cran: SAM | Projects | Ecosyste.ms: Papers

10.1111/jns.12228

Clinical and genetic diversities of Charcot-Marie-Tooth disease withMFN2mutations in a large case study
Cited by: 31
Author(s): Masahiro Ando, Akihiro Hashiguchi, Yuji Okamoto, Akinobu Yoshimura, Yoshihiro Hiramatsu, Jun‐Hui Yuan, Yujiro Higuchi, Jun Mitsui, Hiroyuki Ishiura, Atsushi Umemura, Koichi Maruyama, Takeshi Matsushige, Shinichi Morishita, Masanori Nakagawa, Shoji Tsuji, Hiroshi Takashima
Software Mentions: 2
Published: about 9 years ago

10.3390/jpm4020282

Differential Transcriptome Profile of Peripheral White Cells to Identify Biomarkers Involved in Oxaliplatin Induced Neuropathy
Cited by: 9
Author(s): Manuel Morales, Julio Ávila, Rebeca González-Fernández, Laia Boronat, M L Soriano, Pablo Martín‐Vasallo
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-213X-13-29

Stage-specific transcription during development of Aedes aegypti
Cited by: 19
Author(s): Brent W. Harker, Susanta K. Behura, Becky deBruyn, Diane D. Lovin, Akio Mori, Jeanne Romero‐Severson, David W. Severson
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2431-13-17

Optimising Ankle Foot Orthoses for children with Cerebral Palsy walking with excessive knee flexion to improve their mobility and participation; protocol of the AFO-CP study
Cited by: 14
Author(s): Yvette L. Kerkum, Jaap Harlaar, Annemieke I. Buizer, Josien C. van den Noort, Jules G. Becher, Merel-Anne Brehm
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2210-8-16

Pharmacokinetics and transcriptional effects of the anti-salmon lice drug emamectin benzoate in Atlantic salmon (Salmo salar L.)
Cited by: 23
Author(s): Pål A. Olsvik, Kai Kristoffer Lie, Eva Mykkeltvedt, Ole Bent Samuelsen, Kjell Petersen, Anne-Kristin Stavrum, Bjørn Tore Lunestad
Software Mentions: 2
Published: about 18 years ago

10.1186/s40360-020-00402-9

Prospects of Indole derivatives as methyl transfer inhibitors: antimicrobial resistance managers
Cited by: 4
Author(s): Suprim Tha, Sapana Shakya, Rajani Malla, Pramod Aryal
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-15-36

uPEPperoni: An online tool for upstream open reading frame location and analysis of transcript conservation
Cited by: 30
Author(s): Adam Skarshewski, Mitchell Stanton-Cook, Thomas Huber, S. Al Mansoori, Ross Smith, Scott A. Beatson, Joseph A. Rothnagel
Software Mentions: 2
Published: over 12 years ago

10.4172/jpb.1000384

Proteome Dynamics of the Specialist Oxalate Degrader Oxalobacter formigenes
Cited by: 13
Author(s): Mellissa L Ellis, James A. Mobley, Ross P. Holmes, John Knight
Software Mentions: 2
Published: over 10 years ago

10.4172/jpb.S9-001

Predicting Protein Model Quality from Sequence Alignments by Support Vector Machines
Cited by: 6
Author(s): Xin Deng, Jilong Li, Jianlin Cheng
Software Mentions: 2
Published: over 12 years ago

10.1016/j.jpsychores.2019.01.011

A longitudinal study on the effects of psychological stress on proteinuria in childhood steroid-sensitive nephrotic syndrome
Cited by: 10
Author(s): Lianne Bakkum, A.M. Willemen, Lydia Zoetebier, Antonia H. Bouts
Software Mentions: 2
Published: over 7 years ago

10.1098/rsif.2014.1111

Micro- and nano-structural details of a spider's filter for substrate vibrations: relevance for low-frequency signal transmission
Cited by: 32
Author(s): Maxim Erko, Osnat Younes‐Metzler, Alexander Rack, Paul Zaslansky, Seth L. Young, Garrett Milliron, Marius Chyasnavichyus, Friedrich G. Barth, Peter Fratzl, Vladimir V. Tsukruk, Igor Zlotnikov, Yael Politi
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-019-3280-9

Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data
Cited by: 37
Author(s): Shifu Chen, Yanqing Zhou, Yaru Chen, Tanxiao Huang, Wenting Liao, Yun Xu, Zhicheng Li, Jia Gu
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0100068

