pypi: package | Projects | Ecosyste.ms: Papers

10.3390/cancers12061453

DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3′-End Usage
Cited by: 16
Author(s): Jamal Elhasnaoui, Valentina Miano, Giulio Ferrero, Elena Doria, Antonette E. Leon, Aline S C Fabrício, Laura Annaratone, Isabella Castellano, Anna Sapino, Michele De Bortoli
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12870-016-0754-z

Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies
Cited by: 72
Author(s): Stéphane Nicolas, Jean‐Pierre Péros, Thierry Lacombe, Amandine Launay, Marie‐Christine Le Paslier, Aurélie Berard, Brigitte Mangin, Sophie Valière, Frédéric Martins, Loïc Le Cunff, Valérie Laucou, Roberto Baciliéri, Alexis Dereeper, Philippe Chatelet, Patrice This, Agnès Doligez
Software Mentions: 7
Published: about 8 years ago

10.15252/msb.20209442

High‐throughput, microscope‐based sorting to dissect cellular heterogeneity
Cited by: 40
Author(s): Nicholas Hasle, Anthony Cooke, Sanjay Srivatsan, Heather Z Huang, Jason J. Stephany, Zachary Krieger, Dana L. Jackson, Weiliang Tang, Sriram Pendyala, Raymond J. Monnat, Cole Trapnell, Emily M. Hatch, Douglas M. Fowler
Software Mentions: 7
Published: almost 4 years ago

10.1186/s40462-020-0194-0

Effects of age on foraging behavior in two closely related albatross species
Cited by: 18
Author(s): Caitlin K. Frankish, Andrea Manica, Richard A. Phillips
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0254293

easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application
Cited by: 4
Author(s): Matteo Di Bernardo, Timothy A. Crombie, Daniel E. Cook, Erik C. Andersen
Software Mentions: 7
Published: over 2 years ago

10.1007/s12020-020-02434-x

Using The Cancer Genome Atlas data to refine the 8th edition of the American Joint Committee on Cancer staging for papillary thyroid carcinoma
Cited by: 3
Author(s): Anello Marcello Poma, Elisabetta Macerola, Liborio Torregrossa, Rossella Elisei, Ferruccio Santini, Fulvio Basolo
Software Mentions: 7
Published: over 3 years ago

10.1186/s13148-020-00837-1

Differential CpG DNA methylation in peripheral naïve CD4+ T-cells in early rheumatoid arthritis patients
Cited by: 21
Author(s): Rujiraporn Pitaksalee, AN Burska, Shoaib Ajaib, Joshua Hugh Rogers, Rekha Parmar, K. Mydlova, Xuanxiao Xie, Alastair Droop, Jagtar Singh Nijjar, P Chambers, Paul Emery, Richard Hodgett, Iain B. McInnes, Frédérique Ponchel
Software Mentions: 7
Published: about 4 years ago

10.1093/molbev/msz154

Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites
Cited by: 51
Author(s): Roy N. Platt, Marina McDew-White, Winka Le Clec’h, Frédéric D. Chevalier, Fiona Allan, Aidan M. Emery, Amadou Garba, Amina Amadou Hamidou, M. Shaali, Joanne P. Webster, David Rollinson, Bonnie L. Webster, Timothy J. Anderson
Software Mentions: 7
Published: almost 5 years ago

10.1002/ece3.5512

Can plant traits predict seed dispersal probability via red deer guts, fur, and hooves?
Cited by: 8
Author(s): Tanja K. Petersen, Hans Henrik Bruun
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12859-019-3224-4

Vertical and horizontal integration of multi-omics data with miodin
Cited by: 35
Author(s): Benjamin Ulfenborg
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms20092075

Deep Learning/Artificial Intelligence and Blood-Based DNA Epigenomic Prediction of Cerebral Palsy
Cited by: 31
Author(s): Ray O. Bahado‐Singh, Sangeetha Vishweswaraiah, Buket Aydas, Nitish K. Mishra, Chittibabu Guda, Uppala Radhakrishna
Software Mentions: 6
Published: about 5 years ago

10.1002/ece3.7453

High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally
Cited by: 7
Author(s): Marjorie Couton, Aurélien Baud, Claire Daguin‐Thiébaut, Erwan Corre, Thierry Comtet, Frédérique Viard
Software Mentions: 6
Published: about 3 years ago

10.3390/microorganisms7120596

Dietary Saccharomyces cerevisiae boulardii CNCM I-1079 Positively Affects Performance and Intestinal Ecosystem in Broilers during a Campylobacter jejuni Infection
Cited by: 22
Author(s): Francesca Romana Massacci, Carmela Lovito, Silvia Tofani, Michele Tentellini, Domenica Anna Genovese, Alessia Arcangela Pia De Leo, Paola Papa, Chiara Francesca Magistrali, Elisabetta Manuali, Massimo Trabalza‐Marinucci, Livia Moscati, Claudio Forte
Software Mentions: 6
Published: over 4 years ago

