Ecosyste.ms: Papers

10.7554/eLife.42675

The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila
Cited by: 20
Author(s): Katrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga Ermakova, Maria Polychronidou, Ingrid Lohmann
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-019-42310-x

Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression
Cited by: 19
Author(s): Christian Kehlmaier, Xiuwen Zhang, Arthur Georges, Patrick D. Campbell, Scott Thomson, Uwe Fritz
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0199274

Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats
Cited by: 25
Author(s): Boris Zybailov, Galina Glazko, Yasir Rahmatallah, Dmitri S. Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D. Byrum, Lisa Orr, Alan J. Tackett, Samuel G. Mackintosh, Ricky D. Edmondson, Dorothy A. Kieffer, Roy J. Martin, Sean H. Adams, Nosratola D. Vaziri, John M. Arthur
Software Mentions: 9
Published: almost 6 years ago

10.7554/eLife.66668

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo
Cited by: 66
Author(s): Marissa M Gaskill, Tyler J. Gibson, Elizabeth D Larson, Melissa M. Harrison
Software Mentions: 7
Published: over 3 years ago

10.3389/fphys.2020.612598

Physiological Network From Anthropometric and Blood Test Biomarkers
Cited by: 7
Author(s): Antonio Barajas-Martínez, Elizabeth Ibarra-Coronado, Martha Patricia Sierra-Vargas, Ivette Cruz-Bautista, Paloma Almeda‐Valdés, Carlos A. Aguilar-Salinas, Rubén Fossión, Christopher R. Stephens, Claudia Vargas-Domínguez, Octavio Gamaliel Atzatzi-Aguilar, Yazmín Debray-García, Rogelio García-Torrentera, Karen Bobadilla, María Augusta Naranjo Meneses, Dulce Abril Mena Orozco, Cesar Lam, Vania Jocelyn Martínez-Garcés, Octavio A. Lecona, Arlex Marín-García, A. Frank, Ana Leonor Rivera
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12859-021-04126-3

Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources
Cited by: 6
Author(s): Neel Patel, William S. Bush
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0089489

Evidence for an Epistatic Effect between TP53 R72P and MDM2 T309G SNPs in HIV Infection: A Cross-Sectional Study in Women from South Brazil
Cited by: 4
Author(s): Fernando Pires Hartwig, Ludmila Gonçalves Entiauspe, Emily Montosa Nunes, Fernanda Martins Rodrigues, Tiago Collares, Fabiana Kömmling Seixas, Mariângela Freitas da Silveira
Software Mentions: 6
Published: over 10 years ago

10.1186/gb-2013-14-11-r124

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation
Cited by: 27
Author(s): Sarah Aldridge, Stephen Watt, Michael A. Quail, Tim Rayner, Margus Lukk, Michael F Bimson, Daniel J. Gaffney, Duncan T. Odom
Software Mentions: 6
Published: almost 12 years ago

10.1371/journal.pone.0198382

Modeling effects of crop production, energy development and conservation-grassland loss on avian habitat
Cited by: 25
Author(s): Jill A. Shaffer, Cali L. Roth, David Mushet
Software Mentions: 6
Published: almost 6 years ago

10.2174/1874104501711010212

Ezqsar: An R Package for Developing QSAR Models Directly From Structures
Cited by: 10
Author(s): Jamal Shamsara
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0226435

The acute myeloid leukemia associated AML1-ETO fusion protein alters the transcriptome and cellular progression in a single-oncogene expressing in vitro induced pluripotent stem cell based granulocyte differentiation model
Cited by: 15
Author(s): Esther Tijchon, Guoqiang Yi, Amit Mandoli, Jos G. A. Smits, Francesco Ferrari, Branco M. H. Heuts, Falco Wijnen, Bowon Kim, Eva M. Janssen-Megens, Jan Jacob Schuringa, Joost H.A. Martens
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12900-016-0063-7

3D QSAR, pharmacophore and molecular docking studies of known inhibitors and designing of novel inhibitors for M18 aspartyl aminopeptidase of Plasmodium falciparum
Cited by: 22
Author(s): Madhuri Kumari, Subhash Chandra, Neeraj Tiwari, Naidu Subbarao
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0245324

InsectOR—Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes
Cited by: 10
Author(s): Snehal D. Karpe, Vikas Tiwari, R. Sowdhamini
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pcbi.0030132

Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes
Cited by: 14
Author(s): Patricia Ryan, Brian W. Kirk, Chad W. Euler, Raymond Schuch, Vincent A. Fischetti
Software Mentions: 5
Published: over 17 years ago

10.3389/fpls.2016.01126

Interpreting the Climatic Effects on Xylem Functional Traits in Two Mediterranean Oak Species: The Role of Extreme Climatic Events
Cited by: 18
Author(s): Angelo Rita, Marco Borghetti, Luigi Todaro, Antonio Saracino
Software Mentions: 4
Published: over 8 years ago

