Ecosyste.ms: Papers

10.1186/s13059-020-02132-x

A systematic evaluation of single-cell RNA-sequencing imputation methods
Cited by: 156
Author(s): Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie Hicks
Software Mentions: 15
Published: about 4 years ago

10.1002/advs.201901850

<i>Mesostigma viride</i> Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta
Cited by: 29
Author(s): Zhe Liang, Yuke Geng, Changmian Ji, Hongwu Du, Chui Eng Wong, Qian Zhang, Ye Zhang, Pingxian Zhang, Adeel Riaz, Sadaruddin Chachar, Yike Ding, Jing Wen, Yun-Wen Wu, Mingcheng Wang, Hongkun Zheng, Yanmin Wu, Viktor Demko, Lisha Shen, Han Xiao, Pengpeng Zhang, Xiaofeng Gu, Hao Yu
Software Mentions: 10
Published: about 5 years ago

10.15252/msb.202110232

Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut
Cited by: 64
Author(s): Sergio Triana, Camila Metz-Zumaran, C. Ramı́rez, Carmon Kee, Patricio Doldan, Mohammed Shahraz, Daniel Schraivogel, Andreas R. Gschwind, Ashwini Kumar Sharma, Lars M. Steinmetz, Carl Herrmann, Theodore Alexandrov, Steeve Boulant, Megan L. Stanifer
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0023947

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction
Cited by: 19
Author(s): Christopher S. Poultney, Glenn L. Butterfoss, Michelle Gutwein, Kevin Drew, David Gresham, Kristin C. Gunsalus, Dennis Shasha, Richard Bonneau
Software Mentions: 8
Published: about 13 years ago

10.15252/msb.20178041

Molecular transitions in early progenitors during human cord blood hematopoiesis
Cited by: 120
Author(s): Shiwei Zheng, Efthymia Papalexi, Andrew Butler, William Stephenson, Rahul Satija
Software Mentions: 7
Published: over 6 years ago

10.1107/S0907444913007051

<i>OpenStructure</i>: an integrated software framework for computational structural biology
Cited by: 82
Author(s): Marco Biasini, Tobias Schmidt, Stefan Bienert, Valerio Mariani, Gabriel Studer, Juergen Haas, Niklaus Johner, Andreas Schenk, Ansgar Philippsen, Torsten Schwede
Software Mentions: 7
Published: over 11 years ago

10.1186/s12866-019-1672-7

An improved bind-n-seq strategy to determine protein-DNA interactions validated using the bacterial transcriptional regulator YipR
Cited by: 26
Author(s): Shi-Qi An, Miguel A. Valvano, Yu Yi, Jeremy S. Webb, Guillermo López–Campos
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-021-85848-5

Abnormal upregulation of cardiovascular disease biomarker PLA2G7 induced by proinflammatory macrophages in COVID-19 patients
Cited by: 18
Author(s): Yang Li, Yongzhong Jiang, Yi Zhang, Naizhe Li, Qiangling Yin, Linlin Liu, Xin Lv, Yan Liu, Aqian Li, Bin Fang, Jiajia Li, Hengping Ye, Gang Ye, Xiaoxian Cui, Yang Liu, Yuanyuan Qu, Chuan Li, Jiandong Li, Dexin Li, Zhongtao Gai, Shiwen Wang, Faxian Zhan, Mifang Liang
Software Mentions: 6
Published: over 3 years ago

10.3389/fpsyg.2021.681945

Comparing the Effect of Product-Based Metrics on the Translation Process
Cited by: 1
Author(s): Bram Vanroy, Moritz Schaeffer, Lieve Macken
Software Mentions: 5
Published: over 3 years ago

10.1093/bib/bbab038

Accurate prediction of inter-protein residue–residue contacts for homo-oligomeric protein complexes
Cited by: 39
Author(s): Yumeng Yan, Sheng‐You Huang
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2021.666771

scGPS: Determining Cell States and Global Fate Potential of Subpopulations
Cited by: 1
Author(s): Michael Thompson, Maika Matsumoto, Tianqi Ma, Anne Senabouth, Nathan J. Palpant, Joseph E. Powell, Quan Nguyen
Software Mentions: 5
Published: over 3 years ago

