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  1. Circular RNAs (circRNAs) constitute a largely unexplored source for biomarker discovery in prostate cancer (PC). Here, we characterize the biomarker potential of circRNAs in PC, where the need for novel diagno...

    Authors: Emma Bollmann Hansen, Jacob Fredsøe, Trine Line Hauge Okholm, Benedicte Parm Ulhøi, Søren Klingenberg, Jørgen Bjerggaard Jensen, Jørgen Kjems, Kirsten Bouchelouche, Michael Borre, Christian Kroun Damgaard, Jakob Skou Pedersen, Lasse Sommer Kristensen and Karina Dalsgaard Sørensen
    Citation: Genome Medicine 2022 14:8
  2. Amyotrophic lateral sclerosis (ALS) is a complex, late-onset, neurodegenerative disease with a genetic contribution to disease liability. Genome-wide association studies (GWAS) have identified ten risk loci to...

    Authors: Restuadi Restuadi, Frederik J. Steyn, Edor Kabashi, Shyuan T. Ngo, Fei-Fei Cheng, Marta F. Nabais, Mike J. Thompson, Ting Qi, Yang Wu, Anjali K. Henders, Leanne Wallace, Chris R. Bye, Bradley J. Turner, Laura Ziser, Susan Mathers, Pamela A. McCombe…
    Citation: Genome Medicine 2022 14:7
  3. Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure ...

    Authors: Christine G. Preston, Matt W. Wright, Rao Madhavrao, Steven M. Harrison, Jennifer L. Goldstein, Xi Luo, Hannah Wand, Bryan Wulf, Gloria Cheung, Mark E. Mandell, Howard Tong, Shaung Cheng, Michael A. Iacocca, Arturo Lopez Pineda, Alice B. Popejoy, Karen Dalton…
    Citation: Genome Medicine 2022 14:6
  4. Lung adenocarcinoma, the most common type of lung cancer, has a high level of morphologic heterogeneity and is composed of tumor cells of multiple histological subtypes. It has been reported that immune cell i...

    Authors: Thinh T. Nguyen, Hyun-Sung Lee, Bryan M. Burt, Jia Wu, Jianjun Zhang, Christopher I. Amos and Chao Cheng
    Citation: Genome Medicine 2022 14:5
  5. Endometrial cancer (EC) is a major gynecological cancer with increasing incidence. It comprises four molecular subtypes with differing etiology, prognoses, and responses to chemotherapy. In the future, clinica...

    Authors: Vanessa F. Bonazzi, Olga Kondrashova, Deborah Smith, Katia Nones, Asmerom T. Sengal, Robert Ju, Leisl M. Packer, Lambros T. Koufariotis, Stephen H. Kazakoff, Aimee L. Davidson, Priya Ramarao-Milne, Vanessa Lakis, Felicity Newell, Rebecca Rogers, Claire Davies, James Nicklin…
    Citation: Genome Medicine 2022 14:3
  6. T and B cell receptor (TCR, BCR) repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Unde...

    Authors: Aviv Omer, Ayelet Peres, Oscar L Rodriguez, Corey T Watson, William Lees, Pazit Polak, Andrew M Collins and Gur Yaari
    Citation: Genome Medicine 2022 14:2
  7. A limited number of studies have characterized genomic properties of hepatocellular carcinoma (HCC) patients in response to anti-PD-1 immunotherapy.

    Authors: Jung Yong Hong, Hee Jin Cho, Jason K. Sa, Xiaoqiao Liu, Sang Yun Ha, Taehyang Lee, Hajung Kim, Wonseok Kang, Dong Hyun Sinn, Geum-Youn Gwak, Moon Seok Choi, Joon Hyeok Lee, Kwang Cheol Koh, Seung Woon Paik, Hee Chul Park, Tae Wook Kang…
    Citation: Genome Medicine 2022 14:1
  8. The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomp...

    Authors: Rebecca L. Walker, Hera Vlamakis, Jonathan Wei Jie Lee, Luke A. Besse, Vanessa Xanthakis, Ramachandran S. Vasan, Stanley Y. Shaw and Ramnik J. Xavier
    Citation: Genome Medicine 2021 13:188
  9. While understanding molecular heterogeneity across patients underpins precision oncology, there is increasing appreciation for taking intra-tumor heterogeneity into account. Based on large-scale analysis of ca...

