Ecosyste.ms: Papers

10.3389/fbioe.2020.00034

A Guide to Conquer the Biological Network Era Using Graph Theory
Cited by: 129
Author(s): Mikaela Koutrouli, Evangelos Karatzas, David Páez-Espino, Georgios A. Pavlopoulos
Software Mentions: 11
Published: almost 5 years ago

10.1002/jia2.25148

Oral abstracts of the 22nd International AIDS Conference, 23-27 July 2018, Amsterdam, the Netherlands
Cited by: 9
Author(s):
Software Mentions: 9
Published: over 6 years ago

10.1126/science.abe9403

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms
Cited by: 461
Author(s): David E. Gordon, Joseph Hiatt, Mehdi Bouhaddou, Veronica V. Rezelj, Svenja Ulferts, Hannes Braberg, Alexander S. Jureka, Kirsten Obernier, Jeffrey Z. Guo, Jyoti Batra, Robyn M. Kaake, Andrew Weckstein, Tristan W. Owens, Meghna Gupta, Sergei Pourmal, Erron W. Titus, Merve Çakır, Margaret Soucheray, Michael McGregor, Zeynep Çakır, Gwendolyn Μ. Jang, Matthew J. O’Meara, Tia A. Tummino, Ziyang Zhang, Helene Foussard, Ajda Rojc, Yuan Zhou, Dmitry Kuchenov, Ruth Hüttenhain, Jiewei Xu, Manon Eckhardt, Danielle L. Swaney, Jacqueline M. Fabius, Manisha R. Ummadi, Beril Tutuncuoglu, Ujjwal Rathore, Maya Modak, Paige Haas, Kelsey M. Haas, Zun Zar Chi Naing, Ernst H. Pulido, Ying Shi, Iñigo Barrio-Hernandez, Danish Memon, Eirini Petsalaki, Alistair S. Dunham, Miguel Marrero, David F. Burke, Cassandra Koh, Thomas Vallet, Jesus A. Silvas, Caleigh M. Azumaya, Christian Billesboelle, Axel F. Brilot, Melody G. Campbell, Amy Diallo, Miles Sasha Dickinson, Devan Diwanji, Nadia Herrera, Nick Hoppe, Huong T. Kratochvil, Yanxin Liu, Gregory E. Merz, Michelle Moritz, Henry C. Nguyen, Carlos Nowotny, Cristina Puchades, Alexandrea N. Rizo, Ursula Schulze‐Gahmen, Amber M. Smith, Ming Sun, I.D. Young, Jianhua Zhao, Daniel Asarnow, J.T. Biel, Alisa Bowen, Julian R. Braxton, Jen Chen, Cynthia M. Chio, Un Seng Chio, Ishan Deshpande, Loan Doan, Bryan Faust, Sebastián Flores, Mingliang Jin, Sun Kyung Kim, Victor Lam, Fei Li, J Li, Yen-Li Li, Yang Li, Xi Liu, Megan Lo, Kyle E. Lopez, Arthur A. Melo, Frank R. Moss, Phuong T. Nguyen, Joana Paulino, Komal Ishwar Pawar, Jessica K. Peters, Thomas H. Pospiech, Maliheh Safari, Smriti Sangwan, Kaitlin Schaefer, Paul Thomas, Aye C. Thwin, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Wang, Natalie Whitis, Zanlin Yu, Kaihua Zhang, Sunny Zhang, Fengbo Zhou, Daniel J. Saltzberg, Anthony J. Hodder, Amber S Shun-Shion, Daniel M. Williams, Kris M. White, Romel Rosales, Thomas Kehrer, Lisa Miorin, Elena Moreno, Arvind H. Patel, Suzannah J. Rihn, Mir M. Khalid, Albert Vallejo-Gracia, Parinaz Fozouni, Camille R. Simoneau, Theodore L. Roth, David Wu, Mohd Anisul Karim, Maya Ghoussaini, Ian Dunham, Francesco Berardi, Sebastian Weigang, Maxime Chazal, Jisoo Park, James Logue, Marisa E. McGrath, Stuart Weston, Robert Haupt, C. James Hastie, Matthew Elliott, Fiona Brown, Kerry Burness, Elaine Reid, Mark Dorward, Clare Johnson, Stuart G. Wilkinson, Anna Geyer, Daniel M. Giesel, Carla Baillie, Samantha L. Raggett, Hannah Leech, Rachel Toth, Nicola Goodman, Kathleen C. Keough, Abigail Lind, Reyna Klesh, Kafi Hemphill, Jared Carlson-Stevermer, Jennifer Oki, Kevin Holden, Travis J. Maures, Katherine S. Pollard, Andrej S̆ali, David A. Agard, Yifan Cheng, James S. Fraser, Adam Frost, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R. Southworth, Robert M. Stroud, Dario R. Alessi, Paul Davies, Matthew B. Frieman, Trey Ideker, Carmen Abate, Nolwenn Jouvenet, Georg Kochs, Brian K Shoichet, Melanie Ott, Massimo Palmarini, Kevan M. Shokat, Adolfo Garcı́a-Sastre, Jeremy A. Rassen, Robert Grosse, Oren S. Rosenberg, Kliment A. Verba, Christopher F. Basler, Marco Vignuzzi, Andrew A. Peden, Pedro Beltrão, Nevan J. Krogan, Tristan W. Owens, Meghna Gupta, Sergei Pourmal, Erron W. Titus, Caleigh M. Azumaya, Christian B. Billesbølle, Axel F. Brilot, Melody G. Campbell, Amy Diallo, Miles Sasha Dickinson, Devan Diwanji, Nadia Herrera, Nick Hoppe, Huong T. Kratochvil, Yanxin Liu, Gregory E. Merz, Michelle Moritz, Henry C. Nguyen, Carlos Nowotny, Cristina Puchades, Alexandrea N. Rizo, Ursula Schulze‐Gahmen, Amber M. Smith, Ming Sun, I.D. Young, Jianhua Zhao, Daniel Asarnow, J.T. Biel, Alisa Bowen, Julian R. Braxton, Jen Chen, Cynthia M. Chio, Un Seng Chio, Ishan Deshpande, Loan Doan, Bryan Faust, Sebastián Flores, Mingliang Jin, Kate Kim, Victor Lam, Fēi Li, Junrui Li, Yen-Li Li, Yang Li, Xi Liu, Megan Lo, Kyle E. Lopez, Arthur A. Melo, Frank R. Moss, Phuong T. Nguyen, Joana Paulino, Komal Ishwar Pawar, Jessica K. Peters, Thomas H. Pospiech, Maliheh Safari, Smriti Sangwan, Kaitlin Schaefer, Paul Thomas, Aye C. Thwin, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Wang, Natalie Whitis, Zanlin Yu, Kaihua Zhang, Zifeng Yang, Fengbo Zhou, Donovan Trinidad, David A. Agard, Yifan Cheng, James S. Fraser, Adam Frost, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R. Southworth, Robert M. Stroud, Oren S. Rosenberg, Kliment A. Verba, Joana Damas, Graham M. Hughes, Kathleen C. Keough, Corrie Painter, Nicole S. Persky, Marco Corbo, Bodgan Kirilenko, Michael Hiller, Klaus‐Peter Koepfli, Irene M. Kaplow, Morgan Wirthlin, Andreas R. Pfenning, Huabin Zhao, Diane P. Genereux, Ross Swofford, Abigail Lind, Katherine S. Pollard, Oliver A. Ryderq, Martin Nweeia, Jennifer R. S. Meadows, Michael X. Dong, Ola Wallerman, Vikki Marinescu, Kerstin Lindblad‐Toh, David A. Ray, Sarahjane Power, Emma C. Teeling, Gaurav Chauhan, Shirley Xue Li, Elinor K. Karlsson, Harris A. Lewin
Software Mentions: 5
Published: about 4 years ago

10.1021/acsomega.1c03681

Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells
Cited by: 5
Author(s): Ankitha Shetty, Santosh D. Bhosale, Subhash Tripathi, Tanja Buchacher, Rahul Biradar, Omid Rasool, Robert Moulder, Sanjeev Galande, Riitta Lahesmaa
Software Mentions: 5
Published: over 3 years ago

10.1002/humu.23674

Allele balance bias identifies systematic genotyping errors and false disease associations
Cited by: 17
Author(s): Francesc Muyas, Mattia Bosio, Anna Puig, Hana Sušak, Laura Domènech, Geòrgia Escaramís, Luís Zapata, German Demidov, Xavier Estivill, Raquel Rabionet, Stephan Ossowski
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-017-00712-9

Longitudinal data analysis for rare variants detection with penalized quadratic inference function
Cited by: 1
Author(s): Hongyan Cao, Li Zhi, Yang Huang, Yuehua Cui, Yanbo Zhang
Software Mentions: 3
Published: over 7 years ago

10.1093/bfgp/elu012

Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits
Cited by: 17
Author(s): Loukas Moutsianas, Andrew P. Morris
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pcbi.1007784

Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation
Cited by: 4
Author(s): Hana Sušak, Laura Serra, German Demidov, Raquel Rabionet, Laura Domènech, Mattia Bosio, Francesc Muyas, Xavier Estivill, Geòrgia Escaramís, Stephan Ossowski
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0154181

Incorporating Non-Coding Annotations into Rare Variant Analysis
Cited by: 9
Author(s): Tom G Richardson, Colin Campbell, Nicholas J. Timpson, Tom R. Gaunt
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0010433

The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments
Cited by: 259
Author(s): Paul Janssen, Rob Van Houdt, Hugo Moors, Pieter Monsieurs, Nicolas Morin, Arlette Michaux, Mohammed Abderrafi Benotmane, Natalie Leys, Tatiana Vallaeys, Alla Lapidus, Sébastien Monchy, Claudine Médigue, Safiyh Taghavi, S. McCorkle, John J. Dunn, Daniël van der Lelie, Max Mergeay
Software Mentions: 3
Published: over 14 years ago

10.3390/cells10030646

Identification of Ku70 Domain-Specific Interactors Using BioID2
Cited by: 2
Author(s): Sanna Abbasi, Caroline Schild-Poulter
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.csbj.2020.10.010

Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses
Cited by: 6
Author(s): Sébastien Leblanc, Marie-Christine Brunet
Software Mentions: 3
Published: almost 5 years ago

10.1002/gepi.22264

Population genetic simulation study of power in association testing across genetic architectures and study designs
Cited by: 6
Author(s): Dominic M. H. Tong, Ryan D. Hernández
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-78511-y

Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data
Cited by: 9
Author(s): Yan Kou, Xiaomin Xu, Zhengnong Zhu, Lei Dai, Yan Tan
Software Mentions: 3
Published: about 4 years ago

10.1128/mBio.01757-19

Distinct Chemotaxis Protein Paralogs Assemble into Chemoreceptor Signaling Arrays To Coordinate Signaling Output
Cited by: 10
Author(s): Lindsey O’Neal, Jessica M. Gullett, Anastasia Aksenova, Adam Keith Hubler, Ariane Briegel, Davi R. Ortega, Andreas Kjær, Grant J. Jensen, Gladys Alexandre
Software Mentions: 3
Published: about 5 years ago

10.1128/mBio.03066-19

How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Cited by: 45
Author(s): José A. Gavira, Vadim M. Gumerov, Míriam Rico-Jiménez, Marharyta Petukh, Amit A. Upadhyay, Álvaro Ortega, Miguel A. Matilla, Igor B. Zhulin, Tino Krell
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1008947

A general framework for functionally informed set-based analysis: Application to a large-scale colorectal cancer study
Cited by: 5
Author(s): Xue Dong, Yu Ru Su, Richard Barfield, Stephanie A. Bien, Qianchuan He, Tabitha A. Harrison, Jeroen R. Huyghe, Temitope O. Keku, Noralane M. Lindor, Clemens Schafmayer, Andrew T. Chan, Stephen B. Gruber, Mark A. Jenkins, Charles Kooperberg, Ulrike Peters, Li Hsu
Software Mentions: 2
Published: over 4 years ago

10.21203/rs.3.rs-515215/v1

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes
Cited by: 6
Author(s): Kliment A. Verba, Meghna Gupta, Caleigh M. Azumaya, Michelle Moritz, Sergei Pourmal, Amy Diallo, Gregory E. Merz, Gwendolyn Μ. Jang, Mehdi Bouhaddou, Andrea Fossati, Axel F. Brilot, Devan Diwanji, Evelyn Hernandez, Nadia Herrera, Huong T. Kratochvil, Victor Lam, Fēi Li, Yang Li, Henry C. Nguyen, Carlos Nowotny, Tristan W. Owens, Jessica K. Peters, Alexandrea N. Rizo, Ursula Schulze‐Gahmen, Amber M. Smith, Iris D. Young, Zanlin Yu, Daniel Asarnow, Christian B. Billesbølle, Melody G. Campbell, Jen Chen, Kuei‐Ho Chen, Un Seng Chio, Miles Sasha Dickinson, Loan Doan, Mingliang Jin, Kate Kim, Junrui Li, Yen-Li Li, Edmond M. Linossi, Yanxin Liu, Megan Lo, Jocelyne Lopez, Kyle E. Lopez, Adamo Mancino, Frank R. Moss, Michael Paul, Komal Ishwar Pawar, Adrian Pelin, Thomas H. Pospiech, Cristina Puchades, Soumya G. Remesh, Maliheh Safari, Kaitlin Schaefer, Ming Sun, Mariano Tabios, Aye C. Thwin, Erron W. Titus, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Feng, Kaihua Zhang, Yang Zhang, Jianhua Zhao, Fengbo Zhou, Yuan Zhou, Lorena Zuliani-Alvarez, David A. Agard, Yifan Cheng, James S. Fraser, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R. Southworth, Robert M. Stroud, Danielle L. Swaney, Nevan J. Krogan, Adam Frost, Oren S. Rosenberg
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0186518

Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data
Cited by: 9
Author(s): Stephanie A. Bien, Paul L. Auer, Tabitha A. Harrison, Conghui Qu, Charles M. Connolly, Peyton G. Greenside, Sai Chen, Sonja I. Berndt, Stéphane Bézieau, Hyun Min Kang, Jeroen R. Huyghe, Hermann Brenner, Graham Casey, Andrew T. Chan, John L. Hopper, Barbara L. Banbury, Jenny Chang–Claude, Stephen J. Chanock, Robert W. Haile, Michael Hoffmeister, Christian Fuchsberger, Mark A. Jenkins, Suzanne M. Leal, Mathieu Lemire, Polly A. Newcomb, Steven Gallinger, John D. Potter, Robert E. Schoen, Martha L. Slattery, Joshua D. Smith, Loı̈c Le Marchand, Emily White, Brent W. Zanke, Gonçalo R. Abecasis, Christopher S. Carlson, Ulrike Peters, Deborah A. Nickerson, Anshul Kundaje, Li Hsu, Ccfr
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1005165

The Power of Gene-Based Rare Variant Methods to Detect Disease-Associated Variation and Test Hypotheses About Complex Disease
Cited by: 123
Author(s): Loukas Moutsianas, Vineeta Agarwala, Christian Fuchsberger, Jason Flannick, Manuel A. Rivas, Kyle J. Gaulton, Patrick K. Albers, Gil McVean, Michael Boehnke, David Altshuler, Mark I. McCarthy
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0169536

Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum
Cited by: 8
Author(s): Vladimir Gorshkov, Stanford Kwenda, Olga Petrova, Elena Osipova, Yuri Gogolev, Lucy N. Moleleki
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2021.680725

The RNA-Binding Proteins SRP14 and HMGB3 Control HIV-1 Tat mRNA Processing and Translation During HIV-1 Latency
Cited by: 5
Author(s): Georges Khoury, Michelle Y. Lee, Sri H. Ramarathinam, James McMahon, Anthony W. Purcell, Secondo Sonza, Sharon R Lewin, Damian F. J. Purcell
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.691847

Diverse ATPase Proteins in Mobilomes Constitute a Large Potential Sink for Prokaryotic Host ATP
Cited by: 9
Author(s): Hyunjin Shim, Haridha Shivram, Shufei Lei, Jennifer A. Doudna, Jillian F. Banfield
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22020532

Mapping the SARS-CoV-2–Host Protein–Protein Interactome by Affinity Purification Mass Spectrometry and Proximity-Dependent Biotin Labeling: A Rational and Straightforward Route to Discover Host-Directed Anti-SARS-CoV-2 Therapeutics
Cited by: 36
Author(s): Rosa Terracciano, Mariaimmacolata Preianò, Annalisa Fregola, Corrado Pelaia, Tiziana Montalcini, Rocco Savino
Software Mentions: 2
Published: almost 4 years ago

10.1101/2020.03.22.002386

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
Cited by: 210
Author(s): David E. Gordon, Gwendolyn Μ. Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Jeffrey Z. Guo, Danielle L. Swaney, Tia A. Tummino, Ruth Hüttenhain, Robyn M. Kaake, Alicia Richards, Beril Tutuncuoglu, Helene Foussard, Jyoti Batra, Kelsey M. Haas, Maya Modak, Minkyu Kim, Paige Haas, Benjamin J. Polacco, Hannes Braberg, Jacqueline M. Fabius, Manon Eckhardt, Margaret Soucheray, M. J. Bennett, Merve Çakır, Michael McGregor, Qiongyu Li, Zun Zar Chi Naing, Yuan Zhou, Shiming Peng, Ilsa T Kirby, James E. Melnyk, John S. Chorba, Kevin Lou, Shizhong Dai, Wenqi Shen, Ying Shi, Ziyang Zhang, Iñigo Barrio-Hernandez, Danish Memon, Claudia Hernández-Armenta, Christopher J.P. Mathy, Tina Perica, Kala Bharath Pilla, Sai J. Ganesan, Daniel J. Saltzberg, Rakesh Ramachandran, Xi Liu, Sara Brin Rosenthal, Lorenzo Calviello, Srivats Venkataramanan, José Liboy-Lugo, Yizhu Lin, Stephanie A. Wankowicz, Markus-Frederik Bohn, Phillip P. Sharp, Raphael Trenker, Janet M. Young, Devin A. Cavero, Joseph Hiatt, Theo Roth, Ujjwal Rathore, Advait Subramanian, Julia Noack, Mathieu Hubert, Ferdinand Roesch, Thomas Vallet, Björn Meyer, Kris M. White, Lisa Miorin, Oren S. Rosenberg, Kliment A. Verba, David A. Agard, Mélanie Ott, Michael Emerman, Davide Ruggero, Adolfo Garc iacute-Sastre, Natalia Jura, Mark von Zastrow, Jack Taunton, Alan Ashworth, Olivier Schwartz, Marco Vignuzzi, Shaeri Mukherjee, Matthew P. Jacobson, Harmit S. Malik, Danica Galonić Fujimori, Trey Ideker, Charles S. Craik, Stephen N. Floor, James S. Fraser, John D. Gross, Andrej Šali, Tanja Kortemme, Pedro Beltrão, Kevan M. Shokat, Brian K. Shoichet, Nevan J. Krogan
Software Mentions: 2
Published: almost 5 years ago

10.3389/fphys.2020.00081

Editorial: Integrated Omics for Defining Interactomes
Cited by: 0
Author(s): Sudipto Saha, Rob M. Ewing
Software Mentions: 2
Published: almost 5 years ago

10.3389/fphys.2019.00425

Experimental Analysis of Viral–Host Interactions
Cited by: 18
Author(s): Joseph Gillen, Aleksandra Nita‐Lazar
Software Mentions: 2
Published: over 5 years ago

10.15252/msb.20188792

Mass spectrometry‐based protein–protein interaction networks for the study of human diseases
Cited by: 80
Author(s): Alicia Richards, Manon Eckhardt, Nevan J. Krogan
Software Mentions: 2
Published: almost 4 years ago

10.3390/v9100275

Inference of a Geminivirus−Host Protein−Protein Interaction Network through Affinity Purification and Mass Spectrometry Analysis
Cited by: 24
Author(s): Liping Wang, Xue Ding, Jiajing Xiao, Tamara Jiménez-Gόngora, Renyi Liu, Rosa Lozano‐Durán
Software Mentions: 2
Published: over 7 years ago

10.3390/v12040472

RSV Reprograms the CDK9•BRD4 Chromatin Remodeling Complex to Couple Innate Inflammation to Airway Remodeling
Cited by: 17
Author(s): Allan R. Brasier
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0139355

Weighted Score Tests Implementing Model-Averaging Schemes in Detection of Rare Variants in Case-Control Studies
Cited by: 4
Author(s): Brandon J. Coombes, Saonli Basu, Sharmistha Guha, Nicholas J. Schork
Software Mentions: 2
Published: about 9 years ago

10.1186/s13059-017-1212-4

The impact of rare and low-frequency genetic variants in common disease
Cited by: 256
Author(s): Lorenzo Bomba, Klaudia Walter, Nicole Soranzo
Software Mentions: 2
Published: over 7 years ago

10.1155/2016/2891918

PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data
Cited by: 0
Author(s): Stefan Kalkhof, Stefan Schildbach, Conny Blumert, Friedemann Horn, Martin von Bergen, Dirk Labudde
Software Mentions: 1
Published: almost 9 years ago

10.1002/mbo3.112

Analysis of periplasmic sensor domains from <i>Anaeromyxobacter dehalogenans</i> 2CP-C: Structure of one sensor domain from a histidine kinase and another from a chemotaxis protein
Cited by: 7
Author(s): P.R. Pokkuluri, Jeff Dwulit-Smith, N.E.C. Duke, Rosemarie Wilton, J. Mack, J. Bearden, E. Rakowski, G. Babnigg, Hendrik Szurmant, A. Joachimiak, M. Schiffer
Software Mentions: 1
Published: over 11 years ago

10.1038/msb.2013.58

Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters
Cited by: 152
Author(s): Virgil A. Rhodius, Thomas H. Segall-Shapiro, Brian D. Sharon, Amar Ghodasara, Ekaterina Orlova, Hannah Tabakh, David H Burkhardt, Kevin Clancy, Todd C. Peterson, Carol A. Gross, Christopher A. Voigt
Software Mentions: 1
Published: almost 12 years ago

10.3390/pathogens10091155

Interactome Analysis of the Nucleocapsid Protein of SARS-CoV-2 Virus
Cited by: 19
Author(s): Xin Zheng, Zeyu Sun, Liang Yu, Danrong Shi, Miaojin Zhu, Hang‐Ping Yao, Lanjuan Li
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1008344

A region-based gene association study combined with a leave-one-out sensitivity analysis identifies SMG1 as a pancreatic cancer susceptibility gene
Cited by: 9
Author(s): Cavin Wong, Fei Chen, Najmeh Alirezaie, Yifan Wang, Adeline Cuggia, Ayelet Borgida, Spring Holter, Tatiana Lenko, Céline Domecq, Alzheimer’s Disease Neuroimaging Initiative, Gloria M. Petersen, Sapna Syngal, Randall E. Brand, Anil K. Rustgi, Michele L. Coté, Elena M. Stoffel, Sara H. Olson, Nicholas J. Roberts, Mohammad Reza Akbari, Jacek Majewski, Alison P. Klein, Celia Greenwood, Steven Gallinger, George Zogopoulos
Software Mentions: 1
Published: over 5 years ago

10.1128/mBio.00931-18

An Aspartate-Specific Solute-Binding Protein Regulates Protein Kinase G Activity To Control Glutamate Metabolism in Mycobacteria
Cited by: 28
Author(s): Nabanita Bhattacharyya, Irene Nkumama, Zaccheus Newland-Smith, Li‐Ying Lin, Weiguo Yin, Rebecca E. Cullen, Jack S. Griffiths, Alexander R. Jarvis, Mike Price, Pei Ying Chong, Russell Wallis, Helen M. O’Hare
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms22084167

Structural and Functional Remodeling of Mitochondria in Cardiac Diseases
Cited by: 19
Author(s): Xiaonan Sun, Jalen Alford, Hongyu Qiu
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0094088

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting
Cited by: 9
Author(s): Kaushik Bhattacharjee, S. R. Joshi
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0003878

Survival in Nuclear Waste, Extreme Resistance, and Potential Applications Gleaned from the Genome Sequence of Kineococcus radiotolerans SRS30216
Cited by: 58
Author(s): Christopher E. Bagwell, Swapna Bhat, Gary M. Hawkins, Bryan W. Smith, Tapan Biswas, Timothy R. Hoover, Elizabeth Saunders, Cliff Han, Oleg V. Tsodikov, Lawrence J. Shimkets
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-10-315

P2CS: a two-component system resource for prokaryotic signal transduction research
Cited by: 59
Author(s): Mohamed Barakat, Philippe Ortet, Cécile Jourlin-Castelli, Mireille Ansaldi, Vincent Méjean, David E. Whitworth
Software Mentions: 1
Published: almost 16 years ago

10.1155/2013/890123

SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species
Cited by: 19
Author(s): Marine Peralta, Marie‐Christine Combes, Alberto Cenci, Philippe Lebailly, Alexis Dereeper
Software Mentions: 1
Published: over 11 years ago

10.1186/s12918-017-0452-y

A two-step framework for inferring direct protein-protein interaction network from AP-MS data
Cited by: 8
Author(s): Bo Tian, Can Zhao, Feiyang Gu, Zengyou He
Software Mentions: 1
Published: over 7 years ago

10.3389/fcimb.2021.574067

Dengue Virus Non-Structural Protein 5 as a Versatile, Multi-Functional Effector in Host–Pathogen Interactions
Cited by: 14
Author(s): Priya Bhatnagar, Gopinathan Pillai Sreekanth, Kaja Murali‐Krishna, Anmol Chandele, Ramakrishnan Sitaraman
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2021.615165

The CD147 Protein Complex Is Involved in Entry of Chikungunya Virus and Related Alphaviruses in Human Cells
Cited by: 15
Author(s): Lien De Caluwé, Sandra Coppens, Katleen Vereecken, Simon Daled, Maarten Dhaenens, Xaveer Van Ostade, Dieter Deforce, Kevin K. Ariën, Koen Bartholomeeusen
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2148-11-34

Evolutionary history of the OmpR/IIIA family of signal transduction two component systems in Lactobacillaceae and Leuconostocaceae
Cited by: 10
Author(s): Manuel Zúñiga, Ciara Luna Gómez-Escoín, Fernando Gónzález-Candelas
Software Mentions: 1
Published: almost 14 years ago

10.21203/rs.3.rs-114758/v1

Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation.
Cited by: 20
Author(s): Kang-Lin Hsieh, Yinyin Wang, Luyao Chen, Zhongming Zhao, Sean I Savitz, Xiaoqian Jiang, Jing Tang, Yejin Kim
Software Mentions: 1
Published: about 4 years ago

10.1186/1742-4690-9-33

Proteomic analysis of HIV-1 Nef cellular binding partners reveals a role for exocyst complex proteins in mediating enhancement of intercellular nanotube formation
Cited by: 74
Author(s): Joya Mukerji, Kevin Olivieri, Vikas Misra, Kristin Agopian, Dana Gabuzda
Software Mentions: 1
Published: over 12 years ago

10.1186/s12866-018-1197-5

Disbiome database: linking the microbiome to disease
Cited by: 123
Author(s): Yorick Janssens, Joachim Nielandt, Antoon Bronselaer, Nathan Debunne, Evelien Wynendaele, Filip Van Immerseel, Yves-Paul Vandewynckel, Guy De Tré
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.19032

Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106
Cited by: 41
Author(s): Barbara Celona, John Von Dollen, Sarat C. Vatsavayai, Risa Kashima, Jeffrey R. Johnson, Y. Amy Tang, Akiko Hata, Bruce L. Miller, Eric J. Huang, Nevan J. Krogan, William W. Seeley, Brian L. Black
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-11-720

The genetic organisation of prokaryotic two-component system signalling pathways
Cited by: 41
Author(s): Robert H. Williams, David E. Whitworth
Software Mentions: 1
Published: about 14 years ago

10.1186/1756-0381-4-10

Using graph theory to analyze biological networks
Cited by: 516
Author(s): Georgios A. Pavlopoulos, Maria Secrier, Charalampos Moschopoulos, Theodoros Soldatos, Σοφία Κοσσίδα, Jan Aerts, Reinhard Schneider, Pantelis G. Bagos
Software Mentions: 1
Published: over 13 years ago