cran: SAM | Projects | Ecosyste.ms: Papers

10.1038/s41598-018-34812-x

A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence
Cited by: 35
Author(s): Patrick Lypaczewski, Johanna Hoshizaki, Wen-Wei Zhang, Laura-Isobel McCall, John Torcivia-Rodriguez, Vahan Simonyan, Amanpreet Kaur, Ken Dewar, Greg Matlashewski
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-019-40739-8

Featherweight long read alignment using partitioned reference indexes
Cited by: 13
Author(s): Hasindu Gamaarachchi, Sri Parameswaran, Martin A. Smith
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-23168-x

Identification of p38 MAPK as a novel therapeutic target for Friedreich’s ataxia
Cited by: 9
Author(s): M. Grazia Cotticelli, Shujuan J. Xia, Avinash Kaur, Daniel W. Lin, Yongping Wang, Eric Ruff, John W. Tobias, Robert B. Wilson
Software Mentions: 2
Published: over 8 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

10.1038/s41598-018-23337-y

Comparative whole-genome sequence analysis of Mycobacterium tuberculosis isolated from tuberculous meningitis and pulmonary tuberculosis patients
Cited by: 21
Author(s): Kiatichai Faksri, Eryu Xia, Rick Twee‐Hee Ong, Jun Tan, Ditthawat Nonghanphithak, Nampueng Makhao, Nongnard Thamnongdee, Arirat Thanormchat, Arisa Phurattanakornkul, Somcharn Rattanarangsee, Chate Ratanajaraya, Prapat Suriyaphol, Therdsak Prammananan, Yik-Ying Teo, Angkana Chaiprasert
Software Mentions: 2
Published: over 8 years ago

10.1186/s40478-021-01118-5

Molecular analysis of pediatric CNS-PNET revealed nosologic heterogeneity and potent diagnostic markers for CNS neuroblastoma with FOXR2-activation
Cited by: 19
Author(s): Andrey Korshunov, Konstantin Okonechnikov, Felix Schmitt-Hoffner, Marina Ryzhova, Felix Sahm, Damian Stichel, Daniel Schrimpf, David Reuß, Philipp Sievers, Abigail K Suwala, Ella Kumirova, Olga Zheludkova, Andrey Golanov, David Jones, Stefan M. Pfister, Marcel Kool, Andreas von Deimling
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-8-S7-S24

ProtQuant: a tool for the label-free quantification of MudPIT proteomics data
Cited by: 47
Author(s): Susan M. Bridges, G Bryce Magee, Nan Wang, W. Paul Williams, Shane C. Burgess, Bindu Nanduri
Software Mentions: 2
Published: almost 19 years ago

10.1038/s41598-018-20727-0

Differential long non-coding RNA expression profiles in human oocytes and cumulus cells
Cited by: 51
Author(s): Julien Bouckenheimer, Patricia Fauque, Charles-Henri Lecellier, Céline Bruno, Thérèse Commes, Jean-Marc Lemaı̂tre, John De Vos, Saïd Assou
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-21608-2

Flexible migratory choices of Cory’s shearwaters are not driven by shifts in prevailing air currents
Cited by: 10
Author(s): Gaia Dell’Ariccia, Simon Benhamou, Maria P. Dias, José Pedro Granadeiro, Joël Sudre, Paulo Catry, Francesco Bonadonna
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-019-41672-6

Utilization of NGS technologies to investigate transcriptomic and epigenomic mechanisms in trastuzumab resistance
Cited by: 7
Author(s): Miguel Nava, Pranabananda Dutta, Robin Farias‐Eisner, Jaydutt V. Vadgama, Yanyuan Wu
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-15516-0

Identification of selection signals by large-scale whole-genome resequencing of cashmere goats
Cited by: 35
Author(s): Xiaokai Li, Rui Su, Wenting Wan, Wenguang Zhang, Jiang Huai-zhi, Xuguang Qiao, Yixing Fan, Yanjun Zhang, Ruijun Wang, Zhihong Liu, Zhiying Wang, Bin Liu, Yue Ma, Hongping Zhang, Qianjun Zhao, Tao Zhong, Ran Di, Yu Jiang, Wei Chen, Wen Wang, Yang Dong, Jinquan Li
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2164-13-62

Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter
Cited by: 108
Author(s): Bridget M. Barker, Kristin Kroll, Martin Vödisch, Aurélien Mazurie, Olaf Kniemeyer, Robert A. Cramer
Software Mentions: 2
Published: over 14 years ago

10.1038/s41598-017-16700-y

A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness
Cited by: 10
Author(s): John Lai, Leire Moya, Jiyuan An, Andrea Hoffman, Srilakshmi Srinivasan, Janaththani Panchadsaram, Carina Walpole, Joanna Perry-Keene, Suzanne K. Chambers, Melanie Lehman, Colleen C. Nelson, Judith A. Clements, Jyotsna Batra
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-09247-5

Prevalence of Rare Genetic Variations and Their Implications in NGS-data Interpretation
Cited by: 17
Author(s): Yangrae Cho, Chul‐Ho Lee, Eun-Goo Jeong, Minho Kim, Jong Hui Hong, Yun Woong Ko, Bomnun Lee, Gilly Yun, Byong Joon Kim, Jongcheol Jung, Jongsun Jung, Jin Sung Lee
Software Mentions: 2
Published: about 9 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

10.1186/1471-2431-13-17

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

10.1038/s41598-017-10493-w

Functional proteomics outlines the complexity of breast cancer molecular subtypes
Cited by: 48
Author(s): Angelo Gámez‐Pozo, Lucía Trilla-Fuertes, Julia Berges-Soria, Nathalie Selevsek, Rocío López-Vacas, Mariana Díaz-Almirón, Paolo Nanni, Jorge M. Arevalillo, Hilario Navarro, Jonas Grossmann, Francisco Gayá Moreno, Rubén Gómez Rioja, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Paloma Maı́n, Jaime Feliú, Purificación Martínez del Prado, Pilar Zamora, Eva Ciruelos, Enrique Espinosa, Juan Ángel Fresno Vara
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-09285-z

Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat
Cited by: 11
Author(s): Xuguang Qiao, Rui Su, Yan Wang, Ruijun Wang, Ting Yang, Xiaokai Li, Wei Chen, Shiyang He, Yu Jiang, Qiwu Xu, Wenting Wan, Yaolei Zhang, Wenguang Zhang, Chen Jiang, Bin Liu, Xin Liu, Yixing Fan, Duoyuan Chen, Jiang Huai-zhi, Dongming Fang, Zhihong Liu, Xiaowen Wang, Yanjun Zhang, Danqing Mao, Zhiying Wang, Ran Di, Qianjun Zhao, Tao Zhong, Huanming Yang, Jian Wang, Wen Wang, Yang Dong, Xiaoli Chen, Xun Xu, Jinquan Li
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-08492-y

Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts
Cited by: 55
Author(s): Natallia Shved, Gregor Warsow, Felix Eichinger, David Hoogewijs, Simone Brandt, Peter J. Wild, Matthias Kretzler, Clemens D. Cohen, Maja T. Lindenmeyer
Software Mentions: 2
Published: about 9 years ago

10.1186/s12859-017-1810-x

Robust gene selection methods using weighting schemes for microarray data analysis
Cited by: 14
Author(s): Seok Kang, Jongwoo Song
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-00788-3

Multimodal Regulation Orchestrates Normal and Complex Disease States in the Retina
Cited by: 13
Author(s): Ana María Olivares, Austin S. Jelcick, James B. Reinecke, Barrett Leehy, Ali Haider, Margaux A. Morrison, Lin Cheng, D. F. Chen, Margaret M. DeAngelis, Neena B. Haider
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-09089-1

Accelerating next generation sequencing data analysis with system level optimizations
Cited by: 14
Author(s): Nagarajan Kathiresan, Ramzi Temanni, Hakeem Almabrazi, Najeeb Syed, Puthen V. Jithesh, Rashid Al‐Ali
Software Mentions: 2
Published: about 9 years ago