10.15252/embj.2019103852

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic <scp>sRNA</scp> activation in competence control
Cited by: 47
Author(s): Jens Hör, Geneviève Garriss, Silvia Di Giorgio, Lisa-Marie Hack, Jens T. Vanselow, Konrad U. Förstner, Andreas Schlösser, Birgitta Henriques‐Normark, Jörg Vogel
Software Mentions: 5
Published: over 4 years ago

10.15252/msb.20199198

Enhancing scientific discoveries in molecular biology with deep generative models
Cited by: 28
Author(s): Romain Lopez, Adam Gayoso, Nir Yosef
Software Mentions: 5
Published: about 4 years ago

10.15252/msb.20209946

The transcriptome dynamics of single cells during the cell cycle
Cited by: 28
Author(s): Daniel Schwabe, Sara Formichetti, Jan Philipp Junker, Martin Falcke, Nikolaus Rajewsky
Software Mentions: 4
Published: about 4 years ago

10.1002/iid3.362

What has single‐cell RNA sequencing revealed about microglial neuroimmunology?
Cited by: 15
Author(s): Norwin Kubick, Patrick C. Henckell Flournoy, Pavel Klimovich, Gina Manda, Michel‐Edwar Mickael
Software Mentions: 4
Published: about 4 years ago

10.1002/bit.26891

Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture
Cited by: 35
Author(s): Inmaculada Hernández, Heena Dhiman, Gerald Klanert, Vaibhav Jadhav, Norbert Auer, Michael Hanscho, Martina Baumann, Anna Esteve‐Codina, Marc Dabad, Jessica Gómez, Tyler Alioto, Angelika Merkel, Emanuele Raineri, Simon Heath, Daniel Rico, Nicole Borth
Software Mentions: 3
Published: almost 6 years ago

10.1002/advs.202002825

Engineered Tools to Study Intercellular Communication
Cited by: 30
Author(s): Benjamin Yang, Trisha M. Westerhof, Kaitlyn Sabin, Sofía D. Merajver, Carlos A. Aguilar
Software Mentions: 3
Published: almost 4 years ago

10.1111/acel.13428

Single‐oocyte transcriptome analysis reveals aging‐associated effects influenced by life stage and calorie restriction
Cited by: 13
Author(s): Tomobumi Mishina, Namine Tabata, Tetsutaro Hayashi, Mika Yoshimura, Mana Umeda, Midori Mori, Yayoi Ikawa, Hiroshi Hamada, Itoshi Nikaido, Tomoya S. Kitajima
Software Mentions: 3
Published: over 3 years ago

10.1111/mec.14560

Patterns of Z chromosome divergence among <i>Heliconius</i> species highlight the importance of historical demography
Cited by: 62
Author(s): Steven M. Van Belleghem, Margarita Baquero, Riccardo Papa, Camilo Salazar, W. Owen McMillan, Brian A. Counterman, Chris D. Jiggins, Simon H. Martin
Software Mentions: 3
Published: over 6 years ago

10.15252/msb.20188584

Path‐seq identifies an essential mycolate remodeling program for mycobacterial host adaptation
Cited by: 49
Author(s): Eliza J.R. Peterson, Rebeca Bailo, Alissa C. Rothchild, Mario L. Arrieta-Ortiz, Amardeep Kaur, Min Pan, Dat Mai, Abrar A. Abidi, Charlotte Cooper, Alan Aderem, Apoorva Bhatt, Nitin S. Baliga
Software Mentions: 3
Published: over 5 years ago

10.1002/wsbm.1467

Functional genomic approaches to elucidate the role of enhancers during development
Cited by: 13
Author(s): Genevieve E. Ryan, Emma K. Farley
Software Mentions: 3
Published: almost 5 years ago

10.1111/pbi.12685

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

10.1002/ctm2.308

Understanding cell‐cell communication and signaling in the colorectal cancer microenvironment
Cited by: 40
Author(s): Shaikha AlMusawi, Mehreen Ahmed, Abdolrahman S. Nateri
Software Mentions: 3
Published: almost 4 years ago

10.1111/jcmm.13238

State of the art technologies to explore long non-coding RNAs in cancer
Cited by: 57
Author(s): Saeede Salehi, Mohammad Taheri, Negar Azarpira, Abdolhossein Zare, Abbas Behzad-Behbahani
Software Mentions: 3
Published: over 7 years ago