10.3389/fphys.2020.587994

Metabolic Physiological Networks: The Impact of Age
Cited by: 15
Author(s): Antonio Barajas-Martínez, Jonathan F. Easton, Ana Leonor Rivera, Ricardo Jesús Martínez‐Tapia, Lizbeth de la Cruz, Adriana Robles-Cabrera, Christopher R. Stephens
Software Mentions: 4
Published: about 4 years ago

10.3390/toxins5122621

Venom Down Under: Dynamic Evolution of Australian Elapid Snake Toxins
Cited by: 54
Author(s): Timothy N. W. Jackson, Kartik Sunagar, Eivind A. B. Undheim, Ivan Koludarov, Angelo H. C. Chan, Kate L. Sanders, Syed Abid Ali, Iwan Hendrikx, Nathan Dunstan, Bryan G. Fry
Software Mentions: 4
Published: almost 11 years ago

10.3233/JAD-200445

Cognitive, Genetic, Brain Volume, and Diffusion Tensor Imaging Markers as Early Indicators of Dementia
Cited by: 4
Author(s): Theresa Müller, Nicola Maria Payton, Grégoria Kalpouzos, Frank Jessen, Giulia Grande, Lars Bäckman, Erika J. Laukka
Software Mentions: 4
Published: about 4 years ago

10.3389/fcimb.2021.723481

Dual RNASeq Reveals NTHi-Macrophage Transcriptomic Changes During Intracellular Persistence
Cited by: 6
Author(s): Jodie Ackland, Ashley Heinson, David W. Cleary, Myron Christodoulides, Tom Wilkinson, Karl J. Staples
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2018.00063

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level
Cited by: 47
Author(s): Michael Schmid, Jonathan Muri, Damianos P. Melidis, Adithi R. Varadarajan, Vincent Somerville, Adrian Wicki, Aline Moser, M Bourqui, Claudia Wenzel, Elisabeth Eugster‐Meier, Juerg E. Frey, Stefan Irmler, Christian H. Ahrens
Software Mentions: 4
Published: almost 7 years ago

10.1242/dev.139857

Cooperative binding of AP-1 and TEAD4 modulates the balance between vascular smooth muscle and hemogenic cell fate
Cited by: 41
Author(s): Nadine Obier, Pierre Cauchy, Salam A. Assi, Jane Gilmour, Michael Lie-A-Ling, Monika Lichtinger, Maarten Hoogenkamp, Laura Noailles, Peter N. Cockerill, Georges Lacaud, Valérie Kouskoff, Constanze Bonifer
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13148-021-01050-4

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA
Cited by: 10
Author(s): Sebastian Lunke, Scott Maxwell, Ishant Khurana, K N Harikrishnan, Jun Okabe, Keith Al-Hasani, Assam El‐Osta
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0178931

In silico discovery of substituted pyrido[2,3-d]pyrimidines and pentamidine-like compounds with biological activity in myotonic dystrophy models
Cited by: 10
Author(s): Àlex L. González, Piotr Konieczny, Beatriz Llamusí, Estefanía Delgado‐Pinar, José I. Borrell, Jordi Teixidó, Enrique García‐España, Manuel Pérez-Alonso, Roger Estrada‐Tejedor, Rubén Artero
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2020.00594

Expansion of Neutrophils and Classical and Nonclassical Monocytes as a Hallmark in Relapsing-Remitting Multiple Sclerosis
Cited by: 23
Author(s): David Haschka, Piotr Tymoszuk, Gabriel Bsteh, Verena Petzer, Klaus Berek, Igor Theurl, Thomas Berger, Günter Weiß
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-018-5016-z

Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation
Cited by: 49
Author(s): Jing Wang, Yue Zhao, Xiaofan Zhou, Scott W. Hiebert, Qi Liu, Yu Shyr
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.16070

Neural pattern change during encoding of a narrative predicts retrospective duration estimates
Cited by: 74
Author(s): Olga Lositsky, Janice Chen, Daniel Toker, Christopher J. Honey, Michael Shvartsman, Jordan Poppenk, Uri Hasson, Kenneth A. Norman
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0255803

In silico identification of natural product inhibitors against Octamer-binding transcription factor 4 (Oct4) to impede the mechanism of glioma stem cells
Cited by: 5
Author(s): Chirasmita Nayak, Sanjeev Kumar Singh
Software Mentions: 4
Published: about 3 years ago

10.3390/molecules24142557

Systematic Assessment of Burst Impurity in Confocal-Based Single-Molecule Fluorescence Detection Using Brownian Motion Simulations
Cited by: 10
Author(s): Dolev Hagai, Eitan Lerner
Software Mentions: 4
Published: over 5 years ago