BRCA1 Haploinsufficiency Leads to Altered Expression of Genes Involved in Cellular Proliferation and Development
Cited by: 16
Author(s): Harriet Feilotter, Claire S. Michel, Paolo Uy, Lauren Bathurst, Scott Davey
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0238231

Treatment outcome of Severe Acute Malnutrition and associated factors among under-five children in outpatient therapeutics unit in Gubalafto Wereda, North Wollo Zone, Ethiopia, 2019
Cited by: 14
Author(s): Biruk Beletew Abate, Befkad Deresse Tilahun, Ayelign Mengesha Kassie, Mesfin Wudu Kassaw
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0008003

Novel Rank-Based Statistical Methods Reveal MicroRNAs with Differential Expression in Multiple Cancer Types
Cited by: 153
Author(s): Roy Navon, Hui Wang, Israel Steinfeld, Anya Tsalenko, Amir Ben-Dor, Zohar Yakhini
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2229-10-273

Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees
Cited by: 37
Author(s): Caroline Côté, Francis Boileau, Vicky Roy, Mario Ouellet, Caroline Levasseur, Marie-Josée Morency, Janice E. K. Cooke, Armand Séguin, John Mackay
Software Mentions: 2
Published: almost 16 years ago

10.1186/1479-5876-6-79

Aurora kinase inhibitors synergize with paclitaxel to induce apoptosis in ovarian cancer cells
Cited by: 61
Author(s): Christopher D. Scharer, Noelani Laycock, Adeboye O. Osunkoya, Sanjay Logani, John F. McDonald, Benedict B. Benigno, Carlos S. Moreno
Software Mentions: 2
Published: almost 18 years ago

10.1186/1472-6785-10-2

Tracing the origins of rescued chimpanzees reveals widespread chimpanzee hunting in Cameroon
Cited by: 66
Author(s): Lora Ghobrial, Felix Lankester, John Kiyang, Akih E Akih, Simone de Vries, Roger Fotso, Elizabeth L. Gadsby, P. D. Jenkins, Mary Katherine Gonder
Software Mentions: 2
Published: over 16 years ago

10.1186/s12870-021-02970-2

BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon
Cited by: 7
Author(s): Kaori Sakai, Sylvie Citerne, Sébastien Antelme, Philippe Le Bris, Sylviane Daniel, Axelle Bouder, Angélina D’Orlando, Amy Cartwright, Frédérique Tellier, Stéphanie Pateyron, Étienne Delannoy, Debbie Laudencia‐Chingcuanco, Grégory Mouille, Jean-Christophe Palauqui, John P. Vogel, Richard Sibout
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2229-11-114

Resistance to Plasmopara viticola in a grapevine segregating population is associated with stilbenoid accumulation and with specific host transcriptional responses
Cited by: 89
Author(s): G. Malacarne, Urška Vrhovšek, L. Zulini, Alessandro Cestaro, M. Stefanini, Fulvio Mattivi, Massimo Delledonne, Riccardo Velasco, C. Moser
Software Mentions: 2
Published: over 15 years ago

10.1186/1479-5876-4-29

Gene expression in acute Stanford type A dissection: a comparative microarray study
Cited by: 44
Author(s): Barbara Theresia Weis-Müller, Olga Modlich, Irina Drobinskaya, Derya Unay, Rita Huber, Hans Bojar, Jochen D. Schipke, P. Feindt, E. Gams, Wolfram Müller, Timm O. Goecke, W. Sandmann
Software Mentions: 2
Published: over 20 years ago

10.1186/s12862-021-01825-6

A comparative genomic approach using mouse and fruit fly data to discover genes involved in testis function in hymenopterans with a focus on Nasonia vitripennis
Cited by: 0
Author(s): Charlotte Lécureuil, Sophie Fouchécourt, Rémi Eliautout, Vanessa Guérin, Kévin Hidalgo, Dorian Neutre, Géraldine Roux, Philippe Monget
Software Mentions: 2
Published: over 5 years ago

10.3813/AAA.919239

Pitch of Harmonic Complex Tones: Rate Coding of Envelope Repetition Rate in the Auditory Midbrain
Cited by: 1
Author(s): Yaqing Su, Bertrand Delgutte
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2105-15-S15-S10

Compression of next-generation sequencing quality scores using memetic algorithm
Cited by: 12
Author(s): Jian Zhou, Zhen Ji, Zexuan Zhu, Shan He
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0019908

