cran: SAM | Projects | Ecosyste.ms: Papers

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/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

10.5808/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

10.1016/j.gpb.2018.03.006

RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes
Cited by: 14
Author(s): Wanfei Liu, Shizhou Wu, Qiang Lin, Shenghan Gao, Feng Ding, Xiaowei Zhang, Hasan Awad Aljohi, Jun Yu, Songnian Hu
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13742-015-0073-6

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant
Cited by: 65
Author(s): Andreas Bremges, Irena Maus, Peter Belmann, Felix Gregor Eikmeyer, Anderson M. Winkler, Andreas Albersmeier, Alfred Pühler, Andreas Schlüter, Alexander Sczyrba
Software Mentions: 2
Published: about 11 years ago

10.1093/gigascience/giy106

Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research
Cited by: 24
Author(s): Zhijin Liu, Xinxin Tan, Pablo Orozco‐terWengel, Xuming Zhou, Liye Zhang, Shilin Tian, Zhongze Yan, Huailiang Xu, Ren Bao-ping, Peng Zhang, Zuofu Xiang, Binghua Sun, Christian Roos, Michael William Bruford, Ming Li
Software Mentions: 2
Published: about 8 years ago

10.1093/gigascience/giy131

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
Cited by: 87
Author(s): Daniel Mapleson, Luca Venturini, Gemy Kaithakottil, David Swarbreck
Software Mentions: 2
Published: almost 8 years ago

10.1093/gigascience/giy157

LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
Cited by: 116
Author(s): Gui-Cai Xu, Tianjun Xu, Rui Zhu, Yan Zhang, Shang-Qi Li, Hongwei Wang, Jiong-Tang Li
Software Mentions: 2
Published: over 7 years ago

10.1093/gigascience/giab007

HTSlib: C library for reading/writing high-throughput sequencing data
Cited by: 147
Author(s): James K. Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan, Andrew Whitwham, Thomas M. Keane, Robert M. Davies
Software Mentions: 2
Published: over 5 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

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

10.1038/s41438-018-0021-6

Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map
Cited by: 23
Author(s): Muqing Yan, David Byrne, Patricia E. Klein, Jianping Yang, Qianni Dong, Natalie Anderson
Software Mentions: 2
Published: over 8 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

10.1186/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/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

10.1038/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

10.1038/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/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

10.1038/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

10.1038/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

10.1038/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/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/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/srep31313

CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs
Cited by: 119
Author(s): Tim Schneider, Lee-Hsueh Hung, Silke Schreiner, Stefan Starke, Heinrich Eckhof, Oliver Roßbach, Stefan Reich, Jan Medenbach, Albrecht Bindereif
Software Mentions: 2
Published: about 10 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/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

10.1038/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

10.1038/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/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/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/srep41312

The choreography of the chemical defensome response to insecticide stress: insights into the Anopheles stephensi transcriptome using RNA-Seq
Cited by: 36
Author(s): Leone De Marco, Davide Sassera, Sara Epis, Valentina Mastrantonio, Marco Ferrari, Irene Ricci, Francesco Comandatore, Claudio Bandi, Daniele Porretta, Sandra Urbanelli
Software Mentions: 2
Published: over 9 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

10.1038/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

10.1038/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/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/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

10.1038/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

10.1038/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/s41598-017-09285-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

10.1038/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

10.1038/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

10.1038/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/s41598-017-15516-0

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

10.1038/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/s41598-018-20727-0

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/s41598-018-23337-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

10.1038/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

10.1038/s41598-018-29190-3

Assembly and Analysis of Unmapped Genome Sequence Reads Reveal Novel Sequence and Variation in Dogs
Cited by: 4
Author(s): Lindsay A. Holden, Meharji Arumilli, Marjo K. Hytönen, Sruthi Hundi, Jarkko Salojärvi, Kim H. Brown, Hannes Lohi
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-29240-w