10.1186/s40168-019-0687-5

Evolution of the gut microbiome following acute HIV-1 infection
Cited by: 61
Author(s): Muntsa Rocafort, Marc Noguera‐Julian, Javier Rivera, Lucía Pastor, Yolanda Guillén, Jost Langhorst, Mariona Parera, Inácio Mandomando, Jorge Carrillo, Víctor Urrea, C. Rodríguez, María Casadellà, M. Luz Calle, Bonaventura Clotet, Julià Blanco, Denise Naniche, Roger Paredes
Software Mentions: 6
Published: about 5 years ago

10.1186/s12862-020-01679-4

Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species
Cited by: 9
Author(s): Erica S. Nielsen, Romina Henriques, Maria Beger, Robert J. Toonen, Sophie von der Heyden
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-015-0107-4

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa
Cited by: 109
Author(s): Pål Trosvik, Eric J. de Muinck
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-021-87365-x

Comparison of Argentinean microbiota with other geographical populations reveals different taxonomic and functional signatures associated with obesity
Cited by: 5
Author(s): Susana Pesoa, Néstor D. Portela, Eduardo Aguilar Fernández, Osvaldo Elbarcha, Martín Gotteland, Fabien Magne
Software Mentions: 6
Published: about 3 years ago

10.1016/j.devcel.2018.06.028

Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development
Cited by: 36
Author(s): Magdalena K. Sznurkowska, Édouard Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher J. Hindley, Jennifer Nichols, Berthold Göttgens, Meritxell Huch, Anna Philpott, Benjamin D. Simons
Software Mentions: 6
Published: almost 6 years ago

10.1111/2041-210X.12917

TreeSim <scp>GM</scp> : Simulating phylogenetic trees under general Bellman–Harris models with lineage‐specific shifts of speciation and extinction in R
Cited by: 17
Author(s): Oskar Hagen, Tanja Stadler
Software Mentions: 6
Published: over 6 years ago

10.1016/j.ccell.2017.07.004

Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets
Cited by: 212
Author(s): Myron G. Best, Nik Sol, Sjors G J G In ‘t Veld, Adrienne Vancura, Mirte Muller, Anna-Larissa N. Niemeijer, Aniko V. Fejes, Lee Ann Tjon Kon Fat, Anna Egberdina Huis In 't Veld, Cyra E. Leurs, Tessa Y. Le Large, Laura L. Meijer, Irsan Kooi, François Rustenburg, Pepijn Schellen, Heleen Verschueren, Edward P. Post, Laurine E. Wedekind, Jillian Wilhelmina Paulina Bracht, Michelle Esenkbrink, Leon J. Wils, Francesca Favaro, Jilian D. Schoonhoven, Jihane Tannous, Hanne Meijers-Heijboer, Geert Kazemier, Elisa Giovannetti, Jaap C. Reijneveld, Sander Idema, Joep Killestein, Michal Heger, Saskia C.A. de Jager, Rolf T. Urbanus, Imo E. Hoefer, Gérard Pasterkamp, Christine Mannhalter, José Gomez-Arroyo, Harm Jan Bogaard, David P. Noske, W. Peter Vandertop, Daan van den Broek, Bauke Ylstra, R. Jonas A. Nilsson, Jelle Wesseling, Niki Karachaliou, Rafael Rosell, Elizabeth Lee-Lewandrowski, Kent Lewandrowski, Bakhos A. Tannous, Adrianus J. de Langen, Egbert F. Smit, Michel M. van den Heuvel, Thomas Würdinger
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pcbi.1008491

Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness
Cited by: 14
Author(s): Iván Cárcamo-Orive, Marc Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D’Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1009506

Comparative analysis reveals distinctive epigenetic features of the human cerebellum
Cited by: 11
Author(s): Elaine E. Guevara, William D. Hopkins, Patrick R. Hof, John J. Ely, Brenda J. Bradley, Chet C. Sherwood
Software Mentions: 6
Published: about 3 years ago

10.1186/s13578-021-00691-5

A single-cell interactome of human tooth germ from growing third molar elucidates signaling networks regulating dental development
Cited by: 7
Author(s): Yueqi Shi, Yinglan Yu, Yuqiong Zhou, Jing Zhao, Wenjie Zhang, Duohong Zou, Weichen Song, Shaoyi Wang
Software Mentions: 6
Published: over 2 years ago

10.1038/s41598-020-64516-0

Cyto-Feature Engineering: A Pipeline for Flow Cytometry Analysis to Uncover Immune Populations and Associations with Disease
Cited by: 7
Author(s): Amy Fox, Taru Dutt, Burton Karger, Mauricio Rojas, Andrés Obregón-Henao, G. Brooke Anderson, Marcela Henao-Tamayo
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0097379

Direct Sequencing from the Minimal Number of DNA Molecules Needed to Fill a 454 Picotiterplate
Cited by: 12
Author(s): Mária Džunková, Marc García-Garcerá, Llúcia Martínez-Priego, Giussepe D’Auria, Francesc Calafell, Andrés Moya
Software Mentions: 6
Published: almost 10 years ago