    Authors: Chayaporn Suphavilai, Shumei Chia, Ankur Sharma, Lorna Tu, Rafael Peres Da Silva, Aanchal Mongia, Ramanuj DasGupta and Niranjan Nagarajan
    Citation: Genome Medicine 2021 13:189
  10. We present Beyondcell, a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments. Our method calcu...

    Authors: Coral Fustero-Torre, María José Jiménez-Santos, Santiago García-Martín, Carlos Carretero-Puche, Luis García-Jimeno, Vadym Ivanchuk, Tomás Di Domenico, Gonzalo Gómez-López and Fátima Al-Shahrour
    Citation: Genome Medicine 2021 13:187
  11. Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic varia...

    Authors: Caitlin T. Fierheller, Laure Guitton-Sert, Wejdan M. Alenezi, Timothée Revil, Kathleen K. Oros, Yuandi Gao, Karine Bedard, Suzanna L. Arcand, Corinne Serruya, Supriya Behl, Liliane Meunier, Hubert Fleury, Eleanor Fewings, Deepak N. Subramanian, Javad Nadaf, Jeffrey P. Bruce…
    Citation: Genome Medicine 2021 13:186
  12. Mutations in certain genes are known to increase breast cancer risk. We study the relevance of rare protein-truncating variants (PTVs) that may result in loss-of-function in breast cancer susceptibility genes ...

    Authors: Peh Joo Ho, Alexis J. Khng, Hui Wen Loh, Weang-Kee Ho, Cheng Har Yip, Nur Aishah Mohd-Taib, Veronique Kiak Mien Tan, Benita Kiat-Tee Tan, Su-Ming Tan, Ern Yu Tan, Swee Ho Lim, Suniza Jamaris, Yirong Sim, Fuh Yong Wong, Joanne Ngeow, Elaine Hsuen Lim…
    Citation: Genome Medicine 2021 13:185
  13. We discuss the current state of genomic medicine in Arab countries of the Middle East, a region with outsized contribution to Mendelian genetics due to inbreeding yet has poor representation in global variome ...

    Authors: Ahmad N. Abou Tayoun, Khalid A. Fakhro, Alawi Alsheikh-Ali and Fowzan S. Alkuraya
    Citation: Genome Medicine 2021 13:184
  14. N6-methyladenosine (m6A) is the most abundant modification of RNA in eukaryotic cells and play critical roles in cancer. While most related studies focus on m6A modifications in linear RNA, transcriptome-wide pro...

    Authors: Ying Ye, Weiyi Feng, Jialiang Zhang, Kaiyu Zhu, Xudong Huang, Ling Pan, Jiachun Su, Yanfen Zheng, Rui Li, Shuang Deng, Ruihong Bai, Lisha Zhuang, Lusheng Wei, Junge Deng, Mei Li, Rufu Chen…
    Citation: Genome Medicine 2021 13:183
  15. Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides add...

    Authors: Themoula Charalampous, Adela Alcolea-Medina, Luke B. Snell, Tom G. S. Williams, Rahul Batra, Christopher Alder, Andrea Telatin, Luigi Camporota, Christopher I. S. Meadows, Duncan Wyncoll, Nicholas A. Barrett, Carolyn J. Hemsley, Lisa Bryan, William Newsholme, Sara E. Boyd, Anna Green…
    Citation: Genome Medicine 2021 13:182
  16. Genetic studies have been tremendously successful in identifying genomic regions associated with a wide variety of phenotypes, although the success of these studies in identifying causal genes, their variants,...

    Authors: Jessy Carol Ntunzwenimana, Gabrielle Boucher, Jean Paquette, Hugues Gosselin, Azadeh Alikashani, Nicolas Morin, Claudine Beauchamp, Louise Thauvette, Marie-Ève Rivard, Frédérique Dupuis, Sonia Deschênes, Sylvain Foisy, Frédéric Latour, Geneviève Lavallée, Mark J. Daly, Ramnik J. Xavier…
    Citation: Genome Medicine 2021 13:181
  17. Cardiorespiratory fitness (CRF) and physical activity (PA) are well-established predictors of morbidity and all-cause mortality. However, CRF is not routinely measured and PA not routinely prescribed as part o...

