pypi: PARS | Projects | Ecosyste.ms: Papers

10.1186/s13059-019-1641-3

dStruct: identifying differentially reactive regions from RNA structurome profiling data
Cited by: 20
Author(s): Krishna Choudhary, Yi-Chun Lai, Elizabeth Tran, Sharon Aviran
Software Mentions: 8
Published: almost 6 years ago

10.7554/eLife.39054

New insights into the cellular temporal response to proteostatic stress
Cited by: 40
Author(s): Justin Rendleman, Zhe Cheng, Shuvadeep Maity, Nicolai Kastelic, Mathias Munschauer, Kristina Allgoewer, Guoshou Teo, Yun Bin Matteo Zhang, Amy Lei, Brian J. Parker, Markus Landthaler, Lindsay Freeberg, Scott Kuersten, Hyungwon Choi, Christine Vogel
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2017.00147

An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences
Cited by: 2
Author(s): Josef Pánek, Martin Modrák, Marek Schwarz
Software Mentions: 5
Published: about 7 years ago

10.1186/s12859-019-2645-4

reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction
Cited by: 5
Author(s): Risa Karakida Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, Jun Sese
Software Mentions: 5
Published: over 5 years ago

10.3390/genes9060300

Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures
Cited by: 10
Author(s): Pierce Radecki, Mirko Ledda, Sharon Aviran
Software Mentions: 3
Published: over 6 years ago

10.3390/genes12020187

Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source
Cited by: 3
Author(s): Carla Gallardo-Benavente, Jessica L. Campo-Giraldo, Juan Castro‐Severyn, Andrés Quiróz, José M. Pérez-Donoso
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0183859

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms
Cited by: 35
Author(s): Kevin A. Meyer, Timothy W. Davis, Susan B. Watson, Vincent J. Denef, Michelle A. Berry, Gregory J. Dick
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-021-07638-7

Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers
Cited by: 5
Author(s): Riccardo Delli Ponti, Marek Mutwil
Software Mentions: 3
Published: over 3 years ago

10.3389/fnins.2020.569517

Dissecting Neuronal Activation on a Brain-Wide Scale With Immediate Early Genes
Cited by: 25
Author(s): Alessandra Franceschini, Irene Costantini, Francesco S. Pavone, Ludovico Silvestri
Software Mentions: 3
Published: about 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

10.1371/journal.pone.0189389

PARS risk charts: A 10-year study of risk assessment for cardiovascular diseases in Eastern Mediterranean Region
Cited by: 24
Author(s): Nizal Sarrafzadegan, Razieh Hassannejad, Hamid Reza Marateb, Mohammad Talaei, Masoumeh Sadeghi, Hamidreza Roohafza, Farzad Masoudkabir, Shahram Oveisgharan, Marjan Mansourian, Mohammad Reza Mohebian, Miguel Ángel Mañanas
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms20225610

Secondary Structural Model of Human MALAT1 Reveals Multiple Structure–Function Relationships
Cited by: 38
Author(s): Phillip J. McCown, Matthew C. Wang, Luc Jaeger, Jessica A. Brown
Software Mentions: 2
Published: about 5 years ago

10.3390/metabo3020259

Getting Your Peaks in Line: A Review of Alignment Methods for NMR Spectral Data
Cited by: 93
Author(s): Trung Nghia Vu, Kris Laukens
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-016-1071-0

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)
Cited by: 15
Author(s): Nathan D. Berkowitz, Ian M. Silverman, Daniel Micah Childress, Hilal Kazan, Li-San Wang, Brian D. Gregory
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms22158252

Revisiting the Proposition of Binding Pockets and Bioactive Poses for GSK-3β Allosteric Modulators Addressed to Neurodegenerative Diseases
Cited by: 6
Author(s): Guilherme M. Silva, Rosivaldo S. Borges, Kelton L. B. Santos, Leonardo Bruno Federico, Isaque Antônio Galindo Francischini, Suzane Quintana Gomes, Mariana Pegrucci Barcelos, Raí C. Silva, Cleydson Breno Rodrigues dos Santos, Carlos Henrique Tomich de Paula da Silva
Software Mentions: 2
Published: over 3 years ago

10.1007/s10928-020-09685-1

Enabling pregnant women and their physicians to make informed medication decisions using artificial intelligence
Cited by: 25
Author(s): Lena Davidson, Mary Regina Boland
Software Mentions: 2
Published: over 4 years ago

10.3389/fpubh.2020.00257

Functionality of Physical Activity Referral Schemes (PARS): A Systematic Review
Cited by: 11
Author(s): Francis A. Albert, Melissa Crowe, A.E.O. Malau‐Aduli, Bunmi S. Malau‐Aduli
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-018-4497-0

RNA secondary structure profiling in zebrafish reveals unique regulatory features
Cited by: 9
Author(s): Kriti Kaushik, Ambily Sivadas, Shamsudheen Karuthedath Vellarikkal, Ankit Verma, Rijith Jayarajan, Satyaprakash Pandey, Tavpritesh Sethi, Souvik Maiti, Vinod Scaria, Sridhar Sivasubbu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-016-1067-9

Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome
Cited by: 28
Author(s): Risa Karakida Kawaguchi, Hisanori Kiryu
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2018.00828

The Genomic Basis of Intrinsic and Acquired Antibiotic Resistance in the Genus Serratia
Cited by: 43
Author(s): Luisa Sandner-Miranda, Pablo Vinuesa, Alejandro Cravioto, Rosario Morales-Espinosa
Software Mentions: 2
Published: over 6 years ago

10.3389/fmolb.2020.586544

Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin
Cited by: 0
Author(s): Irène Pitard, Damien Monet, Pierre L. Goossens, Arnaud Blondel, Thérèse E. Malliavin
Software Mentions: 2
Published: almost 4 years ago

10.3390/s20195595

A Review of Endogenous and Exogenous Contrast Agents Used in Photoacoustic Tomography with Different Sensing Configurations
Cited by: 27
Author(s): Victor T. C. Tsang, Xiufeng Li, Terence T. W. Wong
Software Mentions: 2
Published: about 4 years ago

10.3389/fmolb.2021.666626

Computational Identification of a Putative Allosteric Binding Pocket in TMPRSS2
Cited by: 3
Author(s): Jacopo Sgrignani, Andrea Cavalli
Software Mentions: 2
Published: over 3 years ago

10.1016/j.str.2017.01.008

Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints
Cited by: 40
Author(s): Joe G Greener, Ioannis Filippis, Michael J.E. Sternberg
Software Mentions: 2
Published: over 7 years ago

10.3390/ijerph15112452

PARS: Using Augmented 360-Degree Panoramas of Reality for Construction Safety Training
Cited by: 78
Author(s): Ricardo Eiris, Masoud Gheisari, Behzad Esmaeili
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1005233

The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation
Cited by: 36
Author(s): Lydia M. Castelli, David Talavera, Christopher J. Kershaw, Sarah S. Mohammad‐Qureshi, Joseph L. Costello, William Rowe, Paul F. G. Sims, Chris M. Grant, Simon J. Hubbard, Mark P. Ashe, Graham D. Pavitt
Software Mentions: 2
Published: over 9 years ago

10.1186/s12929-020-00640-3

Functions and properties of nuclear lncRNAs—from systematically mapping the interactomes of lncRNAs
Cited by: 51
Author(s): Chia-Yu Guh, Yu-Hung Hsieh, Hao-Hua Chu
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.ppat.1008184

An RNA thermometer dictates production of a secreted bacterial toxin
Cited by: 22
Author(s): Christian Twittenhoff, Ann Kathrin Heroven, Sabrina Mühlen, Petra Dersch, Franz Narberhaus
Software Mentions: 1
Published: almost 5 years ago

10.1111/phn.12697

The development of a parental attachment recognition scale for mothers nurturing preschool children
Cited by: 1
Author(s): Yôko Tanaka
Software Mentions: 1
Published: almost 5 years ago

10.1186/s40638-018-0090-x

Cognition-based variable admittance control for active compliance in flexible manipulation of heavy objects with a power-assist robotic system
Cited by: 10
Author(s): S. M. Mizanoor Rahman, Ryojun Ikeura
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-019-49849-9

All-optical Reflection-mode Microscopic Histology of Unstained Human Tissues
Cited by: 37
Author(s): Saad Abbasi, Martin Le, Bazil Sonier, Deepak Dinakaran, Gilbert Bigras, Kevan Bell, John R. Mackey, Parsin Haji Reza
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-74160-3

Improving maximal safe brain tumor resection with photoacoustic remote sensing microscopy
Cited by: 24
Author(s): Benjamin R. Ecclestone, Kevan Bell, Saad Abbasi, Deepak Dinakaran, Frank K.H. van Landeghem, John R. Mackey, Paul Fieguth, Parsin Haji Reza
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-76155-6

Reflection-mode virtual histology using photoacoustic remote sensing microscopy
Cited by: 24
Author(s): Kevan Bell, Saad Abbasi, Deepak Dinakaran, Muba Taher, Gilbert Bigras, Frank K.H. van Landeghem, John R. Mackey, Parsin Haji Reza
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-90776-5

Functional and structural ophthalmic imaging using noncontact multimodal photoacoustic remote sensing microscopy and optical coherence tomography
Cited by: 21
Author(s): Zohreh Hosseinaee, Nima Abbasi, Nicholas Pellegrino, Layla Khalili, Lyazzat Mukhangaliyeva, Parsin Haji Reza
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-93222-8

Three-dimensional virtual histology in unprocessed resected tissues with photoacoustic remote sensing (PARS) microscopy and optical coherence tomography (OCT)
Cited by: 8
Author(s): Benjamin R. Ecclestone, Zohreh Hosseinaee, Nima Abbasi, Kevan Bell, Deepak Dinakaran, John R. Mackey, Parsin Haji Reza
Software Mentions: 1
Published: over 3 years ago

10.1186/s40064-016-3076-6

The diversity of mtDNA rns introns among strains of Ophiostoma piliferum, Ophiostoma pluriannulatum and related species
Cited by: 1
Author(s): Iman M. Bilto, Georg Hausner
Software Mentions: 1
Published: over 8 years ago

10.1186/s12966-020-01050-2

A modified Delphi study to gain consensus for a taxonomy to report and classify physical activity referral schemes (PARS)
Cited by: 16
Author(s): Coral L Hanson, Emily J. Oliver, Caroline J. Dodd-Reynolds, Alice Pearsons, Paul Kelly
Software Mentions: 1
Published: almost 4 years ago

10.3390/ijerph17186832

Green Health Partnerships in Scotland; Pathways for Social Prescribing and Physical Activity Referral
Cited by: 14
Author(s): Sheona McHale, Alice Pearsons, Lis Neubeck, Coral L Hanson
Software Mentions: 1
Published: about 4 years ago

10.3390/ijerph18062957

Understanding Leisure Centre-Based Physical Activity after Physical Activity Referral: Evidence from Scheme Participants and Completers in Northumberland UK
Cited by: 3
Author(s): Jordan Bell, Lis Neubeck, Kai Jin, Paul Kelly, Coral L Hanson
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms141223672

Tackling Structures of Long Noncoding RNAs
Cited by: 68
Author(s): Irina Novikova, Scott P. Hennelly, Karissa Y. Sanbonmatsu
Software Mentions: 1
Published: almost 11 years ago

10.3390/ijms17050702

Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures
Cited by: 70
Author(s): Rui Li, Hongliang Zhu, Yane Luo
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms21093099

Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design
Cited by: 128
Author(s): Maria Bzówka, Karolina Mitusińska, Agata Raczyńska, Aleksandra Samol, Jack A. Tuszyński, Artur Góra
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms22010187

Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors
Cited by: 5
Author(s): Pedro Renault, Jesús Giraldo
Software Mentions: 1
Published: almost 4 years ago

10.3390/ijms22105108

Some Dietary Phenolic Compounds Can Activate Thyroid Peroxidase and Inhibit Lipoxygenase-Preliminary Study in the Model Systems
Cited by: 6
Author(s): Ewa Habza-Kowalska, Agnieszka A. Kaczor, Damian Bartuzi, Jacek Piłat, Urszula Gawlik‐Dziki
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms22136730

Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging?
Cited by: 0
Author(s): Paweł Matryba, Kacper Łukasiewicz, Monika Pawłowska, Jacek Tomczuk, Jakub Goła̧b
Software Mentions: 1
Published: over 3 years ago

10.1136/jnnp-2015-311890

The prediagnostic phase of Parkinson's disease
Cited by: 116
Author(s): Alastair Noyce, Andrew J. Lees, Anette-Eleonore Schrag
Software Mentions: 1
Published: almost 9 years ago

10.1155/2016/3136024

In Silico Approach for SAR Analysis of the Predicted Model of DEPDC1B: A Novel Target for Oral Cancer
Cited by: 10
Author(s): Palak Ahuja, K. N. Singh
Software Mentions: 1
Published: over 8 years ago

10.1155/2021/5541753

Schisandrol A Attenuates Myocardial Ischemia/Reperfusion-Induced Myocardial Apoptosis through Upregulation of 14-3-3θ
Cited by: 8
Author(s): Shuaishuai Gong, Jincheng Liu, Shi-Yao Wan, Weiwei Yang, Yuanyuan Zhang, Boyang Yu, Fang Li, Junping Kou
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-14-269

Efficient alignment of RNA secondary structures using sparse dynamic programming
Cited by: 9
Author(s): Cuncong Zhong, Shaojie Zhang
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2105-15-S9-S15

ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search
Cited by: 3
Author(s): Peng Ge, Cuncong Zhong, Shaojie Zhang
Software Mentions: 1
Published: about 10 years ago

10.1186/s12859-015-0771-1

AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis
Cited by: 78
Author(s): Joe G Greener, Michael J.E. Sternberg
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-11-470

Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins
Cited by: 5
Author(s): William N. Kelly, Michael Stumpf
Software Mentions: 1
Published: about 14 years ago

10.1186/s12861-014-0048-3

Improved application of the electrophoretic tissue clearing technology, CLARITY, to intact solid organs including brain, pancreas, liver, kidney, lung, and intestine
Cited by: 67
Author(s): Hyunsu Lee, Jae-Hyung Park, Incheol Seo, Sun-Hyun Park, Shin Kim
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-12-532

Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella
Cited by: 27
Author(s): Elizabeth Skippington, Mark A. Ragan
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-8-154

Highly asymmetric rice genomes
Cited by: 36
Author(s): Jing Ding, Hideki Araki, Qiang Wang, Pengfei Zhang, Sihai Yang, Jian-Qun Chen, Dacheng Tian
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2334-7-98

Association of Escherichia coli O157:H7 tirpolymorphisms with human infection
Cited by: 74
Author(s): James L. Bono, James E. Keen, Marion Clawson, Lisa M. Durso, Michael P. Heaton, William W. Laegreid
Software Mentions: 1
Published: over 17 years ago

10.1186/s12884-018-1973-0

Perinatal death beyond 41 weeks pregnancy: an evaluation of causes and substandard care factors as identified in perinatal audit in the Netherlands
Cited by: 15
Author(s): Joep C. Kortekaas, Anke C. Scheuer, Esteriek de Miranda, Aimée E. van Dijk, Judit K. J. Keulen, Aafke Bruinsma, Ben Willem J. Mol, Frank P.H.A. Vandenbussche, Jeroen van Dillen
Software Mentions: 1
Published: about 6 years ago

10.1186/1752-0509-1-1

Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network
Cited by: 36
Author(s): Ofer Meshi, Tomer Shlomi, Eytan Ruppin
Software Mentions: 1
Published: almost 18 years ago

10.1080/21655979.2017.1373537

Bioengineering of crop plants for improved tetrahydrofolate production
Cited by: 3
Author(s): Bhupendra Chaudhary, Nagendra Singh, Dhananjay Pandey
Software Mentions: 1
Published: about 7 years ago

10.3390/molecules24152766

Thyroid Peroxidase Activity is Inhibited by Phenolic Compounds—Impact of Interaction
Cited by: 13
Author(s): Ewa Habza-Kowalska, Agnieszka A. Kaczor, Justyna Żuk, Dariusz Matosiuk, Urszula Gawlik‐Dziki
Software Mentions: 1
Published: over 5 years ago

10.13918/j.issn.2095-8137.2017.004

Does mRNA structure contain genetic information for regulating co-translational protein folding?
Cited by: 3
Author(s): Jinfu Yang
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.pacs.2019.100141

Review on practical photoacoustic microscopy
Cited by: 179
Author(s): Seungwan Jeon, Jongbeom Kim, Dong-Hyun Lee, Jin Woo Baik, Chulhong Kim
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1005613

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function
Cited by: 167
Author(s): Cristian Del Campo, Alexander Bartholomäus, Ivan Fedyunin, Zoya Ignatova
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1001064

Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction
Cited by: 603
Author(s): Vincent Croset, Raphael Rytz, Scott F. Cummins, Aidan Budd, David Brawand, Henrik Kaessmann, Toby J. Gibson, Richard Benton
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0173023

The impact of RNA secondary structure on read start locations on the Illumina sequencing platform
Cited by: 9
Author(s): Adam Price, Jaishree Garhyan, Cynthia Gibas
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0041318

Mycobacterium tuberculosis Population in Northwestern Russia: An Update from Russian-EU/Latvian Border Region
Cited by: 35
Author(s): Igor Mokrousov, Anna Vyazovaya, Tatiana Otten, Viacheslav Zhuravlev, Еlena Pavlova, Larisa Tarashkevich, Valery Krishevich, Boris Vishnevsky, Olga Narvskaya
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0137078

Helicobacter pylori bab Paralog Distribution and Association with cagA, vacA, and homA/B Genotypes in American and South Korean Clinical Isolates
Cited by: 19
Author(s): Aeryun Kim, Stephanie L. Servetas, Jieun Kang, Jinmoon Kim, Sungil Jang, Jin Huang, Wan Jin Lee, June Kim, Judith Romero–Gallo, Richard M. Peek, D. Scott Merrell, Jeong Heon
Software Mentions: 1
Published: about 9 years ago

10.22074/cellj.2019.5684

A Simple Technique for Three-Dimensional Imaging and Segmentation of Brain Vasculature U sing Fast Free-of-Acrylamide Clearing Tissue in Murine.
Cited by: 7
Author(s): Arezoo Khoradmehr, Fahime Mazaheri, Morteza Anvari, Amin Tamadon
Software Mentions: 1
Published: over 5 years ago

10.1007/s00259-021-05270-x

Just another “Clever Hans”? Neural networks and FDG PET-CT to predict the outcome of patients with breast cancer
Cited by: 23
Author(s): Manuel Weber, David Kersting, Lale Umutlu, Michael Schäfers, Christoph Rischpler, Wolfgang P. Fendler, Irène Buvat, Ken Herrmann, Robert Seifert
Software Mentions: 1
Published: over 3 years ago

10.3389/fmed.2021.628179

Evaluation of an Automatic Classification Algorithm Using Convolutional Neural Networks in Oncological Positron Emission Tomography
Cited by: 19
Author(s): Pierre Pinochet, Florian Eude, Stéphanie Becker, Vijay Shah, Ludovic Sibille, Mathieu Nessim Toledano, Romain Modzelewski, Pierre Véra, Pierre Decazes
Software Mentions: 1
Published: over 3 years ago

10.3389/fpls.2018.00671

New Era of Studying RNA Secondary Structure and Its Influence on Gene Regulation in Plants
Cited by: 27
Author(s): Xiaofei Yang, Minglei Yang, Huiyong Deng, Yiliang Ding
Software Mentions: 1
Published: over 6 years ago

10.1117/1.JBO.26.5.056007

Single acquisition label-free histology-like imaging with dual-contrast photoacoustic remote sensing microscopy
Cited by: 5
Author(s): Benjamin R. Ecclestone, Deepak Dinakaran, Parsin Haji Reza
Software Mentions: 1
Published: over 3 years ago

10.1117/1.JBO.26.6.069801

Single acquisition label-free histology-like imaging with dual-contrast photoacoustic remote sensing microscopy (Errata)
Cited by: 1
Author(s): Benjamin R. Ecclestone, Deepak Dinakaran, Parsin Haji Reza
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: PARS

Papers Mentioning PARS 73