10.1186/s12915-021-01002-7

A cell-to-patient machine learning transfer approach uncovers novel basal-like breast cancer prognostic markers amongst alternative splice variants
Cited by: 12
Author(s): Jean-Philippe Villemin, Claudio Lorenzi, Marie-Sarah Cabrillac, Andrew Oldfield, William Ritchie, Reini F. Luco
Software Mentions: 6
Published: about 3 years ago

10.3389/fonc.2020.01496

Development and Validation of a Clinical Prognostic Model Based on Immune-Related Genes Expressed in Clear Cell Renal Cell Carcinoma
Cited by: 11
Author(s): Shengxiang Ren, Wei Wang, Hanyu Shen, Chenlin Zhang, Haiyan Hao, Mengjing Sun, Yingjing Wang, Xiaojing Zhang, Bing Lu, Chen Chen, Ziheng Wang
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0243420

Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands
Cited by: 9
Author(s): Pamela Vega-Polo, María Mercedes Cobo, Andrea Argudo, Bernardo Gutiérrez, Jennifer K. Rowntree, María de Lourdes Torres
Software Mentions: 6
Published: over 3 years ago

10.1128/AEM.02707-20

New Endohyphal Relationships between Mucoromycota and Burkholderiaceae Representatives
Cited by: 17
Author(s): Alicja Okrasińska, Aleksandra Bokus, Katarzyna Duk, Aleksandra Gęsiorska, B Sokolowska, Aleksandra Miłobędzka, Marta Wrzosek, Julia Pawłowska
Software Mentions: 6
Published: about 3 years ago

10.3389/fneur.2020.00285

Neoplastic and Non-neoplastic Acute Intracerebral Hemorrhage in CT Brain Scans: Machine Learning-Based Prediction Using Radiomic Image Features
Cited by: 13
Author(s): Jawed Nawabi, Helge Kniep, Reza Kabiri, Gabriel Broocks, Tobias D Faizy, Christian J. Thaler, Gerhard Schön, Jens Fiehler, Uta Hanning
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-016-3199-8

Identification of novel targets of diabetic nephropathy and PEDF peptide treatment using RNA-seq
Cited by: 29
Author(s): Ana Rubín, Anna C. Salzberg, Yuka Imamura, Anzor Grivitishvilli, Joyce Tombran-Tink
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pcbi.1005694

PCSF: An R-package for network-based interpretation of high-throughput data
Cited by: 34
Author(s): Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-021-07819-4

Stage- and sex-specific transcriptome analyses reveal distinctive sensory gene expression patterns in a butterfly
Cited by: 7
Author(s): David A. Ernst, Erica L. Westerman
Software Mentions: 6
Published: almost 3 years ago

10.3389/fimmu.2021.705646

On Deep Landscape Exploration of COVID-19 Patients Cells and Severity Markers
Cited by: 9
Author(s): Aarón Vázquez-Jiménez, Ugo Enrique Avila-Ponce De León, Meztli Matadamas-Guzmán, Erick Andrés Muciño-Olmos, Yoscelina Estrella Martínez-López, Thelma Escobedo-Tapia, Osbaldo Reséndis-Antonio
Software Mentions: 6
Published: over 2 years ago

10.1007/s00415-020-09859-4

Posterior circulation stroke: machine learning-based detection of early ischemic changes in acute non-contrast CT scans
Cited by: 12
Author(s): Helge Kniep, Peter Sporns, Gabriel Broocks, André Kemmling, Jawed Nawabi, Thilo Rusche, Jens Fiehler, Uta Hanning
Software Mentions: 6
Published: about 4 years ago

10.3389/fcimb.2018.00020

Genetic Separation of Listeria monocytogenes Causing Central Nervous System Infections in Animals
Cited by: 20
Author(s): Lisandra Aguilar-Bultet, Pamela Nicholson, Lorenz Rychener, Margaux Dreyer, Bulent Gözel, Francesco C. Origgi, Anna Oevermann, Joachim Frey, Laurent Falquet
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2016.00183

Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans
Cited by: 78
Author(s): Benjamin Mayne, Tina Bianco‐Miotto, Sam Buckberry, James Breen, Vicki L. Clifton, Cheryl Shoubridge, Claire T. Roberts
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2021.614957

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains
Cited by: 34
Author(s): Camila Gazolla Volpiano, Fernando Hayashi Sant’Anna, Adriana Ambrosini, Jackson Freitas Brilhante de São José, Anelise Beneduzi, William B. Whitman, Emanuel Maltempi de Souza, Bruno Brito Lisboa, Luciano Kayser Vargas, Luciane Maria Pereira Passaglia
Software Mentions: 6
Published: about 3 years ago