The Transcriptome of Human Epicardial, Mediastinal and Subcutaneous Adipose Tissues in Men with Coronary Artery Disease
Cited by: 42
Author(s): Sandra Guauque-Olarte, Nathalie Gaudreault, Marie-Ève Piché, Dominique Fournier, Pascale Mauriège, Patrick Mathieu, Yohan Bossé
Software Mentions: 2
Published: over 15 years ago

10.1186/s12862-019-1531-z

Geographic body size variation of a tropical anuran: effects of water deficit and precipitation seasonality on Asian common toad from southern Asia
Cited by: 6
Author(s): Guo Cheng, Shuai Gao, Ali Krzton, Long Zhang
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12937-018-0382-6

Severely malnourished children with a low weight-for-height have a higher mortality than those with a low mid-upper-arm-circumference: III. Effect of case-load on malnutrition related mortality– policy implications
Cited by: 9
Author(s): Emmanuel Grellety, Michael Golden
Software Mentions: 2
Published: about 8 years ago

10.1186/s12937-018-0384-4

Severely malnourished children with a low weight-for-height have a higher mortality than those with a low mid-upper-arm-circumference: I. Empirical data demonstrates Simpson’s paradox
Cited by: 23
Author(s): Emmanuel Grellety, Michael Golden
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2105-15-165

Cache-Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER
Cited by: 11
Author(s): Miguel Ferreira, Nuno Roma, Luís M. S.Russo
Software Mentions: 2
Published: over 12 years ago

10.1107/S2059798317013596

FlexED8: the first member of a fast and flexible sample-changer family for macromolecular crystallography
Cited by: 13
Author(s): Gergely Papp, Franck Felisaz, Clement Sorez, Marcos Lopez-Marrero, Robert Janocha, Babu A. Manjasetty, Alexandre Gobbo, Hassan Belrhali, Matthew W. Bowler, F. Cipriani
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0062767

Observational Bias during Nutrition Surveillance: Results of a Mixed Longitudinal and Cross-Sectional Data Collection System in Northern Nigeria
Cited by: 11
Author(s): Emmanuel Grellety, Francisco J. Luquero, Christopher Mambula, Hassana H. Adamu, Greg J. Elder, Klaudia Porten
Software Mentions: 2
Published: over 13 years ago

10.3390/nu10091255

Lactobacillus acidophilus DDS-1 Modulates the Gut Microbiota and Improves Metabolic Profiles in Aging Mice
Cited by: 57
Author(s): Ravichandra Vemuri, Rajaraman Eri, Rohit Gundamaraju, Shakuntla Gondalia, Avinash V. Karpe, David J. Beale, Christopher Martoni, Rajaraman Eri
Software Mentions: 2
Published: about 8 years ago

10.3390/nu9040390

Novel Genetic Variants Associated with Child Refractory Esophageal Stricture with Food Allergy by Exome Sequencing
Cited by: 1
Author(s): Min Yang, Min Xiong, Huan Chen, Lanlan Geng, Peiyu Chen, Jing Xie, Shui Qing Ye, Ding‐You Li, Sitang Gong
Software Mentions: 2
Published: over 9 years ago

10.3390/nu13062120

Untargeted Plasma Metabolomics Unravels a Metabolic Signature for Tissue Sensitivity to Glucocorticoids in Healthy Subjects: Its Implications in Dietary Planning for a Healthy Lifestyle
Cited by: 4
Author(s): Nicolas C. Nicolaides, Maria-Konstantina Ioannidi, Eleni Koniari, Ifigeneia Papageorgiou, Αnastasia Bartzeliotou, Amalia Sertedaki, Maria I. Klapa, Evangelia Charmandari
Software Mentions: 2
Published: about 5 years ago

10.1186/s12862-018-1127-z

Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
Cited by: 26
Author(s): Jonna Sofia Eriksson, Filipe de Sousa, Yann Bertrand, Alexandre Antonelli, Bengt Oxelman, Bernard E. Pfeil
Software Mentions: 2
Published: over 8 years ago

10.1155/2020/8841681

Hierarchical Multimodal Adaptive Fusion (HMAF) Network for Prediction of RGB-D Saliency
Cited by: 2
Author(s): Yiliang Lv, Wujie Zhou
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12284-016-0109-2

Detection of Novel QTLs Regulating Grain Size in Extra-Large Grain Rice (Oryza sativa L.) Lines
Cited by: 16
Author(s): Shuhei Segami, Tatsuya Yamamoto, Katsuyuki Oki, Tomonori Noda, Hajime Kanamori, Harumi Sasaki, Satomi Mori, Motoyuki Ashikari, Hidemi Kitano, Yūichi Katayose, Yukimoto Iwasaki, Kotaro Miura
Software Mentions: 2
Published: about 10 years ago

