Ecosyste.ms: Papers

10.1186/1471-2105-12-S13-S22

Non-nucleosidic inhibition of Herpes simplex virus DNA polymerase: mechanistic insights into the anti-herpetic mode of action of herbal drug withaferin A
Cited by: 45
Author(s): Abhinav Grover, Vibhuti Agrawal, Ashutosh Shandilya, Virendra S. Bisaria, Durai Sundar
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-10-S1-S41

Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses
Cited by: 40
Author(s): Jhang Wei Huang, Chwan-Chuen King, Jinn-Moon Yang
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-10-32

VASCo: computation and visualization of annotated protein surface contacts
Cited by: 70
Author(s): Georg Steinkellner, Robert Rader, Gerhard G. Thallinger, Christoph Kratky, Karl Gruber
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12859-018-2317-9

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures
Cited by: 11
Author(s): Maciej Antczak, Tomasz Żok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak, Marta Szachniuk
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-12-S13-S23

In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC)
Cited by: 26
Author(s): Usman Sumo Friend Tambunan, N. Bramantya, Arli Aditya Parikesit
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-11-306

Beyond rotamers: a generative, probabilistic model of side chains in proteins
Cited by: 45
Author(s): Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E. Johansson, Thomas Hamelryck
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-016-1371-4

SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides
Cited by: 11
Author(s): Tamara Vasylenko, Yi Fan Liou, Po Chin Chiou, Hsiao Wei Chu, Yung Sung Lai, Yu Ling Chou, Hui Ling Huang, Shinn-Ying Ho
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-014-0370-6

PyTMs: a useful PyMOL plugin for modeling common post-translational modifications
Cited by: 77
Author(s): Andreas Warnecke, Tatyana Sandalova, Adnane Achour, Robert A. Harris
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12859-016-1033-6

Evolutionary relationships between heme-binding ferredoxin α + β barrels
Cited by: 8
Author(s): Giriraj Acharya, Gurmeet Kaur, S. Subramanian
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-016-1124-4

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server
Cited by: 18
Author(s): Luciano A. Abriata, Christophe Bovigny, Matteo Dal Peraro
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-015-0724-8

Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method
Cited by: 16
Author(s): Andrés H. Gutiérrez, William Martin, Chris Bailey‐Kellogg, Frances Terry, Leonard Moise, Anne S. De Groot
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-6-202

PALSSE: A program to delineate linear secondary structural elements from protein structures
Cited by: 59
Author(s): Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin
Software Mentions: 1
Published: over 19 years ago

10.1186/1741-7007-10-62

Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx
Cited by: 80
Author(s): Sonja Wilke, J. Krausze, Konrad Büssow
Software Mentions: 1
Published: over 12 years ago

10.1186/s12915-020-00885-2

Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes
Cited by: 4
Author(s): Ryan T. Bell, Yuri I. Wolf, Eugene V. Koonin
Software Mentions: 1
Published: about 4 years ago

10.1186/s12915-020-00936-8

Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity
Cited by: 28
Author(s): Kristýna Pluháčková, Andreas Hörner
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12915-016-0313-y

Oligomeric interface modulation causes misregulation of purine 5´-nucleotidase in relapsed leukemia
Cited by: 9
Author(s): Aleš Hnı́zda, Jana Škerlová, Milan Fábry, Petr Pachl, Martina Šinalová, Lukáš Vrzal, Petr Man, Petr Novák, P. Řezáčová, Václav Veverka
Software Mentions: 1
Published: about 8 years ago

10.1186/s12915-017-0464-5

Outer membrane protein folding from an energy landscape perspective
Cited by: 55
Author(s): Bob Schiffrin, David J. Brockwell, Sheena E. Radford
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12915-020-00920-2

Crystal structure of the yeast heterodimeric ADAT2/3 deaminase
Cited by: 15
Author(s): Xiwen Liu, Ruoyu Chen, Yujie Sun, Ran Chen, Jie Zhou, Qingnan Tian, Xiaoma Tao, Zhang Zhang, Guan‐Zheng Luo, Wei Xie
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12915-020-00896-z

Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda
Cited by: 10
Author(s): Liang Xu, Jian Yang, Meng Xu, Dai Shan, Zhongdao Wu, Dongjuan Yuan
Software Mentions: 1
Published: almost 4 years ago

10.1186/1741-7007-8-134

The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain
Cited by: 48
Author(s): Robert O. J. Weinzierl
Software Mentions: 1
Published: about 14 years ago

10.1186/1741-7007-8-70

Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family
Cited by: 124
Author(s): Daniel H. Haft, Malay Kumar Basu, Douglas A. Mitchell
Software Mentions: 1
Published: over 14 years ago

10.1186/s12915-017-0446-7

A yeast two-hybrid system for the screening and characterization of small-molecule inhibitors of protein–protein interactions identifies a novel putative Mdm2-binding site in p53
Cited by: 28
Author(s): Jin Huei Wong, Mohammad Alfatah, Mei Fang Sin, Hong May Sim, Chandra Verma, David P. Lane, Prakash Arumugam
Software Mentions: 1
Published: about 7 years ago

10.1186/1741-7007-9-7

The activation mechanism of Irga6, an interferon-inducible GTPase contributing to mouse resistance against Toxoplasma gondii
Cited by: 28
Author(s): Nikolaus Pawlowski, Aliaksandr Khaminets, Julia P. Hunn, Natasa Papic, Andreas Schmidt, Revathy C. Uthaiah, Rita Lange, Gabriela Vopper, Sascha Martens, Eva Wolf, Jonathan C. Howard
Software Mentions: 1
Published: almost 14 years ago

10.1186/2046-1682-5-13

A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors
Cited by: 7
Author(s): Subhodeep Moitra, Kalyan Tirupula, Judith Klein‐Seetharaman, Christopher J. Langmead
Software Mentions: 1
Published: over 12 years ago

10.1186/2046-1682-5-2

Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations
Cited by: 23
Author(s): Haina Qin, Liangzhong Lim, Jianxing Song
Software Mentions: 1
Published: almost 13 years ago

10.1186/1472-6750-13-71

Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiaeidentifies mutants with improved heterologous exocellulase activity and host secretion
Cited by: 31
Author(s): Tzi‐Yuan Wang, Chih-Jen Huang, Hsin‐Liang Chen, Po-Chun Ho, Huei-Mien Ke, Hsing-Yi Cho, Sz-Kai Ruan, Kuo-Yen Hung, I-Li Wang, Ya-Wun Cai, Huang‐Mo Sung, Wen-Hsiung Li, Ming-Che Shih
Software Mentions: 1
Published: about 11 years ago

10.1186/s12896-015-0217-x

Defining the complementarities between antibodies and haptens to refine our understanding and aid the prediction of a successful binding interaction
Cited by: 13
Author(s): Mohammed M. Al Qaraghuli, Soumya Palliyil, Gillian Broadbent, David C. Cullen, Keith A. Charlton, A.J. Porter
Software Mentions: 1
Published: about 9 years ago

10.1186/s12896-018-0420-7

Effects of substrate binding site residue substitutions of xynA from Bacillus amyloliquefaciens on substrate specificity
Cited by: 10
Author(s): Anil S. Prajapati, V A Pawar, Ketankumar Panchal, Ankit P. Sudhir, Bhaumik R. Dave, Darshan H. Patel, R. B. Subramanian
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12896-019-0520-z

Surface patches on recombinant erythropoietin predict protein solubility: engineering proteins to minimise aggregation
Cited by: 7
Author(s): Manuel Alejandro Carballo-Amador, Edward A. McKenzie, Alan J. Dickson, Jim Warwicker
Software Mentions: 1
Published: over 5 years ago

10.1186/s12896-015-0214-0

A novel eurythermic and thermostale lipase LipM from Pseudomonas moraviensis M9 and its application in the partial hydrolysis of algal oil
Cited by: 22
Author(s): Wuyi Yang, Cao Hai, Li Xu, Houjin Zhang, Yunjun Yan
Software Mentions: 1
Published: about 9 years ago

