R. Jones, Marat Khairoutdinov, Dae Hyun Kim, Zane Martin, Shuhei Matsugishi, Brian Medeiros, Hiroaki Miura, Yumin Moon, Sebastian K. Müller, Tomoki Ohno, Max Popp, Thara Prabhakaran, David A. Randall, Rosimar Ríos-Berríos, Nicolas Rochetin, Romain Roehrig, David M. Romps, James H. Ruppert, Masaki Satoh, Levi G. Silvers, Martin S. Singh, Björn Stevens, Lorenzo Tomassini, Chiel C. van Heerwaarden, Shuguang Wang, Ming Zhao
Software Mentions: 3
Published: about 4 years ago

10.1007/s13361-016-1544-4

Prognostic Metabolite Biomarkers for Soft Tissue Sarcomas Discovered by Mass Spectrometry Imaging
Cited by: 37
Author(s): Sha Lou, Benjamin Balluff, Arjen H.G. Cleven, Judith V.M.G. Bovée, Liam A. McDonnell
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pcbi.1007543

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
Cited by: 6
Author(s): Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Mitchell D. Probasco, Ning Leng, Bret Duffin, John Steill, Scott Swanson, Brian E. McIntosh, Ron Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher
Software Mentions: 3
Published: almost 5 years ago

10.26508/lsa.201800082

Mitochondrial ubiquinone–mediated longevity is marked by reduced cytoplasmic mRNA translation
Cited by: 12
Author(s): Marte Molenaars, Georges E. Janssens, Toon Santermans, Marco Lezzerini, Rob Jelier, Alyson W. MacInnes, Riekelt H. Houtkooper
Software Mentions: 3
Published: about 6 years ago

10.1120/jacmp.v17i3.6370

2016 AAPM Spring Clinical Meeting - Abstracts
Cited by: 0
Author(s):
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.ppat.1005943

Cathelicidin Insufficiency in Patients with Fatal Leptospirosis
Cited by: 21
Author(s): Janet C. Lindow, Elsio A. Wunder, Stephen J. Popper, Jinsoo Min, Praveen Mannam, Anup Srivastava, Yi Yao, Kathryn P. Hacker, Khadir Raddassi, Patty J Lee, Ruth R. Montgomery, Albert C. Shaw, José E. Hagan, Guilherme C. Araújo, Nívison Nery, David A. Relman, Charles C. Kim, Mitermayer Galvão dos Reis, Albert I. Ko
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-017-02329-4

Expression Profiling of mRNAs and Long Non-Coding RNAs in Aged Mouse Olfactory Bulb
Cited by: 11
Author(s): Ming Wang, Wei Liu, Jian Jiao, Jingyun Li, Chengshuo Wang, Luo Zhang
Software Mentions: 3
Published: over 7 years ago

10.1029/2019RG000686

Spaceborne Cloud and Precipitation Radars: Status, Challenges, and Ways Forward
Cited by: 65
Author(s): Alessandro Battaglia, Pavlos Kollias, Ranvir Dhillon, Richard Roy, Simone Tanelli, Katia Lamer, Mircea Grecu, Matthew Lebsock, Daniel Watters, Kamil Mróz, Gerald M. Heymsfield, Lihua Li, Katsuko Furukawa
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.ppat.1006510

Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
Cited by: 50
Author(s): Gustavo H. Kijak, Eric Sanders‐Buell, Agnès‐Laurence Chenine, Michael A. Eller, Nilu Goonetilleke, Rasmi Thomas, Sivan Leviyang, Elizabeth A. Harbolick, Meera Bose, Phuc Pham, Celina Oropeza, Kultida Poltavee, Anne Marie O’Sullivan, Erik Billings, Mélanie Merbah, Margaret C. Costanzo, Joanna Warren, Bonnie M. Slike, Hui Li, Kristina K. Peachman, Will Fischer, Feng Gao, Claudia Cicala, James Arthos, Leigh Anne Eller, Robert J. O’Connell, Samuel Sinei, Lucas Maganga, Hannah Kibuuka, Sorachai Nitayaphan, Mangala Rao, Mary Marovich, Shelly J. Krebs, Morgane Rolland, Bette T. Korber, George M. Shaw, Nelson L. Michael, Merlin L. Robb, Sodsai Tovanabutra, Jerome H. Kim
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2019.01624