10.1186/s13029-016-0058-6

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing
Cited by: 4
Author(s): Takuji Takeuchi, Atsuo Yamada, Takashi Aoki, Kunihiro Nishimura
Software Mentions: 2
Published: about 10 years ago

10.1038/srep41544

Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features
Cited by: 90
Author(s): Andrés Lanzós, Joana Carlevaro-Fita, Loris Mularoni, Ferrán Reverter, Emilio Palumbo, Roderic Guigó, Rory Johnson
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2202-8-95

Gene expression profiling in a mouse model of infantile neuronal ceroid lipofuscinosis reveals upregulation of immediate early genes and mediators of the inflammatory response
Cited by: 28
Author(s): Xingwen Qiao, Jui Yun Lu, Sandra L. Hofmann
Software Mentions: 2
Published: almost 19 years ago

10.1038/srep41711

Therapeutic properties of Scutellaria baicalensis in db/db mice evaluated using Connectivity Map and network pharmacology
Cited by: 18
Author(s): Bu-Yeo Kim, Kwang Hoon Song, Chi-Yeon Lim, Su-In Cho
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2156-10-48

Single-feature polymorphism discovery by computing probe affinity shape powers
Cited by: 11
Author(s): Wayne Xu, Seungho Cho, Sungjin Yang, Yung–Tsi Bolon, Hatice Bilgiç, Haiyan Jia, Yongqiang Xiong, Gary J. Muehlbauer
Software Mentions: 2
Published: about 17 years ago

10.1038/srep38639

Transient appearance of circulating tumor DNA associated with de novo treatment
Cited by: 7
Author(s): Kikuya Kato, Junji Uchida, Yoji Kukita, Toru Kumagai, Kazumi Nishino, Tomio Inoue, Masashi Kimura, Fumio Imamura
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep41923

A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis
Cited by: 8
Author(s): Zheng Yang, Helen L. Bullifent, Karen Moore, Konrad Paszkiewicz, Richard J. Saint, Stephanie J. Southern, Olivia L. Champion, Nicola J. Senior, Mitali Sarkar‐Tyson, Petra C. F. Oyston, Timothy P. Atkins, Richard W. Titball
Software Mentions: 2
Published: over 9 years ago

10.1038/srep35100

Translation Elongation Factor eEF1A2 is a Novel Anticancer Target for the Marine Natural Product Plitidepsin
Cited by: 68
Author(s): Alejandro Losada, María José Muñoz-Alonso, Carlos Tejerizo García, Pedro A. Sánchez‐Murcia, Juan Fernando Martínez-Leal, Juan M. Domínguez, M. Pilar Lillo, Federico Gago, Carlos M. Galmarini
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12883-018-1044-1

Protocol for promoting recovery optimization of walking activity in stroke (PROWALKS): a randomized controlled trial
Cited by: 16
Author(s): Henry Wright, Tamara Wright, Ryan T. Pohlig, Scott E. Kasner, Jonathan Raser-Schramm, Darcy S. Reisman
Software Mentions: 2
Published: over 8 years ago

10.1038/srep35108

Analysis of the brain mural cell transcriptome
Cited by: 166
Author(s): Liqun He, Michael Vanlandewijck, Elisabeth Raschperger, Maarja Andaloussi Mäe, Bongnam Jung, Thibaud Lebouvier, Koji Ando, Jennifer Hofmann, Annika Keller, Christer Betsholtz
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep32562

Crystal structure of the two-subunit tRNA m1A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae
Cited by: 15
Author(s): Mingxing Wang, Yuwei Zhu, Chongyuan Wang, Xia Fan, Xuping Jiang, Mohammad Ebrahimi, Zhi Qiao, Liwen Niu, Maikun Teng, Xu Li
Software Mentions: 2
Published: about 10 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