    Authors: Ken B. Hanscombe, Elodie Persyn, Matthew Traylor, Kylie P. Glanville, Mark Hamer, Jonathan R. I. Coleman and Cathryn M. Lewis
    Citation: Genome Medicine 2021 13:180
  18. Targeted therapies in oncology are promising but variants of uncertain significance (VUS) limit their use for clinical management and necessitate functional testing in vitro. Using BRCA1 and BRCA2 variants, which...

    Authors: Amandine Billaud, Louise-Marie Chevalier, Paule Augereau, Jean-Sebastien Frenel, Christophe Passot, Mario Campone and Alain Morel
    Citation: Genome Medicine 2021 13:174
  19. Hundreds of thousands of cancer patients have had targeted (panel) tumor sequencing to identify clinically meaningful mutations. In addition to improving patient outcomes, this activity has led to significant ...

    Authors: Alexander Gusev, Stefan Groha, Kodi Taraszka, Yevgeniy R. Semenov and Noah Zaitlen
    Citation: Genome Medicine 2021 13:179
  20. Ensuring accordance with principles of healthcare ethics requires improved communication of pathogen genomic data. This could include educating healthcare professionals in communicating pathogen genomic inform...

    Authors: Angeline S Ferdinand, Jane S Hocking, Justin T. Denholm, Benjamin P. Howden and Deborah A. Williamson
    Citation: Genome Medicine 2021 13:178
  21. Cancer is a somatic evolutionary disease and adenocarcinomas of the stomach and gastroesophageal junction (GC) may serve as a two-dimensional model of cancer expansion, in which tumor subclones are not evenly ...

    Authors: Christoph Röcken, Anu Amallraja, Christine Halske, Luka Opasic, Arne Traulsen, Hans-Michael Behrens, Sandra Krüger, Anne Liu, Jochen Haag, Jan-Hendrik Egberts, Philip Rosenstiel and Tobias Meißner
    Citation: Genome Medicine 2021 13:177
  22. Vaginal microbiota (VMB) composition is altered in women with cervical intra-epithelial neoplasia (CIN) compared to healthy controls and is associated with disease progression. However, the impact of CIN excis...

    Authors: Anita Mitra, David A. MacIntyre, Maria Paraskevaidi, Anna-Barbara Moscicki, Vishakha Mahajan, Ann Smith, Yun S. Lee, Deirdre Lyons, Evangelos Paraskevaidis, Julian R. Marchesi, Phillip R. Bennett and Maria Kyrgiou
    Citation: Genome Medicine 2021 13:176
  23. The human leukocyte antigen class I (HLA-I) genotype has been linked with differential immune responses to infectious disease and cancer. However, the clinical relevance of germline HLA-mediated immunity in ga...

    Authors: Zhihao Lu, Huan Chen, Xi Jiao, Yujiao Wang, Lijia Wu, Huaibo Sun, Shuang Li, Jifang Gong, Jian Li, Jianling Zou, Keyan Yang, Ying Hu, Beibei Mao, Lei Zhang, Xiaotian Zhang, Zhi Peng…
    Citation: Genome Medicine 2021 13:175
  24. Mutational signatures are key to understanding the processes that shape cancer genomes, yet their analysis requires relatively rich whole-genome or whole-exome mutation data. Recently, orders-of-magnitude spar...

    Authors: Itay Sason, Yuexi Chen, Mark D.M. Leiserson and Roded Sharan
    Citation: Genome Medicine 2021 13:173
  25. Deletions and duplications of the multigenic 16p11.2 and 22q11.2 copy number variant (CNV) regions are associated with brain-related disorders including schizophrenia, intellectual disability, obesity, bipolar...

    Authors: Mikhail Vysotskiy, Xue Zhong, Tyne W. Miller-Fleming, Dan Zhou, Nancy J. Cox and Lauren A. Weiss
    Citation: Genome Medicine 2021 13:172
  26. Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen subdivided into lineages termed sequence types (STs). Since the 1950s, successive waves of STs have appeared and replaced previous...