10.3390/ijms20246120

CRK5 Protein Kinase Contributes to the Progression of Embryogenesis of Arabidopsis thaliana
Cited by: 22
Author(s): Abu Imran Baba, Ildikó Valkai, Nitin M. Labhane, Lilla Koczka, Norbert Andrási, Éva Klement, Zsuzsanna Darula, Katalin F. Medzihradszky, László Szabados, Attila Fehér, Gábor Rigó, Ágnes Cséplő
Software Mentions: 2
Published: almost 7 years ago

10.1093/bioinformatics/btz041

SVIM: structural variant identification using mapped long reads
Cited by: 148
Author(s): David Heller, Martin Vingron
Software Mentions: 2
Published: over 7 years ago

10.1186/s12284-020-00416-1

Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq
Cited by: 59
Author(s): Lei Lei, Hongliang Zheng, Yanli Bi, Liuqing Yang, Hualong Liu, Jingguo Wang, Jian Sun, Hongwei Zhao, Xianwei Li, Jiaming Li, Yongcai Lai, Detang Zou
Software Mentions: 2
Published: about 6 years ago

10.5808/GI.2019.17.4.e40

Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data
Cited by: 1
Author(s): Yu Na Lee, Kiejung Park, Insong Koh
Software Mentions: 2
Published: over 6 years ago

10.1155/2014/354703

Hypergraph-Based Recognition Memory Model for Lifelong Experience
Cited by: 0
Author(s): Hyoungnyoun Kim, Ji‐Hyung Park
Software Mentions: 2
Published: over 12 years ago

10.1155/2014/891761

Dynamic Regulatory Network Reconstruction for Alzheimer’s Disease Based on Matrix Decomposition Techniques
Cited by: 10
Author(s): Wei Kong, Xiaoyang Mou, Xiefei Zhi, Xing Zhang, Yang Yang
Software Mentions: 2
Published: over 12 years ago

10.1093/bioinformatics/btaa760

OGRE: Overlap Graph-based metagenomic Read clustEring
Cited by: 5
Author(s): Marleen Balvert, Xiao Luo, Ernestina Hauptfeld, Alexander Schönhuth, Bas E. Dutilh
Software Mentions: 2
Published: about 6 years ago

10.1186/1741-7015-9-130

A diagnostic algorithm combining clinical and molecular data distinguishes Kawasaki disease from other febrile illnesses
Cited by: 41
Author(s): Xuefeng B. Ling, Kenneth Lau, John T. Kanegaye, Pan Zheng, Syd S. Peng, Jun Ji, Gigi Liu, Yuichiro Sato, Tom Yu, John C. Whitin, James Schilling, Jane C. Burns, Harvey J. Cohen
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0065571

Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia
Cited by: 36
Author(s): Qiaojun Wen, Linda Y. Liu, Ting Yang, Cantas Alev, Shao-Yi Wu, David K. Stevenson, Guojun Sheng, Atul J. Butte, Xuefeng B. Ling
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0041224

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads
Cited by: 37
Author(s): Colin Davenport, Jens Neugebauer, Nils Beckmann, Benedikt Friedrich, Burim Kameri, Svea Kokott, Malte Paetow, Björn Siekmann, Matthias Wieding-Drewes, Markus Wienhöfer, S. Wolf, Burkhard Tümmler, Volker Ahlers, Frauke Sprengel
Software Mentions: 2
Published: about 14 years ago

10.18632/oncotarget.11754

A characteristic biosignature for discrimination of gastric cancer from healthy population by high throughput GC-MS analysis
Cited by: 42
Author(s): Yinan Chen, Jun Zhang, Li Guo, Lei Liu, Jingran Wen, Lu Xu, Min Yan, Zuofeng Li, Xiaoyan Zhang, Nan Peng, Jinling Jiang, Jun Ji, Jianian Zhang, Wei Cai, Huisheng Zhuang, Yan Wang, Zhenggang Zhu, Yingyan Yu
Software Mentions: 2
Published: about 10 years ago

10.1186/s13054-018-2275-7

Plasma mitochondrial DNA and metabolomic alterations in severe critical illness
Cited by: 28
Author(s): Pär I. Johansson, Kiichi Nakahira, Angela Rogers, Michael J. McGeachie, Rebecca M. Baron, Laura E. Fredenburgh, John S. Harrington, Augustine M.K. Choi, Kenneth B. Christopher
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0254796