10.1038/srep32006

Genome-wide identification of cassava R2R3 MYB family genes related to abscission zone separation after environmental-stress-induced abscission
Cited by: 26
Author(s): Wenbin Liao, Yiling Yang, Yayun Li, Gan Wang, Ming Peng
Software Mentions: 2
Published: about 10 years ago

10.1038/srep37452

Non-coding RNAs match the deleted genomic regions in humans
Cited by: 3
Author(s): Boseon Byeon, Igor Kovalchuk
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep43109

miR-125b-5p enhances chemotherapy sensitivity to cisplatin by down-regulating Bcl2 in gallbladder cancer
Cited by: 62
Author(s): Dong Yang, Ming Zhan, Tao Chen, Wei Chen, Yunhe Zhang, Sunwang Xu, Jinchun Yan, Qihong Huang, Jian Wang
Software Mentions: 2
Published: over 9 years ago

10.1038/srep26719

Involvement of Auxin and Brassinosteroid in Dwarfism of Autotetraploid Apple (Malus × domestica)
Cited by: 69
Author(s): Yue Ma, Xue Hou, Lei Zhang, Feng Zhang, C. Ou, Feng Wang, Zhihong Zhang
Software Mentions: 2
Published: over 10 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

10.1038/srep25031

Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China
Cited by: 27
Author(s): Ting Wang, Zhen Wang, Fan Xia, Yingjuan Su
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

10.1186/s12862-015-0378-1

Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)8 isomerase evolutionary intermediates from a diverse metagenome
Cited by: 16
Author(s): Lianet Noda‐Garcia, Ana Lilia Juárez-Vázquez, María C. Ávila-Arcos, E.A. Verduzco-Castro, Gabriela M. Montero-Morán, Paul Gaytán, Mauricio Carrillo‐Tripp, Francisco Barona‐Gómez
Software Mentions: 2
Published: over 11 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

10.1186/s12866-019-1663-8

Thymol tolerance in Escherichia coli induces morphological, metabolic and genetic changes
Cited by: 9
Author(s): Fatemah Al-Kandari, Rabeah Al-Temaimi, Arnoud H. M. van Vliet, Martin J. Woodward
Software Mentions: 2
Published: almost 7 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

10.1038/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

10.1186/1471-2105-11-483

Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types
Cited by: 14
Author(s): Noor Dawany, Aydın Tözeren
Software Mentions: 2
Published: almost 16 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

10.1038/srep30867

Ameloblastoma Phenotypes Reflected in Distinct Transcriptome Profiles
Cited by: 7
Author(s): Shijia Hu, Joel S. Parker, Kimon Divaris, Ricardo Padilla, Valerie A. Murrah, J. Timothy Wright
Software Mentions: 2
Published: about 10 years ago

10.1038/srep44389

A novel strategy for clustering major depression individuals using whole-genome sequencing variant data
Cited by: 16
Author(s): Chenglong Yu, Bernhard T. Baune, Júlio Licinio, Ma Li Wong
Software Mentions: 2
Published: over 9 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

10.1186/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

10.1186/1471-2105-14-S11-S3

Efficient digest of high-throughput sequencing data in a reproducible report
Cited by: 4
Author(s): Zhe Zhang, Jeremy Leipzig, Ariella Sasson, Angela M Yu, Juan C. Perín, Hongbo Xie, Mahdi Sarmady, Patrick V. Warren, Peter S. White
Software Mentions: 2
Published: about 13 years ago

10.1186/1465-9921-14-80

Microarray profiling reveals suppressed interferon stimulated gene program in fibroblasts from scleroderma-associated interstitial lung disease
Cited by: 81
Author(s): Gisela Lindahl, Carmel Stock, Shiwen Xu, Patricio Clark Di Leoni, Piersante Sestini, Sarah Howat, George Bou‐Gharios, Andrew G. Nicholson, Christopher P. Denton, Jan C. Grutters, Toby M. Maher, Adrian Wells, David Abraham, Elisabetta A. Renzoni
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2105-14-358

Fragment assignment in the cloud with eXpress-D
Cited by: 24
Author(s): Anjeanette Roberts, Harvey Feng, Lior Pachter
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2105-13-S15-S4

Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
Cited by: 12
Author(s): Joseph S. Reddy, Ranjit Kumar, James Watt, Mark L. Lawrence, Shane C. Burgess, Bindu Nanduri
Software Mentions: 2
Published: about 14 years ago

10.1186/1748-717X-4-17

Constitutive gene expression profile segregates toxicity in locally advanced breast cancer patients treated with high-dose hyperfractionated radical radiotherapy
Cited by: 32
Author(s): Luis Alberto Henríquez Hernández, Pedro C. Lara, B. Pinar, Elisa Bordón, Carlos Rodríguez-Gallego, Cristina Bilbao, Leandro Fernández Pérez, Amílcar Flores Morales
Software Mentions: 2
Published: over 17 years ago

10.1098/rsos.160059

The dynamics of emotions in online interaction
Cited by: 28
Author(s): David García, Arvid Kappas, Dennis Küster, Frank Schweitzer
Software Mentions: 2
Published: about 10 years ago

10.1111/anec.12840

Young and early‐onset dilated cardiomyopathy with malignant ventricular arrhythmia and sudden cardiac death induced by the heterozygous LDB3, MYH6, and SYNE1 missense mutations
Cited by: 9
Author(s): Ting Zhao, Yuting Ma, Zuoquan Zhang, Jing Xian, Xiaojing Geng, Feng Wang, Jiana Huang, Zhe Yang, Yi Luo, Yenn‐Jiang Lin
Software Mentions: 2
Published: over 5 years ago

10.1098/rsos.171802

Spatial variability in size at maturity of golden king crab ( <i>Lithodes aequispinus</i> ) and implications for fisheries management
Cited by: 14
Author(s): Andrew Olson, Christopher E. Siddon, Ginny L. Eckert
Software Mentions: 2
Published: over 8 years ago

10.1007/s00709-017-1088-x

Histone H3 and H4 acetylation patterns are more dynamic than those of DNA methylation in Brachypodium distachyon embryos during seed maturation and germination
Cited by: 10
Author(s): Elżbieta Wolny, Agnieszka Brąszewska-Zalewska, Daria Kroczek, Robert Hasterok
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-14-S2-S7

Discovery and analysis of consistent active sub-networks in cancers
Cited by: 12
Author(s): Raj Gaire, Lorey Smith, Patrick O. Humbert, James E. Bailey, Peter J. Stuckey, Izhak Haviv
Software Mentions: 2
Published: over 13 years ago

10.1002/pchj.309

Seeing the forest in order and the trees in disorder: Environmental orderliness versus disorderliness affects the perceptual processing style
Cited by: 2
Author(s): Kaiyun Li, Huijing Yang, Xueyang Wang, Tuo Zhang, Lu Ping, Fengxun Lin
Software Mentions: 2
Published: about 7 years ago

10.1098/rsos.172253

Analysis of the regulation networks in grapevine reveals response to waterlogging stress and candidate gene-marker selection for damage severity
Cited by: 22
Author(s): Xudong Zhu, Xiaopeng Li, Songtao Jiu, Kekun Zhang, Chen Wang, Jinggui Fang
Software Mentions: 2
Published: over 8 years ago

10.1073/pnas.2022928118

Signatures of immune dysfunction in HIV and HCV infection share features with chronic inflammation in aging and persist after viral reduction or elimination
Cited by: 16
Author(s): Cesar J. L. Angel, Edward A. Pham, Huixun Du, Francesco Vallania, Benjamin Fram, Kevin Pérez, Thai Nguyen, Yael Rosenberg-Hasson, Aijaz Ahmed, Cornelia L. Dekker, Philip Grant, Purvesh Khatri, Holden T. Maecker, Jeffrey S. Glenn, Mark M. Davis, David Furman
Software Mentions: 2
Published: over 5 years ago

10.1186/s12920-015-0101-5

Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems
Cited by: 55
Author(s): Pontus Eriksson, Mattias Aine, Srinivas Veerla, Fredrik Liedberg, Gottfrid Sjödahl, Mattias Höglund
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-12-S14-S7