10.7150/thno.44687

miR-182-3p/Myadm contribute to pulmonary artery hypertension vascular remodeling via a KLF4/p21-dependent mechanism
Cited by: 32
Author(s): Lan Sun, Peirong Lin, Ying Chen, Haoying Yu, Shen Ren, Jingrong Wang, Lei Zhao, Guanhua Du
Software Mentions: 3
Published: almost 5 years ago

10.1128/mBio.03399-20

<i>In Vivo</i> Transcriptome of Lactobacillus acidophilus and Colonization Impact on Murine Host Intestinal Gene Expression
Cited by: 11
Author(s): Yong Jun Goh, Rodolphe Barrangou, Todd R. Klaenhammer
Software Mentions: 3
Published: over 3 years ago

10.14338/2331-5180-5-2-000

Proceedings of the 57^th Annual Meeting of the Particle Therapy Cooperative Group (PTCOG)
Cited by: 3
Author(s):
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2105-9-18

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
Cited by: 985
Author(s): David Ellinghaus, Stefan Kurtz, Ute Willhoeft
Software Mentions: 2
Published: almost 17 years ago

10.1002/advs.202101229

Multiplexing Methods for Simultaneous Large‐Scale Transcriptomic Profiling of Samples at Single‐Cell Resolution
Cited by: 24
Author(s): Jiajing Cheng, Jie Liao, Xin Shao, Xiaoyan Lu, Xiaohui Fan
Software Mentions: 2
Published: over 3 years ago

10.1002/advs.201900997

Acrylonitrile‐Mediated Nascent RNA Sequencing for Transcriptome‐Wide Profiling of Cellular RNA Dynamics
Cited by: 13
Author(s): Yuqi Chen, Fan Wu, Zonggui Chen, Zhiyong He, Qi Wei, Weiwu Zeng, Kun Chen, Feng Xiao, Yushu Yuan, Xiaocheng Weng, Yu Zhou, Xiang Zhou
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0223212

Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock
Cited by: 3
Author(s): Matthew L. Chang, Sanny Moussette, Enrique Gamero-Estévez, José Héctor Gálvez, Victoria Chiwara, Indra R. Gupta, Aimee K. Ryan, Anna K. Naumova
Software Mentions: 2
Published: about 5 years ago

10.1002/mgg3.665

<i>BRPF1</i>‐associated intellectual disability, ptosis, and facial dysmorphism in a multiplex family
Cited by: 17
Author(s): Naomi Pode‐Shakked, Ortal Barel, Ben Pode‐Shakked, Aviva Eliyahu, Amihood Singer, Omri Nayshool, Nitzan Kol, Annick Raas‐Rothschild, Elon Pras, Mordechai Shohat
Software Mentions: 2
Published: over 5 years ago

10.1002/1878-0261.12681

Complex context relationships between DNA methylation and accessibility, histone marks, and <i>hTERT</i> gene expression in acute promyelocytic leukemia cells: perspectives for all‐<i>trans</i> retinoic acid in cancer therapy
Cited by: 7
Author(s): Delphine Garsuault, Claire Bouyer, Éric Nguyen, Rohan Kandhari, Martina Prochazkova‐Carlotti, Edith Chevret, Patricia Forgez, Évelyne Ségal-Bendirdjian
Software Mentions: 2
Published: over 4 years ago

10.1186/s13148-016-0303-5

UroMark—a urinary biomarker assay for the detection of bladder cancer
Cited by: 75
Author(s): Andrew Feber, Pawan Dhami, Dong Liang, Patricia de Winter, Wei Shen Tan, Mónica Martínez‐Fernández, Dirk S. Paul, Antony Hynes-Allen, Sheida Rezaee, Pratik Gurung, Simon Rodney, Ahmed Mehmood, Felipe Villacampa, Federico de la Rosa, Charles Jameson, Kar Keung Cheng, Maurice P. Zeegers, Richard T. Bryan, Nicholas D. James, Jesús M. Paramio, Alex Freeman, Stephan Beck, John D. Kelly
Software Mentions: 2
Published: almost 8 years ago

10.1111/1751-7915.13404

Gross transcriptomic analysis of <i>Pseudomonas putida</i> for diagnosing environmental shifts
Cited by: 5
Author(s): Ángeles Hueso-Gil, Belén Calles, George A. O’Toole, Vı́ctor de Lorenzo
Software Mentions: 2
Published: over 5 years ago

10.1089/crispr.2019.0009

Identification of Guide-Intrinsic Determinants of Cas9 Specificity
Cited by: 16
Author(s): Nicholas C. Huston, Josh Tycko, Eric L. Tillotson, Christopher J. Wilson, Vic E. Myer, Hariharan Jayaram, Barrett E. Steinberg
Software Mentions: 2
Published: over 5 years ago

10.1186/1751-0473-2-2

HitKeeper, a generic software package for hit list management
Cited by: 9
Author(s): Jörg Hau, Michael Müller, Marco Pagni
Software Mentions: 2
Published: over 17 years ago

10.1042/BJ20150612

The solution structures of native and patient monomeric human IgA1 reveal asymmetric extended structures: implications for function and IgAN disease
Cited by: 21
Author(s): Gar Kay Hui, David W. Wright, Owen L. Vennard, Lucy E. Rayner, Melisa Pang, See Cheng Yeo, Jayesh Gor, Karen Molyneux, Jonathan Barratt, Stephen J. Perkins
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-021-07572-8

Genome-scale analyses of transcriptional start sites in Mycobacterium marinum under normoxic and hypoxic conditions
Cited by: 3
Author(s): Shuo Huang, Wei Zhou, Wei Tang, Yong Zhang, Yangbo Hu, Shiyun Chen
Software Mentions: 2
Published: over 3 years ago

10.1002/ece3.5646

Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species
Cited by: 21
Author(s): Sara Kurland, Christopher W. Wheat, Maria de la Paz Celorio‐Mancera, Verena E. Kutschera, Jason Hill, Anastasia Andersson, Carl-Johan Rubin, Leif Andersson, Nils Ryman, Linda Laikre
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0042761

A Novel Approach for Transcription Factor Analysis Using SELEX with High-Throughput Sequencing (TFAST)
Cited by: 14
Author(s): D. Reiss, Frederick M. Howard, Harry L. T. Mobley
Software Mentions: 2
Published: over 12 years ago

10.1186/s13395-020-00239-0

X-linked muscular dystrophy in a Labrador Retriever strain: phenotypic and molecular characterisation
Cited by: 12
Author(s): I. Barthélémy, Nadège Calmels, Robert B. Weiss, Laurent Tiret, Adeline Vulin, Nicolas Wein, Cécile Peccate, Carole Drougard, Christophe Béroud, Nathalie Deburgrave, Jean-Laurent Thibaud, Catherine Escriou, Isabel Punzón, Luis Garcı́a, Jean‐Claude Kaplan, Kevin M. Flanigan, F. Leturcq, Stéphane Blot
Software Mentions: 2
Published: over 4 years ago

10.1002/ece3.2174

Genetic structure and diversity of natural and domesticated populations of<i>Citrus medica</i>L. in the Eastern Himalayan region of Northeast India
Cited by: 19
Author(s): Atiqur Rahman Barbhuiya, M. L. Khan, Selvadurai Dayanandan
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-019-5966-9

Genome-wide localization of the polyphenol quercetin in human monocytes
Cited by: 8
Author(s): Dana Atrahimovich, Avraham O. Samson, Yifthah Barsheshet, Jacob Vaya, Soliman Khatib, Eli Reuveni
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-11-417

FACT: Functional annotation transfer between proteins with similar feature architectures
Cited by: 27
Author(s): Tina Koestler, Arndt von Haeseler, Ingo Ebersberger
Software Mentions: 2
Published: over 14 years ago

10.3389/fpls.2015.01124

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress
Cited by: 16
Author(s): Anne-Antonella Serra, Ivan Couée, David Heijnen, Sophie Michon-Coudouel, Cécile Sulmon, Gwenola Gouesbet
Software Mentions: 2
Published: almost 9 years ago

10.1002/wrna.1622

Functions and mechanisms of <scp>RNA</scp> tailing by metazoan terminal nucleotidyltransferases
Cited by: 24
Author(s): Vladyslava Liudkovska, Andrzej Dziembowski
Software Mentions: 1
Published: over 4 years ago