Removal of peptidoglycan and inhibition of active cellular processes leads to daptomycin tolerance in Enterococcus faecalis
Cited by: 7
Author(s): Rachel D. Johnston, Brittni M. Woodall, Johnathan Harrison, Shawn R. Campagna, Elizabeth Fozo
Software Mentions: 2
Published: about 5 years ago

10.1186/1755-8794-1-51

Expression-based Pathway Signature Analysis (EPSA): Mining publicly available microarray data for insight into human disease
Cited by: 15
Author(s): Jessica D. Tenenbaum, Michael G. Walker, Paul J. Utz, Atul J. Butte
Software Mentions: 2
Published: almost 18 years ago

10.1186/1755-8794-5-33

The effects of MicroRNA transfections on global patterns of gene expression in ovarian cancer cells are functionally coordinated
Cited by: 29
Author(s): Shubin Shahab, Lilya V. Matyunina, Christopher G. Hill, Limin Wang, Roman Mezencev, L. DeEtte Walker, John F. McDonald
Software Mentions: 2
Published: about 14 years ago

10.1186/gm494

A simple consensus approach improves somatic mutation prediction accuracy
Cited by: 33
Author(s): David Goode, Sally M. Hunter, Maria A. Doyle, Tao Ma, Simone M. Rowley, David Y.H. Choong, Georgina L Ryland, Ian Campbell
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0147369

Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform
Cited by: 21
Author(s): Tariq Pervaiz, Haifeng Jia, Muhammad Salman Haider, Cheng Zhang, Mengjie Cui, Mengqi Wang, Liwen Cui, Xicheng Wang, Jinggui Fang
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-020-02229-3

Reference flow: reducing reference bias using multiple population genomes
Cited by: 29
Author(s): Nae-Chyun Chen, Brad Solomon, Taher Mun, Sheila Iyer, Ben Langmead
Software Mentions: 2
Published: over 5 years ago

10.1186/1745-6150-1-18

Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples
Cited by: 21
Author(s): Jaroslav Novák, Mia Miller, Douglas A. Bell
Software Mentions: 2
Published: about 20 years ago

10.1371/journal.pone.0041001

Transcriptome Profiling of the Cancer, Adjacent Non-Tumor and Distant Normal Tissues from a Colorectal Cancer Patient by Deep Sequencing
Cited by: 65
Author(s): Yanan Wu, Xuetao Wang, WU Fang-bo, Ruolei Huang, Fangqin Xue, Guantao Liang, Min Tao, Peng Cai, Yi Huang
Software Mentions: 2
Published: about 14 years ago

10.1186/s13059-019-1910-1

Transcriptome assembly from long-read RNA-seq alignments with StringTie2
Cited by: 734
Author(s): Sam Kovaka, Aleksey V. Zimin, Geo Pertea, Roham Razaghi, Steven L. Salzberg, Mihaela Pertea
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12920-017-0255-4

CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data
Cited by: 15
Author(s): Zhenhua Yu, Ao Li, Minghui Wang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0083674

Behaviorally Activated mRNA Expression Profiles Produce Signatures of Learning and Enhanced Inhibition in Aged Rats with Preserved Memory
Cited by: 31
Author(s): Rebecca P. Haberman, Carlo Colantuoni, Ming Teng Koh, Michela Gallagher
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0013453

Reversible Block of Mouse Neural Stem Cell Differentiation in the Absence of Dicer and MicroRNAs
Cited by: 66
Author(s): Therése Andersson, Sabhi Rahman, Stephen N. Sansom, Jessica Alsiö, Masahiro Kaneda, James Smith, Dónal O’Carroll, Alexander Tarakhovsky, Frederick J. Livesey
Software Mentions: 2
Published: almost 16 years ago

10.1038/srep09064

Structure, Function and Inhibition of the Phosphoethanolamine Methyltransferases of the Human Malaria Parasites Plasmodium vivax and Plasmodium knowlesi
Cited by: 22
Author(s): Aayushi Garg, T. Lukk, Vidya P. Kumar, Jae Yeon Choi, Yoann Augagneur, Dennis R. Voelker, Satish K. Nair, Choukri Ben Mamoun
Software Mentions: 2
Published: over 11 years ago