10.1016/j.celrep.2020.107628

Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth
Cited by: 156
Author(s): Sarah Davidson, Mirjana Efremova, Angela Riedel, Bidesh Mahata, Jhuma Pramanik, Jani Huuhtanen, Gozde Kar, Roser Vento‐Tormo, Tzachi Hagai, Xi Chen, Muzlifah Haniffa, Jacqueline D. Shields, Sarah A. Teichmann
Software Mentions: 6
Published: about 4 years ago

10.1111/eva.13291

A comparison of microsatellites and genome‐wide SNPs for the detection of admixture brings the first molecular evidence for hybridization between Mustela eversmanii and M. putorius (Mustelidae, Carnivora)
Cited by: 11
Author(s): Lajos Szatmári, Tamás Cserkész, Levente Laczkó, József Lanszki, Cino Pertoldi, Alexei V. Abramov, Morten Elmeros, Barnabás Ottlecz, Zsolt Hegyeli, Gábor Sramkó
Software Mentions: 6
Published: over 2 years ago

10.1186/s12859-021-04264-8

mLoc-mRNA: predicting multiple sub-cellular localization of mRNAs using random forest algorithm coupled with feature selection via elastic net
Cited by: 6
Author(s): Prabina Kumar Meher, Anil Rai, Atmakuri Ramakrishna Rao
Software Mentions: 6
Published: almost 3 years ago

10.1002/1878-0261.13014

imPlatelet classifier: image‐converted RNA biomarker profiles enable blood‐based cancer diagnostics
Cited by: 10
Author(s): Krzysztof Pastuszak, Anna Supernat, Myron G. Best, Sjors G J G In ‘t Veld, Sylwia Łapińska‐Szumczyk, Anna Łojkowska, Robert Różański, Anna Żaczek, Jacek Jassem, Thomas Würdinger, Tomasz Stokowy
Software Mentions: 6
Published: almost 3 years ago

10.1186/s13072-020-00379-z

DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna
Cited by: 15
Author(s): Jack Hearn, Fiona A. Plenderleith, Tom J. Little
Software Mentions: 6
Published: over 3 years ago

10.1111/eva.13198

Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure
Cited by: 2
Author(s): Zahra Salem Taboun, Ryan P. Walter, Jennifer R. Ovenden, Daniel D. Heath
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0221355

Effects of road salt on microbial communities: Halophiles as biomarkers of road salt pollution
Cited by: 17
Author(s): Wolf T. Pecher, M. Emad Al Madadha, Priya DasSarma, Folasade Ekulona, Eric J. Schott, Kelli Crowe, Bojana Stojkovic Gut, Shiladitya DasSarma
Software Mentions: 6
Published: over 4 years ago

10.1007/s10705-018-9958-y

Fertilizer response and nitrogen use efficiency in African smallholder maize farms
Cited by: 56
Author(s): Stephen M. Ichami, Keith D. Shepherd, Andrew Sila, J.J. Stoorvogel, Ellis Hoffland
Software Mentions: 6
Published: over 5 years ago

10.1186/s13229-019-0287-z

A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood
Cited by: 12
Author(s): Charles E. Mordaunt, Bo Y. Park, Kelly M. Bakulski, Jason I. Feinberg, Lisa Croen, Christine Ladd‐Acosta, Craig J. Newschaffer, Heather E. Volk, Sally J Ozonoff, Irva Hertz‐Picciotto, Janine M. LaSalle, Rebecca Jean Schmidt, M. Daniele Fallin
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-018-4876-6

The arrhythmogenic cardiomyopathy-specific coding and non-coding transcriptome in human cardiac stromal cells
Cited by: 14
Author(s): Johannes Michael Rainer, Viviana Meraviglia, Hagen Blankenburg, Chiara Piubelli, Peter P. Pramstaller, Adolfo Paolin, Elisa Cogliati, Giulio Pompilio, Elena Sommariva, Francisco S. Domingues, Alessandra Rossini
Software Mentions: 6
Published: almost 6 years ago

10.3390/nu13020549

Circulating Metabolites Associated with Postprandial Satiety in Overweight/Obese Participants: The SATIN Study
Cited by: 5
Author(s): Lucia Camacho-Barcía, Jesús García‐Gavilán, Christopher Papandreou, Thorsten Hansen, Jo Harrold, Graham Finlayson, John Blundell, Anders Sjödin, Jason C.G. Halford, Mònica Bulló
Software Mentions: 6
Published: over 3 years ago

10.3390/genes12040491

Dissection of the Genetic Association between Anorexia Nervosa and Obsessive–Compulsive Disorder at the Network and Cellular Levels
Cited by: 4
Author(s): Weichen Song, Weidi Wang, Shunying Yu, Guan Ning Lin
Software Mentions: 6
Published: about 3 years ago

10.1038/sdata.2017.185

An RNA-Seq atlas of gene expression in mouse and rat normal tissues
Cited by: 95
Author(s): Julia F. Söllner, Germán Leparc, Tobias Hildebrandt, H. Klein, Leo Thomas, Elia Stupka, Eric J. Simon
Software Mentions: 6
Published: over 6 years ago