Urine-derived cells: a promising diagnostic tool in Fabry disease patients
Cited by: 22
Author(s): Gisela G. Slaats, Fabian Braun, Martin Hoehne, Laura E. Frech, Linda Blomberg, Thomas Benzing, Bernhard Schermer, Markus M. Rinschen, Christine Kurschat
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-33752-w

The pathogenic mechanisms of Tilletia horrida as revealed by comparative and functional genomics
Cited by: 13
Author(s): Ai‐Jun Wang, Linxiu Pang, Na Wang, Peng Ai, Desuo Yin, Shuangcheng Li, Qi Deng, Jun Zhu, Yueyang Liang, Jianqing Zhu, Ping Li, Anqi Zheng
Software Mentions: 2
Published: almost 8 years ago

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/s41598-019-39808-9

High density linkage map construction and QTL mapping for runner production in allo-octoploid strawberry Fragaria × ananassa based on ddRAD-seq derived SNPs
Cited by: 17
Author(s): Mohammad Rashed Hossain, Sathishkumar Natarajan, Hoy‐Taek Kim, Denison Michael Immanuel Jesse, Lee Cheol-Gyu, Jong-In Park, Ill–Sup Nou
Software Mentions: 2
Published: over 7 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/s41598-019-41672-6

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/s41598-019-47218-0

E2F1 Drives Breast Cancer Metastasis by Regulating the Target Gene FGF13 and Altering Cell Migration
Cited by: 48
Author(s): Daniel P. Hollern, Matthew Swiatnicki, Jonathan Rennhack, Sean A. Misek, Brooke C. Matson, Andrew McAuliff, Kathleen A. Gallo, Kathleen M. Caron, Eran R. Andrechek
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-47318-x

Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice
Cited by: 3
Author(s): Lin Cheng, Kyu‐Won Kim, Yong‐Jin Park
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-50897-4

Enhanced glacial discharge from the eastern Antarctic Peninsula since the 1700s associated with a positive Southern Annular Mode
Cited by: 24
Author(s): William A. Dickens, Gerhard Kuhn, Melanie J. Leng, Alastair G C Graham, Julian A. Dowdeswell, Michael P. Meredith, C. D. Hillenbrand, Dominic A. Hodgson, Roberts Sj, Hilary J. Sloane, James A Smith
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-59207-9

Relationships Between Environmental Conditions And Fish Assemblages In Tropical Savanna Headwater Streams
Cited by: 11
Author(s): Thiago Bernardi Vieira, Francisco Leonardo Tejerina‐Garro
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59375-8

Full annual monitoring of Subantarctic Emiliania huxleyi populations reveals highly calcified morphotypes in high-CO2 winter conditions
Cited by: 17
Author(s): Andrés S. Rigual-Hernández, Thomas W. Trull, José-Abel Flores, Scott D. Nodder, Ruth Eriksen, Diana M. Davies, Gustaaf M. Hallegraeff, Francisco J. Sierro, Shramik Patil, Aleix Cortina, Anne-Marie Ballegeer, Lisa C. Northcote, F. Abrantes, Marta M. Rufino
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-61942-y

Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome
Cited by: 13
Author(s): Leila Ghanbari Maman, Fahimeh Palizban, Fereshteh Fallah Atanaki, Naser Elmi, Shohreh Ariaeenejad, Mohammad Reza Ghaffari, Kaveh Kavousi
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-62467-0

The trends in land surface heat fluxes over global monsoon domains and their responses to monsoon and precipitation
Cited by: 11
Author(s): Jian Zeng, Qiang Zhang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-62975-z

Metabolomic alternations of follicular fluid of obese women undergoing in-vitro fertilization treatment
Cited by: 14
Author(s): Jing-Yan Song, Shufen Xiang, Conghui Pang, Jiayin Guo, Zhen‐Gao Sun
Software Mentions: 2
Published: over 6 years ago

10.3390/s20164551

CNN and LSTM-Based Emotion Charting Using Physiological Signals
Cited by: 50
Author(s): Muhammad Najam Dar, M. Usman Akram, Sajid Gul Khawaja, Amit N. Pujari
Software Mentions: 2
Published: about 6 years ago