10.1038/srep10624

Lipidome and Transcriptome Profiling of Pneumolysin Intoxication Identifies Networks Involved in Statin-Conferred Protection of Airway Epithelial Cells
Cited by: 4
Author(s): Sarah Statt, Jhen-Wei Ruan, Chih Ting Huang, Reen Wu, Cheng–Yuan Kao
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms21072417

Transcriptomic Profiling in Fins of Atlantic Salmon Parasitized with Sea Lice: Evidence for an Early Imbalance Between Chalimus-Induced Immunomodulation and the Host’s Defense Response
Cited by: 18
Author(s): Navaneethaiyer Umasuthan, Xi Xue, Albert Caballero‐Solares, Surendra Kumar, JD Westcott, Z Chen, Stanko Škugor, Barbara F. Nowak, RG Taylor, ML Rise
Software Mentions: 2
Published: over 6 years ago

10.3389/fpsyg.2017.01709

Rhythmic Density Affects Listeners' Emotional Response to Microtiming
Cited by: 9
Author(s): Olivier Senn, Claudia Bullerjahn, Lorenz Kilchenmann, Richard von Georgi
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0106054

Extracellular Matrix Defects in Aneurysmal Fibulin-4 Mice Predispose to Lung Emphysema
Cited by: 17
Author(s): Natasja W. M. Ramnath, Koen M. van de Luijtgaarden, Ingrid van der Pluijm, Menno van Nimwegen, Paula M. van Heijningen, Sigrid Swagemakers, Bibi S. van Thiel, Ruziedi Y. Ridwan, Nicole van Vliet, Marcel Vermeij, Lukas J.A.C. Hawinkels, Anne de Munck, Oleh Dzyubachyk, Erik Meijering, Peter van der Spek, Robbert J. Rottier, Hiromi Yanagisawa, Rudi W. Hendriks, Roland Kanaar, Ellen V. Rouwet, Alex KleinJan, Jeroen Essers
Software Mentions: 2
Published: almost 12 years ago

10.1038/srep12995

Identifying miRNA/mRNA negative regulation pairs in colorectal cancer
Cited by: 35
Author(s): Xile Zhou, Xiao Xu, Jinhai Wang, Jie Lin, Wenbin Chen
Software Mentions: 2
Published: about 11 years ago

10.3389/fpsyg.2019.01835

Augmented Reality in Educational Inclusion. A Systematic Review on the Last Decade
Cited by: 79
Author(s): Jairo Quintero, Silvia Baldiris, Rainer Rubira, Jhoni Cerón, Gloria Velez
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-019-1654-y

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling
Cited by: 68
Author(s): Aslihan Karabacak Calviello, Antje Hirsekorn, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-017-1377-x

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
Cited by: 17
Author(s): Gerben Menschaert, Xiaojing Wang, Andrew R. Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W. Deutsch, Tobias Ternent, Juan Antonio Vizcaíno
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms21165745

Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem
Cited by: 0
Author(s): Muhammad Naseem, Özge Osmanoğlu, Martin Kaltdorf, Afnan Ali M A Alblooshi, Jibran Iqbal, Fares M. Howari, Mugdha Srivastava, Thomas Dandekar
Software Mentions: 2
Published: about 6 years ago

10.1038/srep14364

Translational compensation of genomic instability in neuroblastoma
Cited by: 10
Author(s): Erik Dassi, Valentina Greco, Viktoryia Sidarovich, Paola Zuccotti, Natalia Arseni, Paola Scaruffi, Gian Paolo Tonini, Alessandro Quattrone
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pcbi.1008085

Remote homology search with hidden Potts models
Cited by: 20
Author(s): Grey W Wilburn, Sean R. Eddy
Software Mentions: 2
Published: almost 6 years ago

10.1093/database/baw022

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis
Cited by: 56
Author(s): Vahan Simonyan, Konstantin Chumakov, Hayley Dingerdissen, William J. Faison, Scott Goldweber, Anton Golikov, Naila Gulzar, Konstantinos Karagiannis, Phuc Vinh Nguyen Lam, Thomas Maudru, Olesja Muravitskaja, Ekaterina Osipova, Yang Pan, Alexey Pschenichnov, Alexandre Rostovtsev, Luis V. Santana‐Quintero, Krista Smith, Elaine E. Thompson, Valery Tkachenko, John Torcivia-Rodriguez, Alin Voskanian, Qing Wan, Jing Wang, Tsung-Jung Wu, Carolyn A. Wilson, Raja Mazumder
Software Mentions: 2
Published: over 10 years ago