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information
Cited by: 42
Author(s): Shin Suzuki, Tomohiro Yasuda, Yuichi Shiraishi, Satoru Miyano, Masao Nagasaki
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.ppat.1009527

Evaluating the fitness of PA/I38T-substituted influenza A viruses with reduced baloxavir susceptibility in a competitive mixtures ferret model
Cited by: 20
Author(s): Leo Lee, Jie Zhou, Paulina Koszalka, Rebecca Frise, Rubaiyea Farrukee, Keiko Baba, Shahjahan Miah, Toetsu Shishido, Mónica Galiano, Takashi Hashimoto, Shinya Omoto, Takeki Uehara, Edin Mifsud, Neil Collinson, Klaus Kuhlbusch, Barry Clinch, Steffen Wildum, William Barclay, Aeron C. Hurt
Software Mentions: 2
Published: over 5 years ago

10.1186/s12920-015-0090-4

BMP2 response pattern in human lung fibroblasts predicts outcome in lung adenocarcinomas
Cited by: 15
Author(s): Michal Rajski, Annika Sääf, Martin Buess
Software Mentions: 2
Published: over 11 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

10.1371/journal.ppat.1009589

Respiratory syncytial virus M2-1 protein associates non-specifically with viral messenger RNA and with specific cellular messenger RNA transcripts
Cited by: 6
Author(s): Molly R. Braun, Sarah L. Noton, Emmeline L. Blanchard, Afzaal Shareef, Philip J. Santangelo, W. Evan Johnson, Rachel Fearns
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1006365

Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus
Cited by: 54
Author(s): Elizabeth Jaworski, Andrew Routh
Software Mentions: 2
Published: over 9 years ago

10.1186/s12920-020-00733-w

A machine learning framework for genotyping the structural variations with copy number variant
Cited by: 1
Author(s): Zheng Tian, Xiaoyan Zhu, Xuanping Zhang, Zhongmeng Zhao, Xin Yi, Jiayin Wang, Hongle Li
Software Mentions: 2
Published: about 6 years ago

10.18632/aging.202888

Genetic landscape of breast cancer and mutation tracking with circulating tumor DNA in Chinese women
Cited by: 6
Author(s): Yinghao Wang, Lizhi Lin, Linhong Li, Jialiang Wen, Yili Chi, Rutian Hao, Xuanxuan Dai, Yizuo Chen, Du-Ping Huang, Yi-Li Zhou, Jie You, Zhiqiang Ye, Hao Chen, Liping Jin, Danxiang Chen, Fan Yang, Erjie Xia, Xueyan Ma, Fengyu Guo, Yunguang Tong, Min Zheng, Ouchen Wang
Software Mentions: 2
Published: over 5 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

10.1186/1755-8794-5-48

Integrative analysis of neuroblastoma and pheochromocytoma genomics data
Cited by: 15
Author(s): Péter M. Szabó, Miklós Pintér, Dorottya Szabó, Adrienn Zsippai, Attila Patócs, András Falus, Kàroly Rácz, Péter Igaz
Software Mentions: 2
Published: almost 14 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

10.1371/journal.ppat.1002411

Toward an Integrated Model of Capsule Regulation in Cryptococcus neoformans
Cited by: 88
Author(s): Brian C. Haynes, Michael L. Skowyra, Sarah J. Spencer, Stacey R. Gish, M. P. Williams, Elizabeth Held, Michael R. Brent, Tamara L. Doering
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.ppat.1004522

Structure and Specificity of the Bacterial Cysteine Methyltransferase Effector NleE Suggests a Novel Substrate in Human DNA Repair Pathway
Cited by: 24
Author(s): Qing Yao, Li Zhang, Xin Wan, Jing Chen, Liyan Hu, Xiaojun Ding, Lin Li, Jayashree Karar, Hongzhuang Peng, She Chen, Niu Huang, Frank J. Rauscher, Feng Shao
Software Mentions: 2
Published: almost 12 years ago