    Authors: Hongbin Chen, Yuyao Yin, Lucy van Dorp, Liam P. Shaw, Hua Gao, Mislav Acman, Jizhen Yuan, Fengning Chen, Shijun Sun, Xiaojuan Wang, Shuguang Li, Yawei Zhang, Rhys A. Farrer, Hui Wang and Francois Balloux
    Citation: Genome Medicine 2021 13:171
  27. Metastatic breast cancer is a deadly disease with a low 5-year survival rate. Tracking metastatic spread in living patients is difficult and thus poorly understood.

    Authors: Xiaomeng Huang, Yi Qiao, Samuel W. Brady, Rachel E. Factor, Erinn Downs-Kelly, Andrew Farrell, Jasmine A. McQuerry, Gajendra Shrestha, David Jenkins, W. Evan Johnson, Adam L. Cohen, Andrea H. Bild and Gabor T. Marth
    Citation: Genome Medicine 2021 13:170
  28. Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Cor...

    Authors: Carmen Lía Murall, Eric Fournier, Jose Hector Galvez, Arnaud N’Guessan, Sarah J. Reiling, Pierre-Olivier Quirion, Sana Naderi, Anne-Marie Roy, Shu-Huang Chen, Paul Stretenowich, Mathieu Bourgey, David Bujold, Romain Gregoire, Pierre Lepage, Janick St-Cyr, Patrick Willet…
    Citation: Genome Medicine 2021 13:169
  29. In spite of many years of research, our understanding of the molecular bases of Alzheimer’s disease (AD) is still incomplete, and the medical treatments available mainly target the disease symptoms and are har...

    Authors: Eduardo Pauls, Sergi Bayod, Lídia Mateo, Víctor Alcalde, Teresa Juan-Blanco, Marta Sánchez-Soto, Takaomi C. Saido, Takashi Saito, Antoni Berrenguer-Llergo, Camille Stephan-Otto Attolini, Marina Gay, Eliandre de Oliveira, Miquel Duran-Frigola and Patrick Aloy
    Citation: Genome Medicine 2021 13:168
  30. Non-coding regulatory elements (NCREs), such as enhancers, play a crucial role in gene regulation, and genetic aberrations in NCREs can lead to human disease, including brain disorders. The human brain is a co...

    Authors: Soheil Yousefi, Ruizhi Deng, Kristina Lanko, Eva Medico Salsench, Anita Nikoncuk, Herma C. van der Linde, Elena Perenthaler, Tjakko J. van Ham, Eskeatnaf Mulugeta and Tahsin Stefan Barakat
    Citation: Genome Medicine 2021 13:162
  31. Advances in cancer biology are increasingly dependent on integration of heterogeneous datasets. Large-scale efforts have systematically mapped many aspects of cancer cell biology; however, it remains challengi...

    Authors: Christopher Yogodzinski, Abolfazl Arab, Justin R. Pritchard, Hani Goodarzi and Luke A. Gilbert
    Citation: Genome Medicine 2021 13:167
  32. Liver cancer is one of the most commonly diagnosed cancers and the fourth leading cause of cancer-related death worldwide. Broad-spectrum kinase inhibitors like sorafenib and lenvatinib provide only modest sur...

    Authors: Yuchen Guo, Jun Wang, Bente Benedict, Chen Yang, Frank van Gemert, Xuhui Ma, Dongmei Gao, Hui Wang, Shu Zhang, Cor Lieftink, Roderick L. Beijersbergen, Hein te Riele, Xiaohang Qiao, Qiang Gao, Chong Sun, Wenxin Qin…
    Citation: Genome Medicine 2021 13:166
  33. Recent studies have suggested that individual variants do not sufficiently explain the variable expressivity of phenotypes observed in complex disorders. For example, the 16p12.1 deletion is associated with de...

    Authors: Matthew Jensen, Anastasia Tyryshkina, Lucilla Pizzo, Corrine Smolen, Maitreya Das, Emily Huber, Arjun Krishnan and Santhosh Girirajan
    Citation: Genome Medicine 2021 13:163
  34. PTEN is a multi-functional tumor suppressor protein regulating cell growth, immune signaling, neuronal function, and genome stability. Experimental characterization can help guide the clinical interpretation o...