10.3390/s21041138

Open-Design for a Smart Cover of a Night-Time Telescope for Day-Time Use
Cited by: 1
Author(s): R. Cedazo, Alberto Brunete, Hugo R. Albarracin, Esteban González
Software Mentions: 2
Published: over 5 years ago

10.3390/s21051792

Learning Subject-Generalized Topographical EEG Embeddings Using Deep Variational Autoencoders and Domain-Adversarial Regularization
Cited by: 7
Author(s): Juan Lorenzo Hagad, Tsukasa Kimura, Kenichi Fukui, Masayuki Numao
Software Mentions: 2
Published: over 5 years ago

10.3390/s21165279

Rapid Foreign Object Detection System on Seaweed Using VNIR Hyperspectral Imaging
Cited by: 6
Author(s): Donghoon Kwak, Guk-Jin Son, Mi‐Kyung Park, Young-Duk Kim
Software Mentions: 2
Published: about 5 years ago

10.1186/1758-907X-2-2

Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments
Cited by: 83
Author(s): Kevin McCormick, Matthew R. Willmann, Blake C. Meyers
Software Mentions: 2
Published: over 15 years ago

10.1186/1751-0473-7-6

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments
Cited by: 63
Author(s): Ricardo H. Ramírez-González, Raoul Jean Pierre Bonnal, Mario Cáccamo, Dan MacLean
Software Mentions: 2
Published: over 14 years ago

10.1186/s13029-016-0056-8

A new tool for prioritization of sequence variants from whole exome sequencing data
Cited by: 9
Author(s): Brigitte Glanzmann, Hendri Herbst, Craig Kinnear, Marlo Möller, Junaid Gamieldien, Soraya Bardien
Software Mentions: 2
Published: about 10 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

10.1186/s40064-016-3728-6

Characterization of saliva microbiota’s functional feature based on metagenomic sequencing
Cited by: 13
Author(s): Fang Yang, Kang Ning, Xiaowei Zeng, Qian Zhou, Xiaoquan Su, Xiao Yuan
Software Mentions: 2
Published: almost 10 years ago

10.1186/scrt535

Loss of non-coding RNA expression from the DLK1-DIO3 imprinted locus correlates with reduced neural differentiation potential in human embryonic stem cell lines
Cited by: 106
Author(s): Chu Fan Mo, Fang Wu, Kang-Yu Tai, Wei Chun Chang, Kai Wei Chang, Hung‐Chi Kuo, Hong Nerng Ho, H.-F. Chen, Shau-Ping Lin
Software Mentions: 2
Published: over 11 years ago

10.1186/s13287-018-1050-7

Key genes and integrated modules in hematopoietic differentiation of human embryonic stem cells: a comprehensive bioinformatic analysis
Cited by: 11
Author(s): Pengfei Li, Mengyao Wu, Qiwang Lin, Shu Wang, Tong Chen, Hua Jiang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13287-020-01962-7

Co-encapsulation of HNF4α overexpressing UMSCs and human primary hepatocytes ameliorates mouse acute liver failure
Cited by: 14
Author(s): Defu Kong, Huiming Xu, Mo Chen, Yingchun Yu, Yongbing Qian, Tian Qin, Ying Tong, Qiang Xia, Hualian Hang
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13011-021-00404-8

The Alcohol Use Disorders Identification Test (AUDIT) in the Russian language - a systematic review of validation efforts and application challenges
Cited by: 4
Author(s): Maria Neufeld, Anna Bunova, Carina Ferreira‐Borges, Evgeny А. Bryun, E.V. Fadeeva, Artyom Gil, Б. Э. Горный, Daria Khaltourina, Evgenia Koshkina, А. В. Надеждин, Elena Tetenova, Melita Vujnović, Artyom Gil, Elena Yurasova, Jürgen Rehm
Software Mentions: 2
Published: almost 5 years ago