10.1111/pbi.13665

BnTIR: an online transcriptome platform for exploring RNA‐seq libraries for oil crop <i>Brassica napus</i>
Cited by: 56
Author(s): Dongxu Liu, Liangqian Yu, Lulu Wei, Pugang Yu, Wang Jing, Hu Zhao, Yuting Zhang, Shuntai Zhang, Zhiquan Yang, Guanqun Chen, Xuan Yao, Yanjun Yang, Yongming Zhou, Xuemin Wang, Shaoping Lu, Cheng Dai, Qingyong Yang, Liang Guo
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1004189

An Evolutionary Analysis of Antigen Processing and Presentation across Different Timescales Reveals Pervasive Selection
Cited by: 35
Author(s): Diego Forni, Rachele Cagliani, Claudia Tresoldi, Diego Forni, Luca De Gioia, Giulia Filippi, Stefania Riva, Giorgia Menozzi, M. Colleoni, Mara Biasin, Sergio Lo Caputo, Francesco Mazzotta, Giacomo P. Comi, Nereo Bresolin, Mario Clerici, Manuela Sironi
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pntd.0005126

Serological and Virological Evidence of Crimean-Congo Haemorrhagic Fever Virus Circulation in the Human Population of Borno State, Northeastern Nigeria
Cited by: 23
Author(s): David Bukbuk, Stuart Dowall, Kuiama Lewandowski, Andrew Bosworth, S. S. Baba, Anitha Varghese, Robert J. Watson, Andrew S. Bell, Barry Atkinson, Roger Hewson
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0037730

Identification, Expression and Target Gene Analyses of MicroRNAs in Spodoptera litura
Cited by: 24
Author(s): Zhongchen Rao, Wenyin He, Lin Liu, Sichun Zheng, Lihua Huang, Qili Feng
Software Mentions: 1
Published: over 12 years ago

10.1002/ece3.5240

Comparing Pool‐seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (<i>Homarus americanus</i>) as a case study
Cited by: 34
Author(s): Yann Dorant, Laura Benestan, Quentin Rougemont, Éric Normandeau, Brian Boyle, Rémy Rochette, Louis Bernatchez
Software Mentions: 1
Published: over 5 years ago

10.1002/ece3.6134

Transposable elements in individual genotypes of<i>Drosophila simulans</i>
Cited by: 8
Author(s): Sarah Signor
Software Mentions: 1
Published: over 4 years ago

10.1111/eva.12436

Understanding and monitoring the consequences of human impacts on intraspecific variation
Cited by: 133
Author(s): M. Mimura, Tetsukazu Yahara, Daniel P. Faith, Ella Vázquez‐Domínguez, Robert I. Colautti, Hideki Araki, Firouzeh Javadi, Juan Núñez–Farfán, Akira Mori, Shi‐Liang Zhou, Peter M. Hollingsworth, Linda E. Neaves, Yuya Fukano, Gideon F. Smith, Yo Ichiro Sato, Hidenori Tachida, Andrew P. Hendry
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms15022305

Genes Involved in the Endoplasmic Reticulum N-Glycosylation Pathway of the Red Microalga Porphyridium sp.: A Bioinformatic Study
Cited by: 27
Author(s): Oshrat Levy‐Ontman, M. Fisher, Yoram Shotland, Yacob Weinstein, Yoram Tekoah, Shoshana Arad
Software Mentions: 1
Published: almost 11 years ago

10.1002/pmic.201600399

Time, space, and disorder in the expanding proteome universe
Cited by: 18
Author(s): David-Paul Minde, A. Keith Dunker, Kathryn S. Lilley
Software Mentions: 1
Published: over 7 years ago

10.1186/1745-6150-7-20

Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes
Cited by: 111
Author(s): Sergei A. Filichkin, Todd C. Mockler
Software Mentions: 1
Published: almost 13 years ago

10.1002/advs.201903463

Dissolvable Polyacrylamide Beads for High‐Throughput Droplet DNA Barcoding
Cited by: 24
Author(s): Yongcheng Wang, Ting Cao, Jina Ko, Yinan Shen, Wei Zong, Kuanwei Sheng, Wenjian Cao, Sijie Sun, Li‐Heng Cai, Ying‐Lin Zhou, Xin‐Xiang Zhang, Chenghang Zong, Ralph Weissleder, David A. Weitz
Software Mentions: 1
Published: almost 5 years ago