10.1038/s41396-019-0508-7

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)
Cited by: 53
Author(s): Adrien Assié, Nikolaus Leisch, Dimitri V. Meier, Harald R. Gruber‐Vodicka, Halina E. Tegetmeyer, Anke Meyerdierks, Manuel Kleiner, Tjorven Hinzke, Samantha B. Joye, Matthew Saxton, Nicole Dubilier, Jillian M. Petersen
Software Mentions: 4
Published: about 5 years ago

10.3390/molecules26071996

Deciphering the Interactions of Bioactive Compounds in Selected Traditional Medicinal Plants against Alzheimer’s Diseases via Pharmacophore Modeling, Auto-QSAR, and Molecular Docking Approaches
Cited by: 25
Author(s): Oluwafemi Adeleke Ojo, Adebola Busola Ojo, Charles E. Okolie, Mary-Ann Chinyere Nwakama, Matthew Iyobhebhe, Ikponmwosa Owen Evbuomwan, Charles Obiora Nwonuma, Rotdelmwa Filibus Maimako, Abayomi Emmanuel Adegboyega, Odunayo Anthonia Taiwo, Khalaf F. Alsharif, Gaber El‐Saber Batiha
Software Mentions: 4
Published: over 3 years ago

10.3389/fpsyt.2019.00953

A Biomarker for Alzheimer’s Disease Based on Patterns of Regional Brain Atrophy
Cited by: 24
Author(s): Stefan Frenzel, Katharina Wittfeld, Mohamad Habes, Johanna Klinger-König, Robin Bülow, Henry Völzke, Hans J. Grabe
Software Mentions: 3
Published: almost 5 years ago

10.1534/g3.120.401014

Independent Whole-Genome Duplications Define the Architecture of the Genomes of the Devastating West African Cacao Black Pod Pathogen <i>Phytophthora megakarya</i> and Its Close Relative <i>Phytophthora palmivora</i>
Cited by: 13
Author(s): Abraham Morales‐Cruz, Shahzad Ali, Andrea Minio, Rosa Figueroa‐Balderas, Jadran F. García, Takao Kasuga, Alina S. Puig, Jean-Philippe Marelli, Bryan A. Bailey, Dario Cantu
Software Mentions: 3
Published: over 4 years ago

10.1186/s12916-015-0416-2

Constitutive phosphorylated STAT3-associated gene signature is predictive for trastuzumab resistance in primary HER2-positive breast cancer
Cited by: 44
Author(s): Amir Sonnenblick, Sylvain Brohée, Debora Fumagalli, Delphine Vincent, David Venet, Michail Ignatiadis, Roberto Salgado, Gert Van den Eynden, Françoise Rothé, Christine Desmedt, Patrick Neven, Sibylle Loibl, Carsten Denkert, Heikki Joensuu, Sherene Loi, Nicolas Sirtaine, Pirkko–Liisa Kellokumpu-Lehtinen, Martine Piccart, Christos Sotiriou
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0149407

An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor
Cited by: 9
Author(s): Gabriele Cordara, André van Eerde, E. Grahn, Harry C. Winter, Irwin J. Goldstein, Ute Krengel
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-017-1364-2

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
Cited by: 83
Author(s): Sabrina Krakau, Hugues Richard, Annalisa Marsico
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0022143

The Two-Component Signal Transduction System CopRS of Corynebacterium glutamicum Is Required for Adaptation to Copper-Excess Stress
Cited by: 35
Author(s): Stephanie Schelder, Daniela Zaade, Boris Litsanov, Michael Bott, Melanie Brocker
Software Mentions: 3
Published: over 13 years ago

10.3389/fneur.2020.595463

Pathomechanisms of HIV-Associated Cerebral Small Vessel Disease: A Comprehensive Clinical and Neuroimaging Protocol and Analysis Pipeline
Cited by: 7
Author(s): Kyle D. Murray, Meera V. Singh, Yuchuan Zhuang, Nasir Uddin, Xing Qiu, Miriam Weber, Madalina E. Tivarus, Henry Z. Wang, Bogachan Sahin, Jianhui Zhong, Sanjay B. Maggirwar, Giovanni Schifitto
Software Mentions: 3
Published: almost 4 years ago

10.15252/msb.156240

Extensive allele‐specific translational regulation in hybrid mice
Cited by: 30
Author(s): Jingyi Hou, Xi Wang, Erik McShane, Henrik Zauber, Wei Sun, Matthias Selbach, Wei Chen
Software Mentions: 3
Published: over 9 years ago

10.1038/s41380-018-0089-2

Stress peptides sensitize fear circuitry to promote passive coping
Cited by: 33
Author(s): Pinelopi Pliota, Vincent Böhm, Florian Grössl, Johannes Griessner, Ornella Valenti, Klaus Kraitsy, Joanna Kaczanowska, Manuel Pasieka, Thomas Lendl, Jan M. Deussing, Wulf Haubensak
Software Mentions: 3
Published: over 6 years ago

10.1242/dmm.041913

Deficiency in the endocytic adaptor proteins PHETA1/2 impair renal and craniofacial development
Cited by: 7
Author(s): Kristin M. Ates, Tong Wang, Trevor Moreland, Rajalakshmi Veeranan-Karmegam, Mingxing Ma, Chelsi Jeter, Paras Anand, Wolfgang Wenzel, Hyung‐Goo Kim, Lynne A. Wolfe, Joshi A. Stephen, David R. Adams, Thomas C. Markello, Cynthia J. Tifft, Robert E. Settlage, William A. Gahl, Graydon B. Gonsalvez, May Christine V. Malicdan, Heather Flanagan-Steet, Y. Albert Pan
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.7514

The adipokinetic hormones and their cognate receptor from the desert locust, Schistocerca gregaria: solution structure of endogenous peptides and models of their binding to the receptor
Cited by: 11
Author(s): Graham E. Jackson, Elumalai Pavadai, Gerd GÄde, N.H. Andersen
Software Mentions: 3
Published: about 5 years ago

10.1016/j.ejrad.2019.01.010

Predictors of segmental myocardial functional recovery in patients after an acute ST-Elevation myocardial infarction
Cited by: 15
Author(s): Kenneth Mangion, David Carrick, Guillaume Clerfond, Christopher Rush, Christie McComb, Keith G. Oldroyd, Mark C. Petrie, Hany Eteiba, Mitchell Lindsay, Margaret McEntegart, Stuart Hood, Stuart Watkins, Andrew Davie, Daniel A. Auger, Xiaodong Zhong, Frederick H. Epstein, Caroline Haig, Colin Berry
Software Mentions: 3
Published: over 5 years ago

10.6026/97320630014414

Screening and analysis of acetyl-cholinesterase (AChE) inhibitors in the context of Alzheimer’s disease
Cited by: 7
Author(s): Mohd Babu Khan, Bhagath Kumar Palaka, Tuleshwori Devi Sapam, Naidu Subbarao, Dinakara Rao Ampasala
Software Mentions: 3
Published: about 6 years ago

10.1111/eva.12515

A phylogenomic analysis of Marek's disease virus reveals independent paths to virulence in Eurasia and North America
Cited by: 37
Author(s): Jakob Trimpert, Nicole Groenke, Maria Jenckel, Shulin He, Dušan Kunec, Moriah L. Szpara, Stephen J. Spatz, Nikolaus Osterrieder, Dino P. McMahon
Software Mentions: 3
Published: about 7 years ago

10.3389/fpls.2021.625670

Duckweed Species Genotyping and Interspecific Hybrid Discovery by Tubulin-Based Polymorphism Fingerprinting
Cited by: 24
Author(s): Luca Braglia, Massimiliano Lauria, Klaus‐J. Appenroth, Manuela Bog, Diego Breviario, A. Grasso, Floriana Gavazzi, Laura Morello
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-15-177

Diversification of a single ancestral gene into a successful toxin superfamily in highly venomous Australian funnel-web spiders
Cited by: 48
Author(s): Sandy S. Pineda, Brianna L. Sollod, David T. Wilson, Aaron E. Darling, Kartik Sunagar, Eivind A.B. Undheim, Laurence Kely, Agostinho Antunes, Bryan G. Fry, Glenn F. King
Software Mentions: 3
Published: over 10 years ago

10.3390/ijms22094493

Methods for Identifying Microbial Natural Product Compounds that Target Kinetoplastid RNA Structural Motifs by Homology and De Novo Modeled 18S rRNA
Cited by: 2
Author(s): Harrison Ndung'u Mwangi, Edward K. Muge, Peter Waiganjo Wagacha, Albert Ndakala, Francis Mulaa
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-016-2585-6

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants
Cited by: 70
Author(s): Marijke J. van Baren, Charles Bachy, Emily Nahas Reistetter, Samuel O. Purvine, Jane Grimwood, Sebastian Sudek, Hang Yu, Camille Poirier, Thomas J. Deerinck, Alan Kuo, Igor V. Grigoriev, Chee-Hong Wong, Richard Smith, Stephen Callister, Chia Lin Wei, Jeremy Schmutz, Alexandra Z. Worden
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0141987

Mixed Inhibition of cPEPCK by Genistein, Using an Extended Binding Site Located Adjacent to Its Catalytic Cleft
Cited by: 6
Author(s): Shashank P. Katiyar, Arpit Jain, Jaspreet Kaur Dhanjal, Durai Sundar
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0138220

A Framework to Simplify Combined Sampling Strategies in Rosetta
Cited by: 10
Author(s): Justin R. Porter, Brian D. Weitzner, Oliver Lange
Software Mentions: 3
Published: about 9 years ago

10.1007/s13361-018-1910-5

Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31
Cited by: 5
Author(s): Andrey Dyachenko, Sem Tamara, Albert J. R. Heck
Software Mentions: 3
Published: over 6 years ago

10.1074/mcp.RA119.001839

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker
Cited by: 32
Author(s): Karl A.T. Makepeace, Yassene Mohammed, Elena L. Rudashevskaya, Evgeniy V. Petrotchenko, F.-Nora Vögtle, Chris Meisinger, Albert Sickmann, Christoph H. Borchers
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0167286

Transcriptomic Analysis of Mouse Cochlear Supporting Cell Maturation Reveals Large-Scale Changes in Notch Responsiveness Prior to the Onset of Hearing
Cited by: 39
Author(s): Juan C. Maass, Rende Gu, Tiantian Cai, Ying-Wooi Wan, Silvia C. Cantellano, Joanna Asprer, Hongyuan Zhang, Hsin-I Jen, Renée K. Edlund, Zhandong Liu, Andrew K. Groves
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-20057-1

Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency
Cited by: 17
Author(s): Naofumi Ito, K. Katoh, Hiroko Kushige, Yutaka Saitô, Terumasa Umemoto, Yu Matsuzaki, Hiroshi Kanazawa, Daiki Kobayashi, Minami Soga, Takumi Era, Nobuhito Araki, Yasuhide Furuta, Toshio Suda, Yasuyuki S. Kida, Kunimasa Ohta
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.23435

Co-expression of xenopsin and rhabdomeric opsin in photoreceptors bearing microvilli and cilia
Cited by: 49
Author(s): Oliver Vöcking, Ioannis Kourtesis, Sharat Chandra Tumu, Harald Hausen
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-015-1991-5

Copy number variations in the genome of the Qatari population
Cited by: 8
Author(s): Khalid Fakhro, Noha A. Yousri, Juan L. Rodríguez-Flores, Amal Robay, Michelle R. Staudt, Francisco Agosto-Perez, Jacqueline Salit, Joel A. Malek, Karsten Suhre, Amin Jayyousi, Mahmoud Zirie, Dora J. Stadler, Jason G. Mezey, Ronald G. Crystal
Software Mentions: 3
Published: about 9 years ago

10.18632/aging.101127

Induction of fibroblast senescence generates a non-fibrogenic myofibroblast phenotype that differentially impacts on cancer prognosis
Cited by: 79
Author(s): Massimiliano Mellone, Christopher J. Hanley, Steve Thirdborough, Toby Mellows, Edwin Garcia, Jeongmin Woo, Jo Tod, Steven J. Frampton, Veronika Jenei, Karwan A. Moutasim, Tasnuva D. Kabir, Peter A. Brennan, Giulia Venturi, Kirsty Ford, Nicolás Herranz, Ka Keat Lim, James Clarke, D Lambert, Stephen S. Prime, Tim Underwood, Pandurangan Vijayanand, Kevin W. Eliceiri, Christopher H. Woelk, Emma V. King, Jesús Gil, Christian Ottensmeier, Gareth J. Thomas
Software Mentions: 2
Published: almost 8 years ago

10.3390/genes11050482

Rising Roles of Small Noncoding RNAs in Cotranscriptional Regulation: In Silico Study of miRNA and piRNA Regulatory Network in Humans
Cited by: 8
Author(s): Massimiliano Chetta, Lorena Di Pietro, Nenad Bukvić, Wanda Lattanzi
Software Mentions: 2
Published: over 4 years ago

10.1002/mbo3.1154

Functional and structural characterization of Hyp730, a highly conserved and dormancy‐specific hypothetical membrane protein
Cited by: 0
Author(s): Stewart Fannin, Jonathan Rangel, Abiodun P. Bodurin, Tannon Yu, Brandon Mistretta, Sujina Mali, Preethi H. Gunaratne, Steven J. Bark, Jerry O. Ebalunode, Arshad Khan, William R. Widger, Mehmet Şen
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2172-8-26

Transcriptional networks in plasmacytoid dendritic cells stimulated with synthetic TLR 7 agonists
Cited by: 72
Author(s): Woubalem Birmachu, Raymond M. Gleason, Barbara J Bulbulian, Christie L Riter, John P. Vasilakos, Kenneth E. Lipson, Yuri Nikolsky
Software Mentions: 2
Published: almost 18 years ago

10.3389/fpls.2018.01840

Metabolomic Analysis of Defense-Related Reprogramming in Sorghum bicolor in Response to Colletotrichum sublineolum Infection Reveals a Functional Metabolic Web of Phenylpropanoid and Flavonoid Pathways
Cited by: 58
Author(s): Fidele Tugizimana, Arnaud T. Djami‐Tchatchou, Paul A. Steenkamp, Lizelle A. Piater, Ian A. Dubery
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes9080372

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes
Cited by: 12
Author(s): Maria Waldl, Bernhard C. Thiel, Roman Ochsenreiter, Alexander Holzenleiter, João Victor de Araújo Oliveira, Maria Emília M. T. Walter, Michael T. Wolfinger, Peter F. Stadler
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-10-35

Characterization of gene expression profiles for different types of mast cells pooled from mouse stomach subregions by an RNA amplification method
Cited by: 14
Author(s): Soken Tsuchiya, Yuki Tachida, Eri Segi-Nishida, Yasushi Okuno, Shigero Tamba, Gozoh Tsujimoto, Satoshi Tanaka, Yukihiko Sugimoto
Software Mentions: 2
Published: almost 16 years ago

10.3389/fpls.2019.00971

Cellular and Transcriptional Responses of Resistant and Susceptible Cultivars of Alfalfa to the Root Lesion Nematode, Pratylenchus penetrans
Cited by: 15
Author(s): Paulo Vieira, Joseph Mowery, J. D. Eisenback, Jonathan Shao, Lev G. Nemchinov
Software Mentions: 2
Published: over 5 years ago

10.26508/lsa.201800052

Pervasive allele-specific regulation on RNA decay in hybrid mice
Cited by: 9
Author(s): Wei Sun, Qingsong Gao, Bernhard Schaefke, Yuhui Hu, Wei Chen
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-020-06866-7

Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus
Cited by: 9
Author(s): Li Ren, Xiaojing Yan, Xin Gao, Jialin Cui, Peiyao Yan, Chang Wu, Wuhui Li, Shaojun Liu
Software Mentions: 2
Published: over 4 years ago

10.1002/brb3.1734

Brain reactions to the use of sensorized hand prosthesis in amputees
Cited by: 5
Author(s): Giuseppe Granata, Riccardo Di Iorio, Francesca Miraglia, Massimo Caulo, Francesco Iodice, Fabrizio Vecchio, Giacomo Valle, Ivo Strauss, Edoardo D’Anna, Francesco Iberite, Liverana Lauretti, Eduardo Fernández, Roberto Romanello, Francesco Maria Petrini, Staniša Raspopović, Silvestro Micera, Paolo Maria Rossini
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2164-9-443

Gene expression profiling of liver from dairy cows treated intra-mammary with lipopolysaccharide
Cited by: 57
Author(s): Li Jiang, Peter Sørensen, Christine M. Røntved, L. Vels, K.L. Ingvartsen
Software Mentions: 2
Published: about 16 years ago

10.1186/s12859-021-04351-w

An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions
Cited by: 0
Author(s): Yongxue Huo, Yikun Zhao, Li‐Wen Xu, Hongmei Yi, Yunlong Zhang, Xianqing Jia, Han Zhao, Jiuran Zhao, Fengge Wang
Software Mentions: 2
Published: about 3 years ago

10.3389/fninf.2016.00048

Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience
Cited by: 9
Author(s): Oliver Rübel, Max Dougherty, Prabhat, P. Denes, David S. Conant, Edward F. Chang, Kristofer E. Bouchard
Software Mentions: 2
Published: about 8 years ago

10.3389/fneur.2019.00358

Smartphone Level Test Measures Disability in Several Neurological Domains for Patients With Multiple Sclerosis
Cited by: 18
Author(s): Alexandra Boukhvalova, Olivia Fan, Ann Marie Weideman, Thomas K. Harris, Emily Kowalczyk, Linh Pham, Péter Kósa, Bibiana Bielekova
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2017.00156

Tet(C) Gene Transfer between Chlamydia suis Strains Occurs by Homologous Recombination after Co-infection: Implications for Spread of Tetracycline-Resistance among Chlamydiaceae
Cited by: 21
Author(s): H. R. Marti, Hoyon Kim, Sandeep J. Joseph, Stacey Dojiri, Timothy D. Read, Deborah Dean
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0207234

Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations
Cited by: 7
Author(s): Xiaopian Tian, Ye Liu, Jianxun Zhu, Zeyang Yu, Jiarui Han, Yan Wang, Han Wang
Software Mentions: 2
Published: about 6 years ago

10.3390/antibiotics9070368

3-(5-Nitrofuran-2-yl)prop-2-en-1-one Derivatives, with Potent Antituberculosis Activity, Inhibit A Novel Therapeutic Target, Arylamine N-acetyltransferase, in Mycobacteria
Cited by: 6
Author(s): Neha Agre, Nilesh R. Tawari, Arundhati Maitra, Antima Gupta, Tulika Munshi, Mariam S. Degani, Sanjib Bhakta
Software Mentions: 2
Published: over 4 years ago

10.3389/fnana.2017.00085

A Connectomic Analysis of the Human Basal Ganglia Network
Cited by: 58
Author(s): Alberto Cacciola, Alessandro Calamuneri, Demetrio Milardi, Enricomaria Mormina, Gaetana Chillemi, Silvia Marıno, Antonino Naro, Giuseppina Rizzo, Giuseppe Anastasi, Angelo Quartarone
Software Mentions: 2
Published: about 7 years ago

10.3389/fneur.2020.603774

Functional Network Profiles in ARSACS Disclosed by Aptamer-Based Proteomic Technology
Cited by: 8
Author(s): Federica Morani, Stefano Doccini, Giovanna Chiorino, Fabiana Fattori, Daniele Galatolo, Elisa Sciarrillo, Federica Gemignani, Stephan Züchner, Enrico Bertini, Filippo M. Santorelli
Software Mentions: 2
Published: almost 4 years ago

10.1002/hbm.25598

Cortical and white matter correlates of language‐learning aptitudes
Cited by: 6
Author(s): Mikael Novén, Hampus Olsson, Gunther Helms, Merle Horne, Markus Nilsson, Mikael Roll
Software Mentions: 2
Published: over 3 years ago

10.3389/fnhum.2016.00374

A Direct Cortico-Nigral Pathway as Revealed by Constrained Spherical Deconvolution Tractography in Humans
Cited by: 33
Author(s): Alberto Cacciola, Demetrio Milardi, Giuseppe Anastasi, Gianpaolo Antonio Basile, Pietro Ciolli, Mariangela Irrera, Giuseppina Cutroneo, Daniele Bruschetta, Giuseppina Rizzo, Stefania Mondello, Placido Bramantı, Angelo Quartarone
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1008581

Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation
Cited by: 11
Author(s): Annabelle Dold, Hong Han, Niankun Liu, Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Heike Hänel, Anke Busch, Petra Beli, Kathi Zarnack, Julian König, Jean‐Yves Roignant, Paul Lasko
Software Mentions: 2
Published: almost 5 years ago

10.3389/fnhum.2020.569973

Case Report of Dual-Site Neurostimulation and Chronic Recording of Cortico-Striatal Circuitry in a Patient With Treatment Refractory Obsessive Compulsive Disorder
Cited by: 25
Author(s): Sarah Olsen, Ishita Basu, Mustafa Taha Bilge, Anish Kanabar, Matthew Boggess, Alexander P Rockhill, Aishwarya Gosai, Elisabeth Hahn, Nir Peled, Michaela Ennis, Ilana Shiff, Katherine Fairbank-Haynes, Joshua D. Salvi, Cristina Cusin, Thilo Deckersbach, Ziv Williams, Justin T. Baker, Darin D. Dougherty, Alik S. Widge
Software Mentions: 2
Published: about 4 years ago

10.6026/97320630014015

Molecular docking based screening of Noggin inhibitors
Cited by: 15
Author(s): Sindhura Gudipati, Ravi Kumar Muttineni, Archana Mankad, Himanshu Pandya, Yogesh T. Jasrai
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-016-1058-x

TopHat-Recondition: a post-processor for TopHat unmapped reads
Cited by: 10
Author(s): Christian Brueffer, Lao H. Saal
Software Mentions: 2
Published: over 8 years ago

10.1111/febs.14973

Light‐induced complex formation of bacteriophytochrome<i>Rp</i>BphP1 and gene repressor<i>Rp</i>PpsR2 probed by SAXS
Cited by: 4
Author(s): Miroslav Z. Papiz, Dom Bellini, Katherine J. Evans, J. Günter Grossmann, Tony Fordham‐Skelton
Software Mentions: 2
Published: over 5 years ago

10.3389/fnagi.2014.00052

Cortical Amyloid Beta in Cognitively Normal Elderly Adults is Associated with Decreased Network Efficiency within the Cerebro-Cerebellar System
Cited by: 18
Author(s): Stefanie C. Steininger, Xinyang Liu, Anton Gietl, Michael Wyss, Simon J. Schreiner, Esmeralda Gruber, Valérie Treyer, Andrea M. Kälin, Sandra E. Leh, Alfred Buck, Roger M. Nitsch, Klaas P. Prüssmann, Christoph Höck, Paul G. Unschuld
Software Mentions: 2
Published: over 10 years ago

10.6026/97320630017369

Molecular docking analysis of antimicrobial peptides with the CXCL1 protein target for colorectal cancer
Cited by: 2
Author(s): Praveen Kumar, P. Shanmughavel
Software Mentions: 2
Published: over 3 years ago

10.1186/s13072-021-00403-w

Programmed suppression of oxidative phosphorylation and mitochondrial function by gestational alcohol exposure correlate with widespread increases in H3K9me2 that do not suppress transcription
Cited by: 4
Author(s): Richard Chang, Kara N. Thomas, Nicole A. Mehta, Kylee J. Veazey, Scott E. Parnell, Michael C. Golding
Software Mentions: 2
Published: over 3 years ago

10.1016/j.dcn.2018.07.003

Individual differences in functional brain connectivity predict temporal discounting preference in the transition to adolescence
Cited by: 23
Author(s): Jeya Anandakumar, Kathryn L. Mills, Eric Earl, Lourdes Irwin, Óscar Miranda-Domínguez, Damion V. Demeter, Alexandra Walton-Weston, Sarah L. Karalunas, Joel T. Nigg, Damien A. Fair
Software Mentions: 2
Published: about 6 years ago

10.12688/f1000research.52531.1

Developing open-source software for bioimage analysis: opportunities and challenges
Cited by: 20
Author(s): Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
Software Mentions: 2
Published: over 3 years ago

10.1042/BCJ20200552

Characterization of the different oligomeric states of the DAN family antagonists SOSTDC1 and SOST
Cited by: 6
Author(s): Gregory R. Gipson, Chandramohan Kattamuri, Magdalena Czepnik, Thomas B. Thompson
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1002170

Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity
Cited by: 58
Author(s): Nir London, Corissa L. Lamphear, James L. Hougland, Carol A. Fierke, Ora Schueler‐Furman
Software Mentions: 2
Published: about 13 years ago

10.15252/msb.20167375

Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation
Cited by: 22
Author(s): Mei-Sheng Xiao, Bin Zhang, Yi-Sheng Li, Qingsong Gao, Wei Sun, Wei Chen
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2164-15-S9-S3

Fragment based group QSAR and molecular dynamics mechanistic studies on arylthioindole derivatives targeting the α-β interfacial site of human tubulin
Cited by: 17
Author(s): Chetna Tyagi, Ankita Gupta, Sumit Goyal, Jaspreet Kaur Dhanjal, Abhinav Grover
Software Mentions: 2
Published: almost 10 years ago

10.3389/fchem.2020.00250

Computational Modeling on Aquaporin-3 as Skin Cancer Target: A Virtual Screening Study
Cited by: 20
Author(s): Dharmendra Kumar Yadav, Surendra Kumar, Eun‐Ha Choi, Sandeep Chaudhary, Mi‐Hyun Kim
Software Mentions: 2
Published: over 4 years ago

10.3389/fnhum.2019.00032

Formant Space Reconstruction From Brain Activity in Frontal and Temporal Regions Coding for Heard Vowels
Cited by: 1
Author(s): Alessandra Cecilia Rampinini, Giacomo Handjaras, Andrea Leo, Luca Cecchetti, Monica Betta, Giovanna Marotta, Emiliano Ricciardi, Pietro Pietrini
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12859-020-3377-1

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
Cited by: 8
Author(s): Ricardo Andrade, Mahdi Doostmohammadi, João Santos, Marie‐France Sagot, Nuno P. Mira, Susana Vinga
Software Mentions: 2
Published: over 4 years ago

10.1016/j.dib.2020.105722

Dataset of allele, genotype and haplotype frequencies of five polymorphisms CDKN2B-AS1 gene in Russian patients with primary open-angle glaucoma
Cited by: 0
Author(s): Natalya V. Eliseeva, Irina Ponomarenko, Evgeny Reshetnikov, А. В. Полоников, Irina Batlutskaya, Inna Aristova, А. В. Елыкова, Н. А. Рудых, М. И. Чурносов
Software Mentions: 2
Published: over 4 years ago

10.15252/msb.20145970

Predominant contribution of <i>cis‐</i> regulatory divergence in the evolution of mouse alternative splicing
Cited by: 35
Author(s): Qingsong Gao, Wei Sun, Marlies Ballegeer, Claude Libert, Wei Chen
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-015-0773-z

Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes
Cited by: 21
Author(s): Magdalena A. Machnicka, Katarzyna Kamińska, Stanisław Dunin-Horkawicz, Janusz M. Bujnicki
Software Mentions: 2
Published: about 9 years ago

10.15252/msb.20188516

A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids
Cited by: 50
Author(s): Roxanne E Debaugny, Aurore Sanchez, Jérôme Rech, Delphine Labourdette, Jérôme Dorignac, Frédéric Geniet, John Palmeri, Andrea Parmeggiani, François Boudsocq, Véronique Anton Leberre, Jean‐Charles Walter, Jean‐Yves Bouet
Software Mentions: 2
Published: about 6 years ago

10.1186/s12917-018-1752-1

Inherited selective cobalamin malabsorption in Komondor dogs associated with a CUBN splice site variant
Cited by: 9
Author(s): John C. Fyfe, Shelby L. Hemker, Alycia Frampton, Karthik Raj, Péter L. Nagy, Kristi J. Gibbon, Urs Giger
Software Mentions: 2
Published: almost 6 years ago