10.1038/srep09506

The effect of music performance on the transcriptome of professional musicians
Cited by: 36
Author(s): Chakravarthi Kanduri, Tuire Kuusi, Minna Ahvenainen, Anju K. Philips, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 2
Published: over 11 years ago

10.1186/2043-9113-2-13

Splitting random forest (SRF) for determining compact sets of genes that distinguish between cancer subtypes
Cited by: 5
Author(s): Xiaowei Guan, Mark R. Chance, Jill S. Barnholtz‐Sloan
Software Mentions: 2
Published: over 14 years ago

10.1111/jcmm.15642

S‐adenosylmethionine in combination with decitabine shows enhanced anti‐cancer effects in repressing breast cancer growth and metastasis
Cited by: 18
Author(s): Niaz Mahmood, Ani Arakelian, David Cheishvili, Moshe Szyf, Shafaat A. Rabbani
Software Mentions: 2
Published: about 6 years ago

10.4172/2153-0602.1000182

Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level
Cited by: 24
Author(s): Da Wei Huang, Castle Raley, Min Jiang, Xin Zheng, Dun Liang, Muhammad T Rehman, Helene Highbarger, Xiaoli Jiao, Brad T. Sherman, Liang Ma, Xiaofeng Chen, Thomas Skelly, Jennifer L. Troyer, Robert M. Stephens, Tomozumi Imamichi, Alice Pau, Richard A. Lempicki, Bao Tran, Dwight V. Nissley, H. Clifford Lane, Robin Dewar
Software Mentions: 2
Published: over 10 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

10.1186/1755-8794-2-57

Evaluation of a new high-dimensional miRNA profiling platform
Cited by: 24
Author(s): Julie M. Cunningham, Ann L. Oberg, Pedro M. Borralho, Betsy T. Kren, Amy J. French, Liang Wang, Brian M. Bot, Bruce W. Morlan, Kevin A.T. Silverstein, Rod Staggs, Yan Zeng, Anne Françoise Lamblin, Christopher A. Hilker, Jie Fan, Clifford J. Steer, Stephen N. Thibodeau
Software Mentions: 2
Published: about 17 years ago

10.1111/jcmm.14284

Augmented CD133 expression in distal margin correlates with poor prognosis in colorectal cancer
Cited by: 7
Author(s): Tapas K. Pradhan, Krishnanand Padmanabhan, Manu Prasad, K Chandramohan, S. Asha Nair
Software Mentions: 2
Published: over 7 years ago

10.1080/14756366.2021.1900160

Modulation of SETDB1 activity by APQ ameliorates heterochromatin condensation, motor function, and neuropathology in a Huntington’s disease mouse model
Cited by: 4
Author(s): Yu Jin Hwang, Seung Jae Hyeon, Young‐Hee Kim, Sungsu Lim, Min Young Lee, Jieun Kim, Ashwini M. Londhe, Lizaveta Gotina, Yunha Kim, Ae Nim Pae, Yong Seo Cho, Jihye Seong, Hyemyung Seo, Yun Kyung Kim, Hyunah Choo, Hoon Ryu, Seungjae Min
Software Mentions: 2
Published: over 5 years ago

10.1186/s40709-015-0032-5

Data integration in biological research: an overview
Cited by: 44
Author(s): Vasileios Lapatas, Michalis Stefanidakis, Rafael C. Jiménez, Allegra Via, Maria Victoria Schneider
Software Mentions: 2
Published: about 11 years ago

10.1074/jbc.M114.561845

Involvement of MicroRNAs in the Regulation of Muscle Wasting during Catabolic Conditions
Cited by: 120
Author(s): Ricardo Soares, Stefano Cagnin, Francesco Chemello, Matteo Silvestrin, Antonio Musarò, Cristiano De Pittà, Gerolamo Lanfranchi, Marco Sandri
Software Mentions: 2
Published: about 12 years ago