10.7150/thno.35882

HIF-1α/Wnt signaling-dependent control of gene transcription regulates neuronal differentiation of glioblastoma stem cells
Cited by: 28
Author(s): Daniele Boso, Elena Rampazzo, Carlo Zanon, Silvia Bresolin, Francesca Maule, Elena Porcù, Alice Cani, Alessandro Della Puppa, Luca Trentin, Giuseppe Basso, Luca Persano
Software Mentions: 2
Published: over 7 years ago

10.7150/thno.37623

Comprehensive characterization of the phosphoproteome of gastric cancer from endoscopic biopsy specimens
Cited by: 19
Author(s): Yuichi Abe, Hidekazu Hirano, Hirokazu Shoji, Asa Tada, Junko Isoyama, Akemi Kakudo, Daigo Gunji, Kazufumi Honda, Narikazu Boku, Jun Adachi, Takeshi Tomonaga
Software Mentions: 2
Published: over 6 years ago

10.1038/s41398-020-01050-7

Translational study of the whole transcriptome in rats and genetic polymorphisms in humans identifies LRP1B and VPS13A as key genes involved in tolerance to cocaine-induced motor disturbances
Cited by: 4
Author(s): Florence Vorspan, Romain Icick, Nawel Mekdad, Cindie Courtin, Vanessa Bloch, Frank Bellivier, Jean‐Louis Laplanche, Nathalie Prince, Dmitry Pishalin, Cyril Firmo, Corinne Blugeon, Bruno Mégarbane, Cynthia Marie-Claire, Nadia Benturquia
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.tplants.2014.02.004

Modelling hormonal response and development
Cited by: 87
Author(s): Ute Voß, Anthony Bishopp, Etienne Farcot, Malcolm J. Bennett
Software Mentions: 2
Published: over 12 years ago

10.1128/mBio.00202-18

Community Development betweenPorphyromonas gingivalisandCandida albicansMediated by InlJ and Als3
Cited by: 65
Author(s): Maryta Sztukowska, Lindsay C. Dutton, Christopher Delaney, Mark Ramsdale, Gordon Ramage, Howard F. Jenkinson, Angela H. Nobbs, Richard J. Lamont
Software Mentions: 2
Published: over 8 years ago

10.1128/mBio.00966-18

cAMP Receptor Protein Controls Vibrio cholerae Gene Expression in Response to Host Colonization
Cited by: 41
Author(s): Jainaba Manneh-Roussel, James R. J. Haycocks, Andrés Magán, Nicolás Pérez-Soto, Kerstin Voelz, Andrew Camilli, Anne Marie Krachler, David C. Grainger
Software Mentions: 2
Published: about 8 years ago

10.1128/mBio.00764-19

Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens
Cited by: 32
Author(s): Andrew Ryan Passer, Marco A. Coelho, R. Blake Billmyre, Minou Nowrousian, Moritz Mittelbach, Andrey Yurkov, Anna Floyd Averette, Christina A. Cuomo, Sheng Sun, Joseph Heitman
Software Mentions: 2
Published: about 7 years ago

10.1128/mBio.00633-21

Genome Scale Analysis Reveals IscR Directly and Indirectly Regulates Virulence Factor Genes in Pathogenic Yersinia
Cited by: 4
Author(s): David Balderas, Erin L. Mettert, Hanh Lam, Rajdeep Banerjee, Tomas Gverzdys, Pablo Álvarez, Geetha Saarunya, N. Kyle Tanner, Adam Zoubedi, Yahan Wei, Patricia J. Kiley, Victoria Auerbuch
Software Mentions: 2
Published: about 5 years ago

10.1128/mSystems.00023-16

Thermus and the Pink Discoloration Defect in Cheese
Cited by: 67
Author(s): Lisa Quigley, Daniel J. O’Sullivan, David F.M. Daly, Órla O’Sullivan, Zuzana Burdíková, Rostislav Váňa, Tom Beresford, R. Paul Ross, Gerald F. Fitzgerald, P.L.H. McSweeney, Linda Giblin, Jeremiah J. Sheehan, Paul D. Cotter
Software Mentions: 2
Published: about 10 years ago