10.1093/gbe/evaa088

Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels
Cited by: 9
Author(s): Rahulsimham Vegesna, Marta Tomaszkiewicz, Oliver A. Ryder, Rebeca Campos-Sánchez, Paul Medvedev, Michael DeGiorgio, Kateryna D. Makova
Software Mentions: 6
Published: about 4 years ago

10.3390/genes12091300

Mitochondrial Genetic Heterogeneity in Leber’s Hereditary Optic Neuropathy: Original Study with Meta-Analysis
Cited by: 7
Author(s): Rajan Kumar Jha, Chhavi Dawar, Qurratulain Hasan, Akhilesh Pujar, Gaurav Gupta, Venugopalan Y Vishnu, Ramesh Kekunnaya, Kumarasamy Thangaraj
Software Mentions: 6
Published: over 2 years ago

10.1186/s43008-020-00036-w

Brassicaceous roots as an unexpected diversity hot-spot of helotialean endophytes
Cited by: 13
Author(s): Jose G. Maciá‐Vicente, Ondřej Koukol
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13059-017-1374-0

Epigenetic supersimilarity of monozygotic twin pairs
Cited by: 76
Author(s): Timothy E. Van Baak, Cristian Coarfa, Pierre Antoine Dugué, Giovanni Fiorito, Eleonora Laritsky, Maria S. Baker, Noah J. Kessler, Jianrong Dong, Jack D. Duryea, Matt J. Silver, Ayden Saffari, Andrew M. Prentice, Sophie E. Moore, Akram Ghantous, Michael N. Routledge, Yun Gong, Zdenko Herceg, Paolo Víneis, Gianluca Severi, John L. Hopper, Melissa C. Southey, Graham G. Giles, Roger L. Milne, Robert A. Waterland
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.ppat.1009769

Virulence and community dynamics of fungal species with vertical and horizontal transmission on a plant with multiple infections
Cited by: 11
Author(s): Kai Fang, Jie Zhou, Lin Chen, Yuxuan Li, Ai-Ling Yang, Xing-Fan Dong, Hanbo Zhang
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13059-021-02451-7

Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data
Cited by: 35
Author(s): Jan Lause, Philipp Berens, Dmitry Kobak
Software Mentions: 5
Published: over 2 years ago

10.1002/jcsm.12643

Single‐cell RNA sequencing and lipidomics reveal cell and lipid dynamics of fat infiltration in skeletal muscle
Cited by: 33
Author(s): Zhonglin Xu, Wenjing You, Wentao Chen, Yanbing Zhou, Qiuyun Nong, Teresa G. Valencak, Yizhen Wang, Tizhong Shan
Software Mentions: 5
Published: over 3 years ago

10.1186/s12263-021-00688-2

An 8-week freeze-dried blueberry supplement impacts immune-related pathways: a randomized, double-blind placebo-controlled trial
Cited by: 7
Author(s): Michèle Rousseau, Justine Horne, Frédéric Guénard, Juan de Toro‐Martín, Véronique Garneau, Valérie Guay, Michèle Kearney, Geneviève Pilon, Denis Roy, Patrick Couture, Charles Couillard, André Marette
Software Mentions: 5
Published: about 3 years ago

10.3390/genes12030385

Maternal Vitamin and Mineral Supplementation and Rate of Maternal Weight Gain Affects Placental Expression of Energy Metabolism and Transport-Related Genes
Cited by: 25
Author(s): Wellison J. S. Diniz, Lawrence P. Reynolds, P. P. Borowicz, Alison K Ward, Kevin K. Sedivec, Kacie L McCarthy, Cierrah J Kassetas, Friederike Baumgaertner, James D Kirsch, Sheri T. Dorsam, Tammi L Neville, J Chris Forcherio, Ronald Scott, J. S. Caton, Carl R Dahlen
Software Mentions: 5
Published: about 3 years ago

10.1073/pnas.2100920118

Single-cell sequencing reveals suppressive transcriptional programs regulated by MIS/AMH in neonatal ovaries
Cited by: 23
Author(s): Marie-Charlotte Meinsohn, Hatice D. Saatcioglu, Lina Wei, Yang Li, Heiko Horn, Maëva Chauvin, Mariko Kano, Ngoc Minh Nguyen, Nicholas Nagykery, A Kashiwagi, Wesley Samore, Dan Wang, Esther Oliva, Guangping Gao, Mary E. Morris, Patricia K. Donahoe, David Pépin
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-017-03489-z

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli
Cited by: 38
Author(s): Tracy H. Hazen, Jane Michalski, Qingwei Luo, Amol C. Shetty, Sean C. Daugherty, James M. Fleckenstein, David A. Rasko
Software Mentions: 5
Published: almost 7 years ago

10.7150/jca.53827

Prognostic Prediction Model for Glioblastoma: A Metabolic Gene Signature and Independent External Validation
Cited by: 6
Author(s): Chuxiang Lei, Wenlin Chen, Yuekun Wang, Binghao Zhao, Penghao Liu, Ziren Kong, Delin Liu, Congxin Dai, Yaning Wang, Yu Wang, Wenbin Ma
Software Mentions: 5
Published: over 3 years ago

10.1038/srep05193

Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies
Cited by: 230
Author(s): Bhagwan Yadav, Tea Pemovska, Agnieszka Szwajda, Evgeny Kulesskiy, Mika Kontro, Reijo Karjalainen, Muntasir Mamun Majumder, Disha Malani, Astrid Murumägi, Jonathan Knowles, Kimmo Porkka, Caroline A. Heckman, Olli Kallioniemi, Krister Wennerberg, Tero Aittokallio
Software Mentions: 5
Published: almost 10 years ago

10.1016/j.meegid.2018.03.011

Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries
Cited by: 16
Author(s): João Perdigão, Carla Silva, Jaciara Diniz, Catarina Pereira, Diana Machado, Jorge Ramos, Hugo Silva, Fernanda Abilleira, Clarice Brinck Brum, Ana Júlia Reis, Maíra Bidart de Macedo, João L. Scaini, Ana B. Silva, Lainister de Oliveira Esteves, Rita Macedo, Fernando Maltêz, Sofia Clemente, Elizabeth Coelho, Sofía Viegas, Paulo Rabna, Amabélia Rodrigues, Nuno Taveira, Luísa Jordão, Afrânio Lineu Kritski, José Roberto Lapa e Silva, Igor Mokrousov, David Couvin, Nalin Rastogi, Isabel Couto, Arnab Pain, Ruth McNerney, Taane G. Clark, Andréa von Groll, Elis R. Dalla-Costa, Maria Lúcia Rosa Rossetti, Pedro E. A. Silva, Miguel Viveiros, Isabel Portugal
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-015-0716-z

Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays
Cited by: 191
Author(s): Matteo Dell’Acqua, Daniel M. Gatti, G. Pea, Federica Cattonaro, Frederik Coppens, Gabriele Magris, Aye L. Hlaing, Htay Htay Aung, Hilde Nelissen, Joke Baute, Elisabetta Frascaroli, Gary A. Churchill, Dirk Inzé, Michèle Morgante, Mario Enrico Pè
Software Mentions: 5
Published: over 8 years ago

10.3390/genes12060842

De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis
Cited by: 5
Author(s): J.M. Córdoba, Emilie Perez, Mick Van Vlierberghe, Amandine Bertrand, Valérian Lupo, Pierre Cardol, Denis Baurain
Software Mentions: 5
Published: almost 3 years ago

10.1371/journal.pone.0072238

Effect of Doxorubicin/Pluronic SP1049C on Tumorigenicity, Aggressiveness, DNA Methylation and Stem Cell Markers in Murine Leukemia
Cited by: 73
Author(s): Daria Y. Alakhova, Yi Zhao, Shu Li, Alexander V. Kabanov
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12864-016-3228-7

RNA-seq based transcriptomic map reveals new insights into mouse salivary gland development and maturation
Cited by: 30
Author(s): Christian Gluck, Sang‐Won Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha, Rose‐Anne Romano
Software Mentions: 5
Published: over 7 years ago

10.1002/ece3.1015

Crater lake cichlids individually specialize along the benthic–limnetic axis
Cited by: 39
Author(s): Henrik Kusche, Hans Recknagel, Axel Meyer
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0136830

Methodological Aspects of the Potential Use of Dendrochronological Techniques When Analyzing the Long-Term Impact of Tourism on Protected Areas
Cited by: 4
Author(s): Szymon Ciapała, Paweł Adamski
Software Mentions: 5
Published: over 8 years ago

10.3390/ijms20225594

Lipid Related Genes Altered in NASH Connect Inflammation in Liver Pathogenesis Progression to HCC: A Canonical Pathway
Cited by: 19
Author(s): Christophe Desterke, Franck Chiappini
Software Mentions: 5
Published: over 4 years ago

10.1002/ece3.3404

Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces
Cited by: 62
Author(s): Kari Kaunisto, Tomas Roslin, Ilari E. Sääksjärvi, Eero J. Vesterinen
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.66018

Information flow, cell types and stereotypy in a full olfactory connectome
Cited by: 82
Author(s): Philipp Schlegel, Alexander Shakeel Bates, Tomke Stürner, Sridhar R. Jagannathan, Nikolas Drummond, Joseph Hsu, Laia Serratosa Capdevila, Alexandre Javier, Elizabeth C. Marin, Asa Barth-Maron, Imaan F M Tamimi, Feng Li, Gerald M. Rubin, Stephen M. Plaza, Marta Costa, Gregory Jefferis
Software Mentions: 5
Published: almost 3 years ago

10.1371/journal.pone.0234505

Comparative genomics of high grade neuroendocrine carcinoma of the cervix
Cited by: 21
Author(s): R. Tyler Hillman, Robert J. Cardnell, Junya Fujimoto, Won Chul Lee, Jianjun Zhang, Lauren A. Byers, Preetha Ramalingam, Mario M. Leitao, Elizabeth M. Swisher, P. Andrew Futreal, Michael Frumovitz
Software Mentions: 5
Published: almost 4 years ago

10.18632/aging.102373

Bioinformatic profiling of prognosis-related genes in the breast cancer immune microenvironment
Cited by: 29
Author(s): Fang Bai, Yu-Chun Jin, Peng Zhang, Hongliang Chen, Yi‐Peng Fu, Mingdi Zhang, Zhen Weng, Kangning Wu
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms20205043

Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco (Nicotiana tabacum L.)
Cited by: 18
Author(s): Ge Bai, Da-Hai Yang, Peijian Cao, Huaiying Yao, Yihan Zhang, Xuejun Chen, Bingguang Xiao, Feng Li, Zhenyu Wang, Jun Yang, He Xie
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-018-0612-3

Design and application of a novel two-amplicon approach for defining eukaryotic microbiota
Cited by: 16
Author(s): Ana Popović, Céline Bourdon, Pauline W. Wang, David S. Guttman, Wieger Voskuijl, Michael E. Grigg, Robert Bandsma, John Parkinson
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2105-12-306

Expression cartography of human tissues using self organizing maps
Cited by: 71
Author(s): Henry Wirth, Markus Löffler, Martin von Bergen, Hans Binder
Software Mentions: 5
Published: almost 13 years ago

10.3390/ani9110970

Enzymatically Digested Food Waste Altered Fecal Microbiota But Not Meat Quality and Carcass Characteristics of Growing-Finishing Pigs
Cited by: 2
Author(s): Cynthia Jinno, Perot Saelao, Elizabeth A. Maga, Arthur S. King, Dan Morash, Steven M. Zicari, Xiang Yang, Yanhong Liu
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-019-2869-3

fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies
Cited by: 1
Author(s): Jiaxing Lin, Alexander B. Sibley, Ivo Shterev, Andrew B. Nixon, Federico Innocenti, Cliburn Chan, Kouros Owzar
Software Mentions: 5
Published: almost 5 years ago

10.1128/mBio.02079-16

Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell Carcinoma
Cited by: 87
Author(s): Gabriel J. Starrett, Christina Marcelus, Paul G. Cantalupo, Joshua P. Katz, Jingwei Cheng, Keiko Akagi, Manisha Thakuria, Guilherme Rabinowits, Linda C. Wang, David E. Symer, James M. Pipas, Reuben S. Harris, James A. DeCaprio
Software Mentions: 5
Published: about 7 years ago

10.1128/mBio.01500-19

Dissecting the Gene Expression, Localization, Membrane Topology, and Function of the Plasmodium falciparum STEVOR Protein Family
Cited by: 38
Author(s): Jan Stephan Wichers, Jochen Scholz, Jan Strauss, Susanne Witt, Andrés Lill, Laura-Isabell Ehnold, Niklas Neupert, Benjamin Liffner, Renke Lühken, Michaela Petter, Stephan Lorenzen, Danny W. Wilson, Christian Löw, Catherine Lavazec, Iris Bruchhaus, Egbert Tannich, Tim‐Wolf Gilberger, Anna Bachmann
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pntd.0005223

MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil
Cited by: 55
Author(s): Kennio Ferreira‐Paim, Leonardo Andrade-Silva, Fernanda Machado Fonseca, Thatiana Bragine Ferreira, Delio José Mora, Juliana Andrade-Silva, Aziza Khan, Aiken Dao, Eduardo C. Reis, Margarete Teresa Gottardo de Almeida, André Luiz Maltos, R. Virmondes, Luciana Trilles, Volker Rickerts, Ariya Chindamporn, Jane E. Sykes, Massimo Cogliati, Kirsten Nielsen, Teun Boekhout, Matthew C. Fisher, June Kwon‐Chung, David M. Engelthaler, Márcia dos Santos Lazéra, Wieland Meyer, Mário León Silva-Vergara
Software Mentions: 5
Published: over 7 years ago

10.1186/s12898-017-0118-z

Puumala hantavirus infections in bank vole populations: host and virus dynamics in Central Europe
Cited by: 30
Author(s): Daniela Reil, Ulrike Rosenfeld, Christian Imholt, Sabrina Schmidt, Rainer G. Ulrich, Jana A. Eccard, Jens Jacob
Software Mentions: 5
Published: about 7 years ago

10.1093/database/baaa096

The IMEx coronavirus interactome: an evolving map of Coronaviridae–host molecular interactions
Cited by: 31
Author(s): Livia Perfetto, Chiara Pastrello, Noemi del-Toro, Margaret Duesbury, Marta Iannuccelli, Max Kotlyar, Luana Licata, Birgit Meldal, Kalpana Panneerselvam, Simona Panni, Negin Rahimzadeh, Sylvie Ricard‐Blum, Łukasz Salwiński, Anjali Shrivastava, Gianni Cesareni, Matteo Pellegrini, Sandra Orchard, Igor Jurišica, Henning Hermjakob, Pablo Porras
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-019-0758-7

Microbiome of vineyard soils is shaped by geography and management
Cited by: 89
Author(s): E. Coller, Alessandro Cestaro, Roberto Zanzotti, D. Bertoldi, Massimo Pindo, Simone Larger, Davide Albanese, E. Mescalchin, Claudio Donati
Software Mentions: 5
Published: over 4 years ago

10.1007/s10126-021-10033-8

Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
Cited by: 5
Author(s): Magnus Alm Rosenblad, Anna Abramova, Ulrika Lind, Pall I. Olason, Stefania Giacomello, Björn Nystedt, Anders Blomberg
Software Mentions: 5
Published: about 3 years ago

10.1186/1471-2229-8-99

Regulon organization of Arabidopsis
Cited by: 95
Author(s): Wieslawa I. Mentzen, Eve Syrkin Wurtele
Software Mentions: 5
Published: over 16 years ago

10.18632/aging.104136

Single cell sequencing reveals cell populations that predict primary resistance to imatinib in chronic myeloid leukemia
Cited by: 5
Author(s): Weilong Zhang, Baofeng Yang, Linqian Weng, Jiangtao Li, Jinfeng Bai, Ting Wang, Jingwen Wang, Yue Jin, Hongmei Jing, Yuchen Jiao, Xixi Chen, Hui Liu, Yi‐Xin Zeng
Software Mentions: 5
Published: over 3 years ago

10.1002/ece3.6650

A landscape‐scale assessment of the relationship between grassland functioning, community diversity, and functional traits
Cited by: 7
Author(s): Hanneke van ‘t Veen, Loïc Chalmandrier, Nadine Sandau, Michael P. Nobis, Patrice Descombes, Achilleas Psomas, Yann Hautier, Loïc Pellissier
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13643-021-01738-x

Cognitive interventions in children and adolescents from low socioeconomic status backgrounds: a systematic review protocol of randomized controlled trials
Cited by: 2
Author(s): Rosalba Company-Córdoba, Antonio Sianes, Ian C. Simpson, Joaquín A. Ibáñez-Alfonso
Software Mentions: 5
Published: almost 3 years ago

10.1038/s41598-019-44254-8

Honey bee predisposition of resistance to ubiquitous mite infestations
Cited by: 17
Author(s): Bart J. G. Broeckx, Lina De Smet, T. Blacquière, Kevin Maebe, Mikalai Khalenkow, Mario Van Poucke, Bjørn Dahle, Peter Neumann, Kim B. Nguyen, Guy Smagghe, Dieter Deforce, Filip Van Nieuwerburgh, Luc Peelman, Dirk C. de Graaf
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-019-40479-9

Egg-laying decisions based on olfactory cues enhance offspring fitness in Stomoxys calcitrans L. (Diptera: Muscidae)
Cited by: 21
Author(s): Steve B. S. Baleba, Baldwyn Torto, Daniel K. Masiga, Christopher W. Weldon, Merid N. Getahun
Software Mentions: 5
Published: about 5 years ago

10.1186/s12866-018-1221-9

Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis
Cited by: 50
Author(s): Deni Ribičić, Kelly M. McFarlin, Roman Netzer, Odd Gunnar Brakstad, Anderson M. Winkler, Mimmi Throne-Holst, Trond Røvik Størseth
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-018-29677-z

Automated analysis of lipid drug-response markers by combined fast and high-resolution whole cell MALDI mass spectrometry biotyping
Cited by: 18
Author(s): David Weigt, Denis A. Sammour, Timon Ulrich, Bogdan Munteanu, Carsten Hopf
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-020-60638-7

Aberrant expression of PAR bZIP transcription factors is associated with epileptogenesis, focus on hepatic leukemia factor
Cited by: 7
Author(s): Lukáš Rambousek, Tilo Gschwind, Carlos Lafourcade, Jean-Charles Paterna, Linda Dib, Jean‐Marc Fritschy, Adriano Fontana
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pcbi.1007481

Bayesian inference of neuronal assemblies
Cited by: 18
Author(s): Giovanni Diana, Thomas T. J. Sainsbury, Martin P. Meyer
Software Mentions: 5
Published: over 4 years ago

10.1186/s12983-015-0109-x

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex
Cited by: 33
Author(s): Andrey Rozenberg, Mrutyunjaya Parida, Florian Leese, Linda C. Weiss, Ralph Tollrian, J. Robert Manak
Software Mentions: 5
Published: almost 9 years ago

10.1186/s42523-020-00058-0

Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides
Cited by: 1
Author(s): Bianca R. P. Brown, Joaquin C. B. Nunez, David M. Rand
Software Mentions: 5
Published: over 3 years ago

Projects: pypi: package

Papers Mentioning package 1,300