pypi: VESPA | Projects | Ecosyste.ms: Papers

10.1093/molbev/msaa057

Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera)
Cited by: 30
Author(s): Elizabeth J. Duncan, Megan Leask, Peter K. Dearden
Software Mentions: 8
Published: over 4 years ago

10.1002/ece3.7959

BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection
Cited by: 2
Author(s): Giobbe Forni, Angelo Ruggieri, Giovanni Piccinini, Andrea Luchetti
Software Mentions: 6
Published: about 3 years ago

10.1186/s12859-016-1204-5

LMAP: Lightweight Multigene Analyses in PAML
Cited by: 12
Author(s): Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 6
Published: about 8 years ago

10.1128/mBio.01496-21

The Interspecific Fungal Hybrid <i>Verticillium longisporum</i> Displays Subgenome-Specific Gene Expression
Cited by: 6
Author(s): Jasper R L Depotter, Fabian van Beveren, Luis Rodríguez‐Moreno, Holger Kramer, Edgar A. Chavarro Carrero, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Thomas A. Wood, Bart P.H.J. Thomma, Michael Seidl
Software Mentions: 5
Published: about 3 years ago

10.1093/molbev/msz099

Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)
Cited by: 72
Author(s): Marc Tollis, Jooke Robbins, Andrew E. Webb, Lukas F. K. Kuderna, Aleah F. Caulin, Jacinda D Garcia, Martine Bérubé, Nader Pourmand, Tomàs Marquès-Bonet, Mary J. O’Connell, Per Palsbøll, Carlo C. Maley
Software Mentions: 5
Published: over 5 years ago

10.1093/molbev/msz063

Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana
Cited by: 16
Author(s): Reetu Tuteja, Peter C. McKeown, Paraic C. Ryan, Claire C. Morgan, Mark T.A. Donoghue, Tim Downing, Mary J. O’Connell, Charles Spillane
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-3800-9

A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M
Cited by: 12
Author(s): Xiaodong Zai, Qiaoling Yang, Kun Liu, Ruihua Li, Mengying Qian, Taoran Zhao, Yaohui Li, Ying Yin, Dayong Dong, Ling Fu, Shanhu Li, Junjie Xu, Wei Chen
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-13-131

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data
Cited by: 31
Author(s): Elena S. Peterson, Lee Ann McCue, Alexandra C. Schrimpe‐Rutledge, Jeffrey L. Jensen, Hyunjoo Walker, Markus A. Kobold, Samantha R Webb, Samuel H. Payne, Charles Ansong, Joshua N. Adkins, W. Roger Cannon, Bobbie-Jo M. Webb-Robertson
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0181680

Probing the compartmentalization of HIV-1 in the central nervous system through its neutralization properties
Cited by: 18
Author(s): Karl Stéfic, Antoine Chaillon, Mélanie Bouvin-Pley, Alain Moreau, Martine Braibant, Frédéric Bastides, Guillaume Gras, Louis Bernard, Françis Barin
Software Mentions: 4
Published: about 7 years ago

10.1186/s12977-014-0065-0

Single genome analysis reveals genetic characteristics of Neuroadaptation across HIV-1 envelope
Cited by: 19
Author(s): Teresa H. Evering, Edwin Kamau, Leslie St. Bernard, Charles B Farmer, Xiang‐Peng Kong, Martin Markowitz
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0080589

Phylogenetic Relatedness of Circulating HIV-1C Variants in Mochudi, Botswana
Cited by: 31
Author(s): Vladimir Novitsky, Hermann Bussmann, Andrew Logan, Sikhulile Moyo, Erik van Widenfelt, Lillian Okui, Mompati Mmalane, Jeannie Baca, Linda B. Buck, Eleanor Phillips, David Todem, Mary Fran McLane, Quanhong Lei, Rui Wang, Joseph Makhema, Shahin Lockman, Victor DeGruttola, Max Essex
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0010213

Restriction of HIV-1 Genotypes in Breast Milk Does Not Account for the Population Transmission Genetic Bottleneck That Occurs following Transmission
Cited by: 40
Author(s): Laura Heath, Susan R. Conway, Laura M. Jones, Katherine Semrau, Kyle J. Nakamura, Jan Walter, W. Don Decker, Jason Hong, Thomas Chen, Marintha Heil, Moses Sinkala, Chipepo Kankasa, Donald M. Thea, Louise Kuhn, James I. Mullins, Grace M. Aldrovandi
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0006949

Evidence for Limited Genetic Compartmentalization of HIV-1 between Lung and Blood
Cited by: 35
Author(s): Laura Heath, Alan Fox, Jan McClure, Kurt Diem, Angélique B. van ’t Wout, Hong Zhao, David R. Park, Jeffrey T. Schouten, Homer L. Twigg, Lawrence Corey, James I. Mullins, John E. Mittler
Software Mentions: 3
Published: about 15 years ago

10.1186/1742-4690-7-92

HIV-1 subtype C envelope characteristics associated with divergent rates of chronic disease progression
Cited by: 18
Author(s): Derseree Archary, Michelle Gordon, Taryn N. Green, Hoosen M. Coovadia, Philip Goulder, Thumbi Ndung’u
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pntd.0006139

New insights into Trypanosoma cruzi evolution, genotyping and molecular diagnostics from satellite DNA sequence analysis
Cited by: 23
Author(s): Juan Carlos Ramı́rez, Carolina Torres, Maria de Los Angeles Curto, Alejandro G. Schijman
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0037853

Phylogeography and Molecular Evolution of Potato virus Y
Cited by: 51
Author(s): José M. Cuevas, Agnès Delaunay, Johan Christiaan Visser, Baoheng Du, Emmanuel Jacquot, Santiago F. Elena
Software Mentions: 2
Published: over 12 years ago

10.1007/s00213-016-4477-5

Brain glutamate in anorexia nervosa: a magnetic resonance spectroscopy case control study at 7 Tesla
Cited by: 23
Author(s): Beata R. Godlewska, Alexandra C. Pike, A L Sharpley, Agnes Ayton, Rebecca J. Park, Philip J. Cowen, Uzay E. Emir
Software Mentions: 2
Published: almost 8 years ago

10.3390/polym13091440

Dynamics & Spectroscopy with Neutrons—Recent Developments & Emerging Opportunities
Cited by: 7
Author(s): Kacper Drużbicki, Mattia Gaboardi, Fernando Bresme
Software Mentions: 2
Published: over 3 years ago

10.1007/s10334-018-0716-6

Short-acquisition-time JPRESS and its application to paediatric brain tumours
Cited by: 2
Author(s): Dominic Carlin, Ben Babourina‐Brooks, Theodoros N. Arvanitis, Martin Wilson, Andrew Peet
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-017-05448-0

DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species
Cited by: 8
Author(s): Adil Salhi, Sónia Negrão, Magbubah Essack, Mitchell J. L. Morton, Salim Bougouffa, Rozaimi Mohamad Razali, Aleksandar Radovanović, Benoı̂t Marchand, Maxat Kulmanov, Robert Hoehndorf, Mark Tester, Vladimir B. Bajic
Software Mentions: 2
Published: about 7 years ago

10.1186/1743-422X-7-130

Prediction of prognostic biomarkers for Interferon-based therapy to Hepatitis C Virus patients: a metaanalysis of the NS5A protein in subtypes 1a, 1b, and 3a
Cited by: 24
Author(s): Mahmoud ElHefnawi, Suher Zada, Iman A. El-Azab
Software Mentions: 2
Published: over 14 years ago

10.3389/fmicb.2020.615721

Non-synonymous Substitutions in HIV-1 GAG Are Frequent in Epitopes Outside the Functionally Conserved Regions and Associated With Subtype Differences
Cited by: 2
Author(s): Babatunde A. Olusola, David O. Olaleye, Georgina N. Odaibo
Software Mentions: 2
Published: over 3 years ago

10.1186/s13014-018-1125-8

A remote EPID-based dosimetric TPS-planned audit of centers for clinical trials: outcomes and analysis of contributing factors
Cited by: 5
Author(s): Narges Miri, Kimberley Legge, Kim Colyvas, Jöerg Lehmann, P Vial, Alisha Moore, Monica Harris, Peter B. Greer
Software Mentions: 1
Published: about 6 years ago

10.1038/tp.2016.239

Elevated brain lactate in schizophrenia: a 7 T magnetic resonance spectroscopy study
Cited by: 94
Author(s): Laura M. Rowland, Subechhya Pradhan, Stephanie A. Korenic, S. Andrea Wijtenburg, L. Elliot Hong, Richard A.E. Edden, Peter B. Barker
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41398-021-01477-6

Brain glutamate concentration in men with early psychosis: a magnetic resonance spectroscopy case–control study at 7 T
Cited by: 16
Author(s): Beata R. Godlewska, Amedeo Minichino, Uzay E. Emir, Ilinca Angelescu, Belinda Lennox, Masa Micunovic, Oliver Howes, Philip J. Cowen
Software Mentions: 1
Published: over 3 years ago

10.7448/IAS.19.1.20095

Sexual risk behaviour among people living with HIV according to the biomedical risk of transmission: results from the ANRS-VESPA2 survey
Cited by: 13
Author(s): Marie Suzan‐Monti, Nicolas Lorente, Baptiste Démoulin, Fabienne Marcellin, Marie Préau, Rosemary Dray‐Spira, Bruno Spire
Software Mentions: 1
Published: over 8 years ago

10.1002/jia2.25024

Gp41 and Gag amino acids linked to HIV-1 protease inhibitor-based second-line failure in HIV-1 subtype A from Western Kenya
Cited by: 10
Author(s): Mia Coetzer, Lauren Ledingham, Lameck Diero, Emmanuel Kemboi, Millicent Orido, Rami Kantor
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms18071444

Lack of Association between Hepatitis C Virus core Gene Variation 70/91aa and Insulin Resistance
Cited by: 2
Author(s): Letícia de Paula Scalioni, Allan Peres da Silva, Juliana Custódio Miguel, Márcia Paschoal do Espírito Santo, Vanessa Alves Marques, Carlos Eduardo Brandão‐Mello, Cristiane Alves Villela-Nogueira, Lia Laura Lewis-Ximenez, Elisabeth Lampe, Lívia Melo Villar
Software Mentions: 1
Published: about 7 years ago

10.1107/S1600577517006907

Very efficient spin polarization analysis (VESPA): new exchange scattering-based setup for spin-resolved ARPES at APE-NFFA beamline at Elettra
Cited by: 45
Author(s): Chiara Bigi, Pranab K. Das, D. Benedetti, Federico Salvador, Damjan Krizmancic, R. Sergo, A. Martin, G. Panaccione, G. Rossi, Jun Fujii, I. Vobornik
Software Mentions: 1
Published: over 7 years ago

10.1128/JVI.00250-17

Feline Immunodeficiency Virus Evolutionarily Acquires Two Proteins, Vif and Protease, Capable of Antagonizing Feline APOBEC3
Cited by: 19
Author(s): Rokusuke Yoshikawa, Junko Takeuchi, Eri Yamada, Yoshiaki Nakano, Naoko Misawa, Yuichi Kimura, Fengrong Ren, Takayuki Miyazawa, Yoshio Koyanagi, Kei Sato
Software Mentions: 1
Published: over 7 years ago

10.1186/s12913-020-05524-8

Implementing a community model of early pregnancy care
Cited by: 4
Author(s): Rebecca Cox, Somia Khalid, Gemma Brierly, Annie Forsyth, Ruth McNamara, Victoria Heppell, Ingrid Granne
Software Mentions: 1
Published: about 4 years ago

10.1186/1746-6148-8-8

Study of compartmentalization in the visna clinical form of small ruminant lentivirus infection in sheep
Cited by: 28
Author(s): Hugo Ramírez, Ramsés Reina, Luigi Bertolotti, Amaia Cenoz, M.M. Hernández, Beatriz San Román, Idoia Glaria, X. de Andrés, Helena Crespo, Paula Jáuregui, Julio Benavides, L. Polledo, Valentín Pérez Pérez, J.F. García-Marín, Sergio Rosati, B. Amorena, D. de Andrés
Software Mentions: 1
Published: over 12 years ago

10.1186/1743-422X-4-79

Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
Cited by: 11
Author(s): Gonzalo Moratorio, Mariela Martínez, María Lucía Lahoz Gutiérrez, Katiuska González, Rodney Colina, Luis Fernando López Tort, Lilia López, Ricardo Recarey, Alejandro G. Schijman, Pilar Moreno, Laura García-Aguirre, Aura R Manascero, Juan Cristina
Software Mentions: 1
Published: about 17 years ago

10.1186/1743-422X-5-14

HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments
Cited by: 15
Author(s): Yung Shwen Ho, Ana Abecasis, Kristof Theys, Koen Deforche, Dominic E. Dwyer, Michael A. Charleston, Anne‐Mieke Vandamme, Nitin K. Saksena
Software Mentions: 1
Published: over 16 years ago

10.1186/1743-422X-6-148

A HIV-1 heterosexual transmission chain in Guangzhou, China: a molecular epidemiological study
Cited by: 10
Author(s): Zhigang Han, Tommy W.C. Leung, Jinkou Zhao, Ming Wang, Fan Liu, Kai Li, Xin-Li Pang, Liang Zhen-bo, Wilina Lim, Huifang Xu
Software Mentions: 1
Published: almost 15 years ago

10.7717/peerj.4234

FUSTr: a tool to find gene families under selection in transcriptomes
Cited by: 10
Author(s): T. Jeffrey Cole, Michael S. Brewer
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0014132

Baseline Prediction of Combination Therapy Outcome in Hepatitis C Virus 1b Infected Patients by Discriminant Analysis Using Viral and Host Factors
Cited by: 28
Author(s): Verónica Saludes, María Alma Bracho, Oliver Valero, Mercé Ardévol, Ramón Planas, Fernando González‐Candelas, V. Ausina, Elisa Martró
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0146084

Delayed P100-Like Latencies in Multiple Sclerosis: A Preliminary Investigation Using Visual Evoked Spread Spectrum Analysis
Cited by: 10
Author(s): Hanni Kiiski, Sinéad Ní Riada, Edmund C. Lalor, Nuno Reis Goncalves, Hugh Nolan, Robert Whelan, Róisín Lonergan, Siobhán Kelly, Marie O’Brien, Katie Kinsella, Jessica Bramham, Teresa Burke, Seán Ó Donnchadha, Michael Hutchinson, Niall Tubridy, Richard B. Reilly
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0174920

Silent dissemination of HTLV-1 in an endemic area of Argentina. Epidemiological and molecular evidence of intrafamilial transmission
Cited by: 13
Author(s): María Celia Frutos, René Gastaldello, Marcos Balangero, Carlos Remondegui, Sebastián Blanco, Koko Otsuki, Ana Carolina Paulo Vicente, David Ernesto, Arnaldo Mangeaud, Silvia Nates, Sandra Gallego
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0109771

Covariance of Charged Amino Acids at Positions 322 and 440 of HIV-1 Env Contributes to Coreceptor Specificity of Subtype B Viruses, and Can Be Used to Improve the Performance of V3 Sequence-Based Coreceptor Usage Prediction Algorithms
Cited by: 12
Author(s): Kieran Cashin, Jasminka Sterjovski, Katherine Harvey, Paul A. Ramsland, Melissa Churchill, Paul R Gorry
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0179035

Occult hepatitis B virus infection in HIV positive patients at a tertiary healthcare unit in eastern India
Cited by: 15
Author(s): Debraj Saha, Ananya Pal, Neelakshi Sarkar, Dipanwita Das, Jason T. Blackard, Subhasish Kamal Guha, Bibhuti Saha, Runu Chakravarty
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0160990

Creatine, Glutamine plus Glutamate, and Macromolecules Are Decreased in the Central White Matter of Premature Neonates around Term
Cited by: 19
Author(s): Mériam Koob, Angèle Viola, Yann Le Fur, Patrick Viout, H. Ratiney, Sylviane Confort‐Gouny, Patrick J. Cozzone, Nadine Girard
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0000411

Discrimination against HIV-Infected People and the Spread of HIV: Some Evidence from France
Cited by: 51
Author(s): Patrick Peretti‐Watel, Bruno Spire, Yolande Obadia, Jean‐Paul Moatti
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0093426

Alterations in HIV-1 gp120 V3 Region Are Necessary but Not Sufficient for Coreceptor Switching in CRF07_BC in China
Cited by: 4
Author(s): Lei Zhang, Liying Ma, Zheng Wang, Yan Wang, Jing Zhang, Haining Wang, Yiming Shao
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0019995

Significantly Longer Envelope V2 Loops Are Characteristic of Heterosexually Transmitted Subtype B HIV-1 in Trinidad
Cited by: 12
Author(s): Aneisha M. Collins-Fairclough, Manhattan Charurat, Yuka Nadai, María A. Pando, María Mercedes Ávila, William A. Blattner, Jean K. Carr
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0003058

Genetic Variability of Hepatitis C Virus before and after Combined Therapy of Interferon plus Ribavirin
Cited by: 17
Author(s): José M. Cuevas, Manuela Torres-Puente, Nuria Jiménez‐Hernández, María Alma Bracho, Inmaculada García-Robles, Boris Wrobel, Fernando Carnicer, Juan del Olmo, Enrique Ortega, Andrés Moya, Fernando González‐Candelas
Software Mentions: 1
Published: about 16 years ago

10.3332/ecancer.2020.1105

Definition and assessment of frailty in older patients: the surgical, anaesthesiological and oncological perspective
Cited by: 3
Author(s): Lorenzo Dottorini, Luca Turati, Luca Mattei, Paolo Formenti
Software Mentions: 1
Published: about 4 years ago

10.1017/S2045796020000396

Poor implementation of the EU clinical trial regulation is a major threat for pragmatic trials in European countries
Cited by: 4
Author(s): Giovanni Ostuzzi, Chiara Gastaldon, Carlo Petrini, Brian Godman, Corrado Barbui
Software Mentions: 1
Published: over 4 years ago

10.1111/j.1460-9568.2007.05968.x

Isolating endogenous visuo-spatial attentional effects using the novel visual-evoked spread spectrum analysis (VESPA) technique
Cited by: 26
Author(s): Edmund C. Lalor, Simon P. Kelly, Barak A. Pearlmutter, Richard B. Reilly, John J. Foxe
Software Mentions: 1
Published: almost 17 years ago

10.3389/fpsyt.2021.656459

Metabolite Alterations in Adults With Schizophrenia, First Degree Relatives, and Healthy Controls: A Multi-Region 7T MRS Study
Cited by: 14
Author(s): S. Andrea Wijtenburg, Min Wang, Stephanie A. Korenic, Shuo Chen, Peter B. Barker, Laura M. Rowland
Software Mentions: 1
Published: over 3 years ago

10.1002/acm2.12521

Remote dosimetric auditing of clinical trials: The need for vendor specific models to convert images to dose
Cited by: 0
Author(s): Narges Miri, P Vial, Peter Greer
Software Mentions: 1
Published: over 5 years ago

Projects: pypi: VESPA

Papers Mentioning VESPA 51