Gene Expression Profiling of the Shoot Meristematic Tissues in Woodland Strawberry Fragaria vesca
Cited by: 8
Author(s): Yongping Li, Jia Feng, Laichao Cheng, Cheng Dai, Qi Gao, Zhongchi Liu, Chunying Kang
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pbio.1000238

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
Cited by: 376
Author(s): David G. Hendrickson, Daniel J. Hogan, Heather McCullough, Jason W. Myers, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: about 15 years ago

10.3389/fpls.2016.01020

Low Temperature and Short-Term High-CO2 Treatment in Postharvest Storage of Table Grapes at Two Maturity Stages: Effects on Transcriptome Profiling
Cited by: 30
Author(s): Raquel Rosales, Irene Romero, Carlos Fernández-Caballero, M. Isabel Escribano, Carmen Merodio, Marı́a T. Sanchez-Ballesta
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.ppat.1003341

Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
Cited by: 132
Author(s): Michael J. Strong, Guiyin Xu, Joseph Coco, Carl Baribault, Dass S. Vinay, Michelle Lacey, Amy L. Strong, Teresa A. Lehman, Michael Seddon, Zhen Lin, Monica Concha, Melody Baddoo, MaryBeth Ferris, Kenneth F. Swan, Deborah E. Sullivan, Matthew E. Burow, Christopher M. Taylor, Erik K. Flemington
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pbio.0050057

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs
Cited by: 501
Author(s): Kristin D. Kasschau, Noah Fahlgren, Elisabeth J. Chapman, Christopher Sullivan, Jason S. Cumbie, Scott A. Givan, James C. Carrington
Software Mentions: 3
Published: almost 18 years ago

10.3389/fpsyg.2020.00953

Global Image Properties Predict Ratings of Affective Pictures
Cited by: 17
Author(s): Christoph Redies, Maria Grebenkina, Mahdi Mohseni, Ali Kaduhm, Christian Dobel
Software Mentions: 3
Published: over 4 years ago

10.1073/pnas.1921055117

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in Arabidopsis
Cited by: 54
Author(s): Christophe Lambing, Pallas Kuo, Andrew J. Tock, Stephanie D. Topp, Ian Henderson
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-21484-w

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias
Cited by: 56
Author(s): Raga Krishnakumar, Anupama Sinha, Sara W. Bird, Harikrishnan Jayamohan, Harrison Edwards, Joseph S. Schoeniger, Kamlesh D. Patel, Steven S. Branda, Michael Bartsch
Software Mentions: 3
Published: almost 7 years ago

10.3389/fpls.2018.01962

Early Detection of Magnaporthe oryzae-Infected Barley Leaves and Lesion Visualization Based on Hyperspectral Imaging
Cited by: 23
Author(s): Ruiqing Zhou, Juanjuan Jin, Qing-Mian Li, Zhen-Zhu Su, Xinjie Yu, Yu Tang, Shaoming Luo, Yong He, Yuanyuan Liu
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0160168

New Cell Adhesion Molecules in Human Ischemic Cardiomyopathy. PCDHGA3 Implications in Decreased Stroke Volume and Ventricular Dysfunction
Cited by: 14
Author(s): Ana Ortega, Carolina Gil-Cayuela, Estefanía Tarazón, María García‐Manzanares, José Montero, Juan Cinca, Manuel Portolés, Miguel Rivera, Esther Roselló‐Lletí
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.15604

NUSAP1 promotes invasion and metastasis of prostate cancer
Cited by: 49
Author(s): Catherine A. Gordon, Xue Gong, Durga Ganesh, James D. Brooks
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-31064-7

Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis
Cited by: 33
Author(s): Johnny A. Sena, Giulia Galotto, Nico Devitt, Melanie C. Connick, Jennifer L. Jacobi, Pooja Umale, Luis Vidali, Callum J. Bell
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-51645-4

Predicting low-concentration effects of pesticides
Cited by: 17
Author(s): Matthias Liess, Sebastian Henz, Saskia Knillmann
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-017-14418-5

Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis
Cited by: 10
Author(s): Emiko Yoshida, Yasuhisa Terao, Noriko Hayashi, Kaoru Mogushi, Atsushi Arakawa, Yuji Tanaka, Yoshiaki Ito, Hiroko Ohmiya, Yoshihide Hayashizaki, Satoru Takeda, Masayoshi Itoh, Hideya Kawaji
Software Mentions: 3
Published: about 7 years ago

10.1186/2049-3002-2-13

Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Cited by: 27
Author(s): Debarshi Roy, Susmita Mondal, Chen Wang, Xiaoping He, Ashwani Khurana, Shailendra Giri, Robert Hoffmann, Deok‐Beom Jung, Sung Hyun Kim, Eduardo N. Chini, Juliana Camacho Periera, Clifford D.L. Folmes, Andrea Mariani, Sean C. Dowdy, Jamie N. Bakkum-Gamez, Shaun M. Riska, Ann L. Oberg, Edward D. Karoly, Lauren N. Bell, Jeremy Chien, Viji Shridhar
Software Mentions: 3
Published: over 10 years ago

10.1186/1746-4811-8-12

Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis
Cited by: 18
Author(s): Kun-Hsiang Liu, Matthew McCormack, Jenq-Yunn Sheen
Software Mentions: 3
Published: almost 13 years ago

10.1186/s13007-020-00588-3

In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing
Cited by: 2
Author(s): Narinder Singh, John Raupp, Dal‐Hoe Koo, Bernd Friebe, Bikram S. Gill, Jesse Poland
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-41625-z

Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data
Cited by: 12
Author(s): Lázaro Betancourt, Krzysztof Pawłowski, Jonatan Eriksson, Attila Marcell Szász, Shamik Mitra, Indira Pla, Charlotte Welinder, Henrik Ekedahl, Per Broberg, Roger Appelqvist, Maria Yakovleva, Y. Sugita, Kenichi Miharada, Christian Ingvar, Lotta Lundgren, Bo Baldetorp, Håkan Olsson, Melinda Rezeli, Elisabet Wieslander, Péter Horvatovich, Johan Malm, Göran Jönsson, György Markó-Varga
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: over 5 years ago

10.1093/jxb/erx010

Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation
Cited by: 48
Author(s): Lekha T. Pazhamala, Shilp Purohit, Rachit K. Saxena, Vanika Garg, L. Krishnamurthy, Jérôme Verdier, Rajeev K. Varshney
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-52395-z

Environmental and ecological factors mediate taxonomic composition and body size of polyplacophoran assemblages along the Peruvian Province
Cited by: 6
Author(s): Christian M. Ibáñez, Melany Waldisperg, Felipe I. Torres, Sergio A. Carrasco, Javier Sellanes, M. Cecilia Pardo‐Gandarillas, Julia D. Sigwart
Software Mentions: 3
Published: about 5 years ago

10.1002/ece3.2213

Is individual consistency in body mass and reproductive decisions linked to individual specialization in foraging behavior in a long‐lived seabird?
Cited by: 13
Author(s): Nina Dehnhard, Marcel Eens, Nicolas Sturaro, Gilles Lepoint, Laurent Demongin, Petra Quillfeldt, Maud Poisbleau
Software Mentions: 3
Published: over 8 years ago

10.1002/ece3.498

New-old hemoglobin-like proteins of symbiotic dinoflagellates
Cited by: 11
Author(s): Nedeljka Rosic, William Leggat, Paulina Kaniewska, Sophie Dove, Ove Hoegh‐Guldberg
Software Mentions: 3
Published: over 11 years ago

10.1111/pbi.12685

Indel‐seq: a fast‐forward genetics approach for identification of trait‐associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan)
Cited by: 57
Author(s): Vikas K. Singh, Aamir W. Khan, Rachit K. Saxena, Pallavi Sinha, Sandip M. Kale, Swathi Parupalli, Vinay Kumar, Annapurna Chitikineni, Suryanarayana Vechalapu, C.V. Sameer Kumar, Mamta Sharma, G. Anuradha, K.N. Yamini, S. Muniswamy, Rajeev K. Varshney
Software Mentions: 3
Published: almost 8 years ago

10.1002/ece3.4504

Methylation divergence of invasiveCionaascidians: Significant population structure and local environmental influence
Cited by: 17
Author(s): Ping Ni, Shiguo Li, Ya‐Ping Lin, Wei Xiong, Xuena Huang, Aibin Zhan
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-53901-z

Blood transcriptome analysis in a buck-ewe hybrid and its parents
Cited by: 1
Author(s): Clemens Falker‐Gieske, C. Knorr, Jens Tetens
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-59541-y

Chronic circadian misalignment accelerates immune senescence and abbreviates lifespan in mice
Cited by: 78
Author(s): Hitoshi Inokawa, Yasuhiro Umemura, Akihiro Shimba, Eiryo Kawakami, Nobuya Koike, Yoshiki Tsuchiya, Masaru Ohashi, Yoichi Minami, Guangwei Cui, T. Asahi, Ryutaro Ono, Yuh Sasawaki, Eiichi Konishi, Seung-Hee Yoo, Chen Zheng, Satoshi Teramukai, Koichi Ikuta, Kazuhiro Yagita
Software Mentions: 3
Published: almost 5 years ago

10.3758/s13421-020-01082-w

The simultaneous recognition of multiple words: A process analysis
Cited by: 4
Author(s): Anne Voormann, Mikhail S. Spektor, Karl Christoph Klauer
Software Mentions: 3
Published: over 3 years ago

10.1002/ece3.8075

High genetic and epigenetic variation of transposable elements: Potential drivers to rapid adaptive evolution for the noxious invasive weed Mikania micrantha
Cited by: 5
Author(s): Yingjuan Su, Qiqi Huang, Zhen Wang, Ting Wang
Software Mentions: 3
Published: about 3 years ago

10.1002/ece3.646

Environmental effects on molecular and phenotypic variation in populations ofEruca sativaacross a steep climatic gradient
Cited by: 31
Author(s): Erik Westberg, Shachar Ohali, Anatoly Shevelevich, Pinchas Fine, Oz Barazani
Software Mentions: 3
Published: over 11 years ago

10.3390/ijms17050696

Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction
Cited by: 31
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms20010016

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools
Cited by: 34
Author(s): Dana Pascovici, Jemma X. Wu, Matthew J. McKay, Chitra Joseph, Zainab Noor, Karthik Shantharam Kamath, Yunqi Wu, Shoba Ranganathan, Vivek Gupta, Mehdi Mirzaei
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-017-02824-8

High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor
Cited by: 8
Author(s): Masahito Yoshihara, Yuzuru Sasamoto, Ryuhei Hayashi, Yuki Ishikawa, Motokazu Tsujikawa, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji, Kohji Nishida
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms16035975

RNA-Seq Transcriptome Analysis of Maize Inbred Carrying Nicosulfuron-Tolerant and Nicosulfuron-Susceptible Alleles
Cited by: 26
Author(s): Xiaomin Liu, Xiaogang Xu, Binghua Li, Xueqing Wang, Guiqi Wang, Yaqian Li
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-31093-2

Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing
Cited by: 23
Author(s): David Jebb, Nicole M. Foley, Conor V. Whelan, Frédéric Touzalin, Sébastien J. Puechmaille, Emma C. Teeling
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-45898-2

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Cited by: 19
Author(s): Rajesh Kumar Gazara, Eduardo Alves Gamosa de Oliveira, B. Calderan Rodrigues, Rodrigo Nunes da Fonseca, Antônia Elenir Amâncio Oliveira, Thiago M. Venancio
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0132642

Spontaneous Deletion of an “ORFanage” Region Facilitates Host Adaptation in a “Photosynthetic” Cyanophage
Cited by: 12
Author(s): Richard John Puxty, Blanca Perez-Sepulveda, Branko Rihtman, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 3
Published: over 9 years ago

10.15252/emmm.202013901

Glycolysis downregulation is a hallmark of HIV‐1 latency and sensitizes infected cells to oxidative stress
Cited by: 23
Author(s): Iart Luca Shytaj, Francesco A. Procopio, Mohammad Tarek, Irene Carlón-Andrés, Hsin‐Yao Tang, Aaron R. Goldman, MohamedHusen Munshi, Virender Kumar Pal, Mattia Forcato, Sheetal Sreeram, Konstantin Leskov, Fengchun Ye, Bojana Lucic, Nicolly Cruz, Lishomwa C. Ndhlovu, Silvio Bicciato, Sergi Padilla‐Parra, Ricardo Sobhie Diaz, Amit Singh, Marina Lušić, Jonathan Karn, David Alvarez-Carbonell, Andrea Savarino
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22169081

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches
Cited by: 10
Author(s): Aljaž Gaber, Miha Pavšič
Software Mentions: 3
Published: about 3 years ago

10.7717/peerj.2105

Constant and seasonal drivers of bird communities in a wind farm: implications for conservation
Cited by: 7
Author(s): Zuzanna M. Rosin, Piotr Skórka, Paweł Szymański, Marcin Tobółka, Andrzej Łuczak, Piotr Tryjanowski
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms20235922

Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies
Cited by: 10
Author(s): Xiaoxiang Zhang, Juan Zhou, Niansheng Huang, Lanjing Mo, Minjia Lv, Yujiao Gao, Chen Chen, Yin Su, Jianhua Ju, Guichun Dong, Yong Zhou, Zefeng Yang, Aihong Li, Yulong Wang, Jianye Huang, Youli Yao
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13637-015-0034-5

Gene expression analysis supports tumor threshold over 2.0 cm for T-category breast cancer
Cited by: 2
Author(s): Hiroko Kato Solvang, Arnoldo Frigessi, Fatemeh Kaveh, Margit Riis, Torben Lüders, Ida Rashida Khan Bukholm, Vessela N. Kristensen, Bettina Kulle Andreassen
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.382

Characterisation of the horse transcriptome from immunologically active tissues
Cited by: 6
Author(s): Joanna Moreton, Sunir Malla, A. Aziz Aboobaker, Rachael Tarlinton, Richard D. Emes
Software Mentions: 3
Published: over 10 years ago

10.1186/1756-0500-1-80

Advanced spot quality analysis in two-colour microarray experiments
Cited by: 10
Author(s): Mikalai M. Yatskou, Eugene Novikov, Guillaume Vetter, Arnaud Muller, Emmanuel Barillot, Laurent Vallar, Evelyne Friederich
Software Mentions: 3
Published: almost 17 years ago

10.1186/1746-1596-9-142

NF-κB signaling and vesicle transport are correlated with the reactivation of the memory trace of morphine dependence
Cited by: 9
Author(s): Junyi Ye, Zhaoyang Yang, Candong Li, Meimei Cai, Daizhan Zhou, Qin Zhang, Wei Y, Ting Wang, Yun Liu
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0173094

Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response
Cited by: 6
Author(s): Alex Yi‐Lin Tsai, Kin Chan, Chi-Yip Ho, Thomas Canam, Resmi Capron, Emma R. Master, Katharina Bräutigam
Software Mentions: 3
Published: over 7 years ago

10.1016/j.dib.2021.107114

RNA-seq and miRNA-seq data from pharmacological inhibition of the G9a/GLP histone methyltransferase complex with UNC0642 in SAMP8 mice
Cited by: 1
Author(s): Shrikant Pawar, Aina Bellver-Sanchis, Christian Griñán-Ferré
Software Mentions: 3
Published: over 3 years ago

Projects: cran: SAM

Papers Mentioning SAM 4,566