10.1093/database/baw137

Cryptosporidium hominisgene catalog: a resource for the selection of novelCryptosporidiumvaccine candidates
Cited by: 11
Author(s): Olukemi O. Ifeonu, Raphael Simon, Sharon M. Tennant, Abhineet S. Sheoran, Maria C. Daly, Victor Felix, Jessica C. Kissinger, Giovanni Widmer, Fred Levine, Saul Tzipori, Joana C. Silva
Software Mentions: 2
Published: over 10 years ago

10.1038/srep16441

Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism
Cited by: 6
Author(s): Hong‐Hsiang Guan, Masato Yoshimura, Phimonphan Chuankhayan, Chien-Chih Lin, Nai-Chi Chen, Ming‐Chi Yang, Asma Ismail, Hoong‐Kun Fun, Chun‐Jung Chen
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0003794

Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells
Cited by: 103
Author(s): Erxi Wu, Nathan Palmer, Ze Tian, Annie P. Moseman, Michal Galdzicki, Xuetao Wang, Bonnie Berger, Hongbing Zhang, Isaac S. Kohane
Software Mentions: 2
Published: almost 18 years ago

10.1093/database/baaa079

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes
Cited by: 2
Author(s): Hong Cui, Limin Zhang, Bruce A. Ford, Hsin Liang Cheng, James Macklin, Anton A. Reznicek, Julian R. Starr
Software Mentions: 2
Published: over 6 years ago

10.3390/genes5020366

Characterization of the Genomic Architecture and Mutational Spectrum of a Small Cell Prostate Carcinoma
Cited by: 9
Author(s): Alan F. Scott, David Mohr, Hua Ling, Robert B. Scharpf, Peng Zhang, Gregory S. Liptak
Software Mentions: 2
Published: over 12 years ago

10.3390/ijms21197386

Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize
Cited by: 16
Author(s): A. B. Jagtap, Yogesh Vikal, Gurmukh S. Johal
Software Mentions: 2
Published: almost 6 years ago

10.1186/gb-2004-5-9-r69

Cited by: 199
Author(s): Jingjing Wang, Laura Kean, Jingli Yang, Adrian K. Allan, Shireen A. Davies, Paweł Herzyk, Julian A. T. Dow
Software Mentions: 2
Published: over 22 years ago

10.7717/peerj.4625

Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume)
Cited by: 12
Author(s): Xiaopeng Ni, Song Xue, Shahid Iqbal, Wanxu Wang, Zhaojun Ni, Muhammad Khalil-Ur-Rehman, Zhihong Gao
Software Mentions: 2
Published: over 8 years ago

10.1186/s13059-016-1096-8

TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells
Cited by: 78
Author(s): Lorenzo de la Rica, Özgen Deniz, Kevin Cheng, Christopher D. Todd, Cristina Cruz, Jonathan Houseley, Miguel R. Branco
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep18429

Single-target high-throughput transcription analyses reveal high levels of alternative splicing present in the FPPS/GGPPS from Plasmodium falciparum
Cited by: 14
Author(s): Heloisa B. Gabriel, Mauro Ferreira de Azevedo, Giuseppe Palmisano, Gerhard Wunderlich, Emı́lia A. Kimura, Alejandro M. Katzin, João M. P. Alves
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.13718

DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival
Cited by: 15
Author(s): Thomas Fleischer, Jovana Klajic, Miriam Ragle Aure, Riku Louhimo, Arne V. Pladsen, Lars Ottestad, Nizar Touleimat, Marko Laakso, Ann Rita Halvorsen, Grethe I.G. Alnæs, Margit Riis, Åslaug Helland, Sampsa Hautaniemi, Per Eystein Lønning, Bjørn Naume, Anne‐Lise Børresen‐Dale, Jörg Tost, Vessela N. Kristensen
Software Mentions: 2
Published: almost 10 years ago

10.3390/ijms21197259

Streamlining Quantitative Analysis of Long RNA Sequencing Reads
Cited by: 1
Author(s): Sebastian Oeck, Alicia I. Tüns, Sebastian Hurst, Alexander Schramm
Software Mentions: 2
Published: almost 6 years ago

10.3390/diagnostics10121077

The Activation of Prothrombin Seems to Play an Earlier Role than the Complement System in the Progression of Colorectal Cancer: A Mass Spectrometry Evaluation
Cited by: 6
Author(s): Maider Beitia, Paolo Romano, Gorka Larrinaga, Jon Danel Solano-Iturri, Annalisa Salis, Gianluca Damonte, Marco Bruzzone, Marcello Ceppi, Aldo Profumo
Software Mentions: 2
Published: almost 6 years ago

10.1155/2021/8884229

Next Generation Exome Sequencing of Pediatric Asthma Identifies Rare and Novel Variants in Candidate Genes
Cited by: 4
Author(s): Neda M. Bogari, Amr Amin, Husni H Rayes, Ahmed Abdelmotelb, Mohiuddin M. Taher, Faisal A. Al‐Allaf, Abdellatif Bouazzaoui, Luke O’Gorman, John W. Holloway
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-015-0666-5

Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo
Cited by: 82
Author(s): Masahiko Imashimizu, Hiroki Takahashi, Taku Oshima, Carl McIntosh, Mikhail Bubunenko, Donald L. Court, Mikhail Kashlev
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0059807

Aridity Modulates N Availability in Arid and Semiarid Mediterranean Grasslands
Cited by: 40
Author(s): Manuel Delgado‐Baquerizo, Fernando T. Maestre, Antonio Gallardo, José L. Quero, Victoria Ochoa, Miguel García‐Gómez, Cristina Escolar, Pablo García‐Palacios, Miguel Berdugo, Enrique Valencia, Beatriz Gozalo, Zouhaier Noumi, Mchich Derak, Matthew D. Wallenstein
Software Mentions: 2
Published: over 13 years ago

10.1242/dmm.025239

Genomic profiling of murine mammary tumors identifies potential personalized drug targets for p53 deficient mammary cancers
Cited by: 27
Author(s): Adam D. Pfefferle, Yash N. Agrawal, Daniel C. Koboldt, Krishna L. Kanchi, Jason I. Herschkowitz, Elaine R. Mardis, Jeffrey M. Rosen, Charles M. Perou
Software Mentions: 2
Published: over 10 years ago

10.1186/gb-2014-15-1-r18

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis
Cited by: 85
Author(s): Beibei Chen, Jonghyun Yun, Min Soo Kim, Joshua T. Mendell, Yang Xie
Software Mentions: 2
Published: over 12 years ago

10.1038/srep20874

Seasonal forecasting of lightning and thunderstorm activity in tropical and temperate regions of the world
Cited by: 43
Author(s): Andrew J. Dowdy
Software Mentions: 2
Published: over 10 years ago

10.1186/gb-2013-14-9-r102

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape
Cited by: 276
Author(s): Kenneth Day, Lindsay L. Waite, Anna Thalacker‐Mercer, Andrew B. West, Marcas M. Bamman, James D. Brooks, R Myers, Devin Absher
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0013865

MEG Responses to the Perception of Global Structure within Glass Patterns
Cited by: 12
Author(s): Jennifer B. Swettenham, Stephen J. Anderson, Ngoc Jade Thai
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0075828

Revealing of Mycobacterium marinum Transcriptome by RNA-seq
Cited by: 15
Author(s): Sen Wang, Xinran Dong, Yaping Zhu, Chuan Wang, Gang Sun, Tāo Luò, Weidong Tian, Huajun Zheng, Qian Gao
Software Mentions: 2
Published: almost 13 years ago

10.1186/gb-2014-15-3-r42

A comprehensive evaluation of assembly scaffolding tools
Cited by: 155
Author(s): Martin Hunt, Chris Newbold, Matthew Berriman, Thomas D. Otto
Software Mentions: 2
Published: over 12 years ago

10.1186/gb-2013-14-6-r54

The plasticity of the grapevine berry transcriptome
Cited by: 148
Author(s): Silvia Dal Santo, Giovanni Battista Tornielli, Sara Zenoni, Marianna Fasoli, Lorenzo Farina, Andrea Anesi, Flavia Guzzo, Massimo Delledonne, Mario Pezzotti
Software Mentions: 2
Published: over 13 years ago

10.1186/gb-2012-13-6-r56

Toward almost closed genomes with GapFiller
Cited by: 915
Author(s): Marten Boetzer, Walter Pirovano
Software Mentions: 2
Published: over 14 years ago

10.1186/gb-2012-13-2-r11

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells
Cited by: 54
Author(s): Najeeb U. Siddiqui, Xiao Li, Hua Luo, Angelo Karaiskakis, Huayun Hou, Thomas Kislinger, J. Timothy Westwood, Quaid Morris, Howard D. Lipshitz
Software Mentions: 2
Published: over 14 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566