10.1186/s12896-017-0389-7

Conversion of an inactive xylose isomerase into a functional enzyme by co-expression of GroEL-GroES chaperonins in Saccharomyces cerevisiae
Cited by: 22
Author(s): Beatriz Temer, Leandro Vieira dos Santos, Victor Augusti Negri, Juliana Pimentel Galhardo, Pedro Henrique Mello Magalhães, Juliana José, Cidnei Marschalk, Thamy Lívia Ribeiro Corrêa, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira
Software Mentions: 1
Published: about 7 years ago

10.1186/s12896-019-0542-6

Improved the expression level of active transglutaminase by directional increasing copy of mtg gene in Pichia pastoris
Cited by: 6
Author(s): Xiaoping Song, Changsheng Shao, Yugang Guo, Yajie Wang, Jingjing Cai
Software Mentions: 1
Published: over 5 years ago

10.1186/s12896-021-00701-x

Optimization of expression, purification and secretion of functional recombinant human growth hormone in Escherichia coli using modified staphylococcal protein a signal peptide
Cited by: 7
Author(s): Garshasb Rigi, Amin Rostami, Habib Ghomi, Gholamreza Ahmadian, V.S. Mirbagheri, Meisam Jeiranikhameneh, Majid Vahed, Sahel Rahimi
Software Mentions: 1
Published: over 3 years ago

10.1186/s12896-016-0310-9

Improvement of alkalophilicity of an alkaline xylanase Xyn11A-LC from Bacillus sp. SN5 by random mutation and Glu135 saturation mutagenesis
Cited by: 19
Author(s): Wenqin Bai, Yufan Cao, Jun Liu, Qinhong Wang, Zhenhu Jia
Software Mentions: 1
Published: about 8 years ago

10.1186/s12896-019-0553-3

Structure-based engineering of heparinase I with improved specific activity for degrading heparin
Cited by: 5
Author(s): Chuan Zhang, Baocheng Yang, Wenting Liu, Zhongyuan Li, Yajian Song, Tongcun Zhang, Xue‐Gang Luo
Software Mentions: 1
Published: over 5 years ago

10.1186/s12896-017-0396-8

Production and purification of chimeric HBc virus-like particles carrying influenza virus LAH domain as vaccine candidates
Cited by: 22
Author(s): Andris Kazāks, I-Na Lu, Sophie Farinelle, Alex Ramirez, Vincenzo Crescente, Benjamin A. F. Bláha, Olotu W. Ogonah, Tarit Mukhopadhyay, Mapi Perez de Obanos, Alejandro Krimer, Ināra Akopjana, Jānis Bogans, Velta Ose, Anna Kirsteina, Tatjana Kazaka, Nicola J. Stonehouse, David J. Rowlands, Claude P. Muller, Kaspars Tārs, William Rosenberg
Software Mentions: 1
Published: about 7 years ago

10.1186/s12885-016-2108-5

Aberrant KDM5B expression promotes aggressive breast cancer through MALAT1 overexpression and downregulation of hsa-miR-448
Cited by: 100
Author(s): Oluwaseun Adebayo Bamodu, Wen Chien Huang, Wei Hwa Lee, Alexander T.H. Wu, Liang Shun Wang, Michael Hsiao, Chi‐Tai Yeh, Tsu Yi Chao
Software Mentions: 1
Published: over 8 years ago

10.1186/s12885-019-6013-6

Parkin gene mutations are not common, but its epigenetic inactivation is a frequent event and predicts poor survival in advanced breast cancer patients
Cited by: 13
Author(s): Khushnuma Wahabi, Ahmad Perwez, Shabeena Kamarudheen, Zafar Iqbal Bhat, Anurag Mehta, M. Moshahid Alam Rizvi
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-019-6477-4

Bag-1 stimulates Bad phosphorylation through activation of Akt and Raf kinases to mediate cell survival in breast cancer
Cited by: 18
Author(s): Tugba Kizilboga, Emine Arzu Baskale, Jale Yıldız, İzzet Mehmet Akçay, Ebru Zemheri, Nisan Denizce Can, C. Ozden, Salih Demir, Fikret Ezbercı, Gizem Dinler Doğanay
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12885-018-5142-7

KRas4B-PDE6δ complex stabilization by small molecules obtained by virtual screening affects Ras signaling in pancreatic cancer
Cited by: 18
Author(s): Diana Casique‐Aguirre, Paola Briseño-Díaz, Ponciano García-Gutiérrez, Claudia H. González-De la Rosa, Reyna Sara Quintero-Barceinas, Arturo Rojo-Domı́nguez, Irene Vergara, L. Medina, José Correa‐Basurto, Martiniano Bello, Rosaura Hernández‐Rivas, María del RocioThompson-Bonilla, Miguel Vargas
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12885-019-5532-5

Protein interaction disruption in cancer
Cited by: 8
Author(s): Matthew Ruffalo, Ziv Bar‐Joseph
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-021-08174-z

Robust expression of LINE-1 retrotransposon encoded proteins in oral squamous cell carcinoma
Cited by: 2
Author(s): Koel Mukherjee, Debpali Sur, Abhijeet Singh, Suresh Rai, Neeladrisingha Das, Rakshanya Sekar, Srinu Narindi, Vandana Dhingra, Bhanwar Lal Jat, K V Vinu Balraam, Saurabh Agarwal, Prabhat Kumar Mandal
Software Mentions: 1
Published: over 3 years ago

10.1186/s12885-018-4704-z

Natural product derivative Gossypolone inhibits Musashi family of RNA-binding proteins
Cited by: 35
Author(s): Lan Lan, Hao Líu, Amber Rae Smith, Carl Appelman, Yu Jiao, Sarah Line Larsen, Rebecca T. Marquez, Xiaoqing Wu, Frank Y. Liu, Philip Gao, Ragul Gowthaman, John Karanicolas, Roberto N. De Guzman, Steven A. Rogers, Jeffrey Aubé, Kristi L. Neufeld, Liang Xu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12885-019-6056-8

Generation of dual specific bivalent BiTEs (dbBIspecific T-cell engaging antibodies) for cellular immunotherapy
Cited by: 7
Author(s): Maciej Kujawski, Lin Li, Supriyo Bhattacharya, Patty Wong, Wen‐Hwa Lee, Lindsay Williams, Harry Li, Junie Chea, Kofi Poku, Nicole Bowles, Nagarajan Vaidehi, Paul J. Yazaki, John E. Shively
Software Mentions: 1
Published: about 5 years ago

10.1186/s12885-019-5845-4

A germline mutation in Rab43 gene identified from a cancer family predisposes to a hereditary liver-colon cancer syndrome
Cited by: 4
Author(s): Yanting Jiang, Yue Sun, Jianbo Hu, Nan Yu, Hui Liu, Jiankun Fan, Xuelian Ning, Yilan Li, Baogang Liu, Yihua Sun, Jinwei Zhang, Xiaohong Qiu, Songbin Fu, Chunlan Zhou, Hui Xu
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2121-14-27

Arginine68 is an essential residue for the C-terminal cleavage of human Atg8 family proteins
Cited by: 16
Author(s): Chao Liu, Hongshen Ma, Jiaxue Wu, Qiang Huang, Jun O. Liu, Yu Liu
Software Mentions: 1
Published: over 11 years ago

10.1186/s13065-021-00758-x

Antibacterial and antioxidant activities of extracts and isolated compounds from the roots extract of Cucumis prophetarum and in silico study on DNA gyrase and human peroxiredoxin 5
Cited by: 8
Author(s): Wario Galma, Milkyas Endale, Emebet Getaneh, Rajalakshmanan Eswaramoorthy, Temesgen Assefa, Yadessa Melaku
Software Mentions: 1
Published: over 3 years ago

10.1186/s13065-021-00766-x

Molecular docking, chemo-informatic properties, alpha-amylase, and lipase inhibition studies of benzodioxol derivatives
Cited by: 12
Author(s): Mohammed Hawash, Nidal Jaradat, Suhaib Shekfeh, Murad Abualhasan, Ahmad Eid, Linda Issa
Software Mentions: 1
Published: over 3 years ago

10.1186/s13065-019-0582-y

Molecular docking and simulation of Zika virus NS3 helicase
Cited by: 15
Author(s): Syed Lal Badshah, Nasir Ahmad, Ashfaq Ur Rehman, Khalid Khan, Asad Ullah, Abdulrhman Alsayari, Abdullatif Bin Muhsinah, Yahia N. Mabkhot
Software Mentions: 1
Published: over 5 years ago

10.1186/s13065-019-0532-8

Design, synthesis and evaluation of novel 3,5-disubstituted benzamide derivatives as allosteric glucokinase activators
Cited by: 14
Author(s): Ajmer Singh Grewal, Rajeev Kharb, Devendra Prasad, Jagdeep Singh Dua, Viney Lather
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12906-018-2312-8

Efficacy of Andrographis paniculata against extended spectrum β-lactamase (ESBL) producing E. coli
Cited by: 28
Author(s): Ubaid Rasool, Shivam Priya, Afsana Parveen, Saroj Kumar Sah, S. Hemalatha
Software Mentions: 1
Published: about 6 years ago

10.1186/1472-6882-14-89

Role of berberine in anti-bacterial as a high-affinity LPS antagonist binding to TLR4/MD-2 receptor
Cited by: 67
Author(s): Ming Chu, Ran Ding, Zhi‐gang Chu, Mingbo Zhang, Xiaoyan Liu, Shao-Hua Xie, Yuanzheng Zhai, Yuedan Wang
Software Mentions: 1
Published: over 10 years ago

10.1186/1472-6823-14-16

A case of Aromatase deficiency due to a novel CYP19A1 mutation
Cited by: 35
Author(s): Lucia Gagliardi, Hamish S. Scott, Feng Jiang, David J. Torpy
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12862-019-1461-9

Insights into body size variation in cetaceans from the evolution of body-size-related genes
Cited by: 10
Author(s): Yingying Sun, Yanzhi Liu, Xiaohui Sun, Yurui Lin, Daiqing Yin, Shixia Xu, Guang Yang
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2148-10-365

Chlorophyll-binding proteins revisited - a multigenic family of light-harvesting and stress proteins from a brown algal perspective
Cited by: 91
Author(s): Simon M. Dittami, Gurvan Michel, Jonas Collén, Catherine Boyen, Thierry Tonon
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12862-015-0490-2

Divergence and adaptive evolution of the gibberellin oxidase genes in plants
Cited by: 41
Author(s): Yuan Huang, Xi Wang, Song Ge, Guang‐Yuan Rao
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2148-12-4

Evolution, expansion and expression of the Kunitz/BPTI gene family associated with long-term blood feeding in Ixodes Scapularis
Cited by: 54
Author(s): Shao‐Xing Dai, Ai-Di Zhang, Jing‐Fei Huang
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2148-11-149

Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution
Cited by: 62
Author(s): Yinhua Huang, Nicholas D. Temperley, Liming Ren, Jacqueline Smith, Ning Li, David W. Burt
Software Mentions: 1
Published: over 13 years ago

10.1186/s12862-015-0337-x

Phylogeny and evolution of plant macrophage migration inhibitory factor/D-dopachrome tautomerase-like proteins
Cited by: 30
Author(s): Ralph Panstruga, Kira Baumgarten, Jürgen Bernhagen
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2148-11-273

The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold
Cited by: 7
Author(s): Francisco Fernández, Fernando Garcés, Miguel López-Estepa, Juan Aguilar, Laura Baldomà, Miquel Coll, Josefa Badı́a, M. Cristina Vega
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2148-12-66

Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures
Cited by: 30
Author(s): Michael L. Hayes, Karolyn Giang, R. Michael Mulligan
Software Mentions: 1
Published: over 12 years ago

10.1186/s12862-016-0823-9

Structural differences and differential expression among rhabdomeric opsins reveal functional change after gene duplication in the bay scallop, Argopecten irradians (Pectinidae)
Cited by: 8
Author(s): Anita J. Porath-Krause, Autum N. Pairett, Davide Faggionato, Bhagyashree S. Birla, Kalyanasundaram Sankar, Jeanne M. Serb
Software Mentions: 1
Published: about 8 years ago

10.1186/s12862-020-01712-6

Directional divergence of Ep300 duplicates in teleosts and its implications
Cited by: 1
Author(s): Xianzong Wang, Junli Yan
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2148-10-207

Evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins
Cited by: 27
Author(s): Jun Okada, Takahiro Okamoto, Atsushi Mukaiyama, Takashi Tadokoro, Dong-Ju You, Hyongi Chon, Yuichi Koga, Kazufumi Takano, Shigenori Kanaya
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2148-12-214

Adaptive evolution of the chrysanthemyl diphosphate synthase gene involved in irregular monoterpene metabolism
Cited by: 22
Author(s): Pingli Liu, Jun‐Nan Wan, Yanping Guo, Song Ge, Guang‐Yuan Rao
Software Mentions: 1
Published: about 12 years ago

10.1186/s12862-015-0506-y

Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes
Cited by: 2
Author(s): Laurent Bianchetti, Yara Tarabay, Odile Lecompte, Roland H. Stote, Olivier Poch, Annick Dejaegere, Stéphane Viville
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2148-8-290

Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components
Cited by: 93
Author(s): Gemma C. Atkinson, Sandra L. Baldauf, Vasili Hauryliuk
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2148-11-321

Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa
Cited by: 84
Author(s): Eric Talevich, Asra Mirza, Natarajan Kannan
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2148-11-225

Lafora disease E3-ubiquitin ligase malin is related to TRIM32 at both the phylogenetic and functional level
Cited by: 23
Author(s): Carlos Romá-Mateo, Daniel Antunes Moreno, Santiago Vérnia, Teresa Rubio, Travis M. Bridges, Matthew S. Gentry, Pascual Sanz
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2148-13-215

Positive selection in glycolysis among Australasian stick insects
Cited by: 22
Author(s): Luke T. Dunning, Alice B. Dennis, Geoffrey Thomson, Brent J. Sinclair, Richard D. Newcomb, Thomas R. Buckley
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12862-017-0909-z

Conservation of estrogen receptor function in invertebrate reproduction
Cited by: 25
Author(s): Brande L. Jones, Chris Walker, Bahareh Azizi, Laren M. Tolbert, Loren Dean Williams, Terry W. Snell
Software Mentions: 1
Published: over 7 years ago

10.1186/s12862-019-1543-8

Human-specific mutations in VMAT1 confer functional changes and multi-directional evolution in the regulation of monoamine circuits
Cited by: 4
Author(s): Daiki X. Sato, Yuu Ishii, Tomoaki Nagai, Kazumasa Ohashi, Masakado Kawata
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2148-13-96

Origin, evolution and classification of type-3 copper proteins: lineage-specific gene expansions and losses across the Metazoa
Cited by: 63
Author(s): Felipe Aguilera, Carmel McDougall, Bernard M. Degnan
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2148-11-198

The evolutionary history of the catenin gene family during metazoan evolution
Cited by: 42
Author(s): Zi-Ming Zhao, Albert B. Reynolds, Eric A. Gaucher
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-017-4420-0

A chelicerate-specific burst of nonclassical Dscam diversity
Cited by: 11
Author(s): Guang Cao, Yang Shi, Jian Zhang, Hongru Ma, Shouqing Hou, Haiyang Dong, Weiling Hong, Shawn Chen, Hao Li, Yandan Wu, Pengjuan Guo, Xu Shao, Bingbing Xu, Feng Shi, Yijun Meng, Yongfeng Jin
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-020-6454-y

Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis
Cited by: 11
Author(s): Chunmiao Shan, Chenkai Wang, Shengxiang Zhang, Yuanyuan Shi, Kelong Ma, Qingshan Yang, Jiawen Wu
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2164-12-S3-S22

A comparative structural bioinformatics analysis of inherited mutations in β-D-Mannosidase across multiple species reveals a genotype-phenotype correlation
Cited by: 13
Author(s): Thi Dan Xuan Huynh, Javed Khan, Shoba Ranganathan
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-15-604

The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles
Cited by: 30
Author(s): Blake T. Hovde, Shawn R. Starkenburg, Heather M. Hunsperger, Laina D. Mercer, Chloe R. Deodato, Ramesh K. Jha, Olga Chertkov, Raymond J. Monnat, Rose Ann Cattolico
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-020-6604-2

The structure, functional evolution, and evolutionary trajectories of the H+-PPase gene family in plants
Cited by: 5
Author(s): Yiming Zhang, Xue Feng, Lihui Wang, Yanping Su, Zhuodong Chu, Yanfang Sun
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-019-5593-5

Genome-wide identification and characterization of abiotic-stress responsive SOD (superoxide dismutase) gene family in Brassica juncea and B. rapa
Cited by: 84
Author(s): Deepika Verma, Neha Lakhanpal, Kashmir Singh
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-9-293

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins
Cited by: 42
Author(s): Phillip Hahn, Jens Böse, S. K. Edler, Andreas Lengeling
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-13-605

The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses
Cited by: 37
Author(s): Mathieu Larroque, Roland Barriot, Arnaud Bottin, Annick Barre, Pierre Rougé, Bernard Dumas, Elodie Gaulin
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-12-75

Comparative genomics allowed the identification of drug targets against human fungal pathogens
Cited by: 89
Author(s): Ana Karina Rodrigues Abadio, Érika Seki Kioshima, Marcus de Melo Teixeira, N. F. Martins, Bernard Maigret, Maria Sueli Soares Felipe
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-6-41

Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family
Cited by: 20
Author(s): Einari A. Niskanen, Vesa P. Hytönen, Alessandro Grapputo, Henri R. Nordlund, Markku S. Kulomaa, Olli H. Laitinen
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2164-11-S4-S2

Predicting RNA-binding residues from evolutionary information and sequence conservation
Cited by: 14
Author(s): Yu‐Feng Huang, Li-Yuan Chiu, Chun-Chin Huang, Chien-Kang Huang
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12864-020-6705-y

Transcriptome of Sphaerospora molnari (Cnidaria, Myxosporea) blood stages provides proteolytic arsenal as potential therapeutic targets against sphaerosporosis in common carp
Cited by: 13
Author(s): Ashlie Hartigan, Anush Kosakyan, Hana Pecková, Edit Eszterbauer, Astrid S. Holzer
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-017-3833-0

Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis
Cited by: 42
Author(s): Philippe Florian, Jérôme Pelloux, Catherine Rayon
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-12-505

Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis
Cited by: 52
Author(s): Kasper Thorsen, Troels Schepeler, Bodil Øster, Mads Heilskov Rasmussen, Søren Vang, Kai Wang, Kristian Q. Hansen, Philippe Lamy, Jakob Skou Pedersen, Asger Eller, Francisco Mansilla, Kirsti Laurila, Carsten Wiuf, Søren Laurberg, Lars Dyrskjøt, Torben F. Ørntoft, Claus Lindbjerg Andersen
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-10-510

Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family
Cited by: 24
Author(s): Marco Vedovato, Valeria Rossi, Joel B. Dacks, F. Filippini
Software Mentions: 1
Published: about 15 years ago

10.1186/s12864-018-4432-4

The genome of a prasinoviruses-related freshwater virus reveals unusual diversity of phycodnaviruses
Cited by: 9
Author(s): Hao Chen, Weijia Zhang, Xiefei Li, Yingjie Pan, Shuling Yan, Yongjie Wang
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2172-10-13

Identification of conformational epitopes for human IgG on Chemotaxis inhibitory protein of Staphylococcus aureus
Cited by: 17
Author(s): Erika Gustafsson, Pieter Jan Haas, Björn Walse, Marcel Hijnen, Christina Furebring, Mats Ohlin, Jos A. G. van Strijp, Kok P. M. van Kessel
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12879-020-05612-4

Molecular epidemiology of SARS-CoV-2 clusters caused by asymptomatic cases in Anhui Province, China
Cited by: 7
Author(s): Yuan Yuan, Jun He, Lei Gong, Weiwei Li, Liangliang Jiang, Jiang Liu, Qingqing Chen, Jianing Yu, Sai Hou, Yuanli Shi, Si-Qi Lu, Zhuhui Zhang, Yinglu Ge, Nan Sa, Lan He, Jiabing Wu, Yong Sun, Zhongfan Liu
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2334-13-173

Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count
Cited by: 9
Author(s): Maria Clara Bizinoto, Shiori Yabe, Élcio Leal, Hirohisa Kishino, Leonardo de Oliveira Martins, Mariana Leão de Lima, Edsel Renata Morais, Ricardo Sobhie Diaz, Luiz Mário Janini
Software Mentions: 1
Published: over 11 years ago

10.1186/s12881-019-0827-6

Case reports: novel TUBG1 mutations with milder neurodevelopmental presentations
Cited by: 9
Author(s): Yue T. K. Yuen, Ilaria Guella, Elke H. Roland, Michael A. Sargent, Cyrus Boelman
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2350-10-51

Mild forms of hypophosphatasia mostly result from dominant negative effect of severe alleles or from compound heterozygosity for severe and moderate alleles
Cited by: 113
Author(s): Delphine Fauvert, Isabelle Brun-Heath, Anne-Sophie Lia-Baldini, Linda Bellazi, A. Taillandier, Jean‐Louis Serre, Philippe de Mazancourt, Étienne Mornet
Software Mentions: 1
Published: over 15 years ago

10.1186/s12881-018-0540-x

Compound heterozygous variants in the multiple PDZ domain protein (MPDZ) cause a case of mild non-progressive communicating hydrocephalus
Cited by: 9
Author(s): Nesreen K. Al-Jezawi, Aisha M. Al‐Shamsi, Jehan Suleiman, Salma Ben-Salem, Anne John, Ranjit Vijayan, Bassam R. Ali, Lihadh Al‐Gazali
Software Mentions: 1
Published: over 6 years ago

10.1186/s12881-019-0933-5

Novel mutations identified in Chinese families with autosomal dominant congenital cataracts by targeted next-generation sequencing
Cited by: 10
Author(s): Shan Li, Jianfei Zhang, Yixuan Cao, Yi You, Xiuli Zhao
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12881-019-0875-y

Whole exome sequencing reveals two novel compound heterozygous mutations in TWNK as a cause of the hepatocerebral form of mitochondrial DNA depletion syndrome: a case report
Cited by: 2
Author(s): Xianghong Li, Liangshan Li, Yaqi Sun, Fuyan Lv, Guoqing Zhang, Wenmiao Liu, Meiyan Zhang, Hong Jiang, Shiguo Liu
Software Mentions: 1
Published: about 5 years ago

10.1186/s12881-015-0240-8

Germline activating MTOR mutation arising through gonadal mosaicism in two brothers with megalencephaly and neurodevelopmental abnormalities
Cited by: 23
Author(s): Cameron Mroske, Kristen Rasmussen, Deepali N. Shinde, Robert Huether, Zöe Powis, Hsiao‐Mei Lu, Ruth Baxter, Elizabeth McPherson, Sha Tang
Software Mentions: 1
Published: about 9 years ago

10.1186/s12881-020-01040-y

A novel COMP mutation in a Chinese family with multiple epiphyseal dysplasia
Cited by: 2
Author(s): Jiashen Shao, Sen Zhao, Zihui Yan, Lianlei Wang, Yuanqiang Zhang, Mao Lin, Chenxi Yu, Shengru Wang, Yuchen Niu, Xiaoxin Li, Guixing Qiu, Jianguo Zhang, Zhihong Wu, Nan Wu
Software Mentions: 1
Published: over 4 years ago