10.1117/1.JBO.25.6.066005

Gastric cancer diagnosis using hyperspectral imaging with principal component analysis and spectral angle mapper
Cited by: 20
Author(s): Ningliang Liu, Yaxiong Guo, Houmin Jiang, Wei Yi
Software Mentions: 2
Published: about 6 years ago

10.1107/S1600576716000649

The Stanford Automated Mounter: pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines
Cited by: 30
Author(s): Silvia Russi, Jianguo Song, S.E. McPhillips, Aina E. Cohen
Software Mentions: 2
Published: over 10 years ago

10.1186/s12920-015-0088-y

Gene expression network analysis reveals new transcriptional regulators as novel factors in human ischemic cardiomyopathy
Cited by: 19
Author(s): Isabel Herrer, Esther Roselló‐Lletí, Ana Ortega, Estefanía Tarazón, Maria Micaela Molina‐Navarro, Juan Carlos Triviño, Luis Martínez‐Dolz, Luís Almenar, Francisca Lago, Ignacio Sánchez‐Lázaro, José Ramón González-Juanatey, Antonio Salvador, Manuel Portolés, Miguel Rivera
Software Mentions: 2
Published: over 11 years ago

10.1107/S1600576716019750

New synchrotron powder diffraction facility for long-duration experiments
Cited by: 35
Author(s): Claire Murray, Joseph L. Potter, Sarah Day, Annabelle R. Baker, Stephen P. Thompson, Jon Kelly, Christopher G. Morris, Sihai Yang, Chiu C. Tang
Software Mentions: 2
Published: over 9 years ago

10.1117/1.JBO.26.10.106002

First-in-human pilot study of snapshot multispectral endoscopy for early detection of Barrett’s-related neoplasia
Cited by: 3
Author(s): Dale J. Waterhouse, Sophia Bano, Władysław Januszewicz, D. Stoyanov, Rebecca Fitzgerald, Massimiliano di Pietro, Sarah E. Bohndiek
Software Mentions: 2
Published: almost 5 years ago

10.1186/1755-8794-5-22

Relation between smoking history and gene expression profiles in lung adenocarcinomas
Cited by: 36
Author(s): Johan Staaf, Göran Jönsson, Mats Jönsson, Anna Karlsson, Sten Isaksson, Annette Salomonsson, Helen Pettersson, Maria Soller, Sven-Börje Ewers, Leif Johansson, Per Jönsson, Maria Planck
Software Mentions: 2
Published: over 14 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

10.3390/insects10030064

The Phylogenetic Relationships of Tiaronthophagus n.gen. (Coleoptera, Scarabaeidae, Onthophagini) Evaluated by Phenotypic Characters
Cited by: 1
Author(s): Angela Roggero, Philippe Moretto, Enrico Barbero, Claudia Palestrini
Software Mentions: 2
Published: over 7 years ago

10.1038/s41438-020-00399-6

The mutation of ent-kaurene synthase, a key enzyme involved in gibberellin biosynthesis, confers a non-heading phenotype to Chinese cabbage (Brassica rapa L. ssp. pekinensis)
Cited by: 20
Author(s): Yue Gao, Shengnan Huang, Gaoyang Qu, Wei Fu, Meidi Zhang, Zhiyong Liu, Hui Feng
Software Mentions: 2
Published: almost 6 years ago

10.1080/19490976.2021.1875774

Effects of colon-targeted vitamins on the composition and metabolic activity of the human gut microbiome– a pilot study
Cited by: 48
Author(s): Van T. Pham, Sophie Fehlbaum, Nicole Seifert, Nathalie Richard, Maaike J. Bruins, Wilbert Sybesma, Ateequr Rehman, Robert E. Steinert
Software Mentions: 2
Published: over 5 years ago

10.1016/j.heliyon.2018.e00813

Reducing electric energy consumption in linear Fresnel collector solar fields coupled to thermal desalination plants by optimal mirror defocusing
Cited by: 13
Author(s): Mohamed Alhaj, Sami G. Al-Ghamdi
Software Mentions: 2
Published: about 8 years ago

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566