10.1128/mSystems.00156-18

Neisseria gonorrhoeae Exposed to Sublethal Levels of Hydrogen Peroxide Mounts a Complex Transcriptional Response
Cited by: 14
Author(s): Sarah J. Quillin, Adam J. Hockenberry, Michael C. Jewett, H. Steven Seifert
Software Mentions: 2
Published: almost 8 years ago

10.1128/mSystems.00920-20

phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
Cited by: 156
Author(s): Harald R. Gruber‐Vodicka, Brandon K. B. Seah, Elmar Pruesse
Software Mentions: 2
Published: almost 6 years ago

10.1007/s00439-016-1658-6

Novel bioinformatic developments for exome sequencing
Cited by: 36
Author(s): Stefan H. Lelieveld, Joris A. Veltman, Christian Gilissen
Software Mentions: 2
Published: over 10 years ago

10.1155/2013/404717

Exploiting Identifiability and Intergene Correlation for Improved Detection of Differential Expression
Cited by: 0
Author(s): J.R. Deller, Hayder Radha, J. Justin McCormick
Software Mentions: 2
Published: over 13 years ago

10.16910/jemr.13.3.6

Fluctuation in pupil size and spontaneous blinks reflect story transportation
Cited by: 4
Author(s): Johanna K. Kaakinen, Jaana Simola
Software Mentions: 2
Published: about 6 years ago

10.1007/s00484-018-1625-0

Local clothing thermal properties of typical office ensembles under realistic static and dynamic conditions
Cited by: 18
Author(s): S Stephanie Vesela, Agnes Psikuta, Ajh Arjan Frijns
Software Mentions: 2
Published: almost 8 years ago

10.1186/s41239-021-00264-z

An associational study: preschool teachers’ acceptance and self-efficacy towards Educational Robotics in a pre-service teacher training program
Cited by: 15
Author(s): Despoina Schina, Cristina Valls, Anna Borrull-Riera, Mireia Usart, Vanessa Esteve-González
Software Mentions: 2
Published: over 5 years ago

10.1029/2019JE006295

Evidence for Multiple Diagenetic Episodes in Ancient Fluvial‐Lacustrine Sedimentary Rocks in Gale Crater, Mars
Cited by: 41
Author(s): C. N. Achilles, E. B. Rampe, Robert T. Downs, T. F. Bristow, D. W. Ming, R. V. Morris, D. T. Vaniman, D. F. Blake, A. S. Yen, A. C. McAdam, B. Sutter, C. M. Fedo, Samantha Gwizd, L. M. Thompson, R. Gellert, S. M. Morrison, Allan H. Treiman, J. A. Crisp, T. S. J. Gabriel, S. J. Chipera, Robert M. Hazen, P. I. Craig, M. T. Thorpe, David J. Des Marais, J. P. Grotzinger, V. Tu, N. Castle, G. W. Downs, T. S. Peretyazhko, R. C. Walroth, P. Sarrazin, John Michael Morookian
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms161226129

Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM™ Platform
Cited by: 33
Author(s): Irene Vanni, Simona Coco, Anna Truini, Marta Rusmini, Maria Giovanna Dal Bello, Angela Alama, Barbara Banelli, Marco Mora, Erika Rijavec, Giulia Barletta, Carlo Genova, Federica Biello, C. Maggioni, Francesco Grossi
Software Mentions: 2
Published: almost 11 years ago

10.3390/ijms18020308

Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification
Cited by: 306
Author(s): Rick Kamps, Rita D. Brandão, Bianca Jc van den Bosch, Aimée D C Paulussen, Sofia Xanthoulea, Marinus J. Blok, Andrea Romano
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms19072001

Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling
Cited by: 31
Author(s): Jinhua Zuo, Yunxiang Wang, Beiwei Zhu, Yunbo Luo, Qing Wang, Lipu Gao
Software Mentions: 2
Published: about 8 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566