    Authors: Kenneth A. Matreyek, Jason J. Stephany, Ethan Ahler and Douglas M. Fowler
    Citation: Genome Medicine 2021 13:165
  35. The receptor-binding domain (RBD) variants of SARS-CoV-2 could impair antibody-mediated neutralization of the virus by host immunity; thus, prospective surveillance of antibody escape mutants and understanding...

    Authors: Chunyan Yi, Xiaoyu Sun, Yixiao Lin, Chenjian Gu, Longfei Ding, Xiao Lu, Zhuo Yang, Yaguang Zhang, Liyan Ma, Wangpeng Gu, Aidong Qu, Xu Zhou, Xiuling Li, Jianqing Xu, Zhiyang Ling, Youhua Xie…
    Citation: Genome Medicine 2021 13:164
  36. Clinical interpretation of genetic variants in the context of the patient’s phenotype is becoming the largest component of cost and time expenditure for genome-based diagnosis of rare genetic diseases. Artific...

    Authors: Francisco M. De La Vega, Shimul Chowdhury, Barry Moore, Erwin Frise, Jeanette McCarthy, Edgar Javier Hernandez, Terence Wong, Kiely James, Lucia Guidugli, Pankaj B. Agrawal, Casie A. Genetti, Catherine A. Brownstein, Alan H. Beggs, Britt-Sabina Löscher, Andre Franke, Braden Boone…
    Citation: Genome Medicine 2021 13:153
  37. Molecular autopsy refers to DNA-based identification of the cause of death. Despite recent attempts to broaden its scope, the term remains typically reserved to sudden unexplained death in young adults. In thi...

    Authors: Hanan E. Shamseldin, Lama AlAbdi, Sateesh Maddirevula, Hessa S. Alsaif, Fatema Alzahrani, Nour Ewida, Mais Hashem, Firdous Abdulwahab, Omar Abuyousef, Hiroyuki Kuwahara, Xin Gao and Fowzan S. Alkuraya
    Citation: Genome Medicine 2021 13:161
  38. Immune checkpoint blockade (ICB) shows lasting benefits in advanced melanoma; however, not all patients respond to this treatment and many develop potentially life-threatening immune-related adverse events (ir...

    Authors: Mykhaylo Usyk, Abhishek Pandey, Richard B. Hayes, Una Moran, Anna Pavlick, Iman Osman, Jeffrey S. Weber and Jiyoung Ahn
    Citation: Genome Medicine 2021 13:160
  39. Tumor mutational burden (TMB) may be a predictive biomarker of immune checkpoint inhibitor (ICI) responsiveness. Genomic landscape heterogeneity is a well-established cancer feature. Molecular characteristics ...

    Authors: Timothy V. Pham, Aaron M. Goodman, Smruthy Sivakumar, Garrett Frampton and Razelle Kurzrock
    Citation: Genome Medicine 2021 13:159
  40. Enhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity...

    Authors: Taotao Sheng, Shamaine Wei Ting Ho, Wen Fong Ooi, Chang Xu, Manjie Xing, Nisha Padmanabhan, Kie Kyon Huang, Lijia Ma, Mohana Ray, Yu Amanda Guo, Ngak Leng Sim, Chukwuemeka George Anene-Nzelu, Mei Mei Chang, Milad Razavi-Mohseni, Michael A. Beer, Roger Sik Yin Foo…
    Citation: Genome Medicine 2021 13:158
  41. Genome-wide association studies (GWASs) have identified thousands of variants associated with asthma and other complex diseases. However, the functional effects of most of these variants are unknown. Moreover,...

    Authors: Marcus M. Soliai, Atsushi Kato, Britney A. Helling, Catherine T. Stanhope, James E. Norton, Katherine A. Naughton, Aiko I. Klinger, Emma E. Thompson, Selene M. Clay, Soyeon Kim, Juan C. Celedón, James E. Gern, Daniel J. Jackson, Matthew C. Altman, Robert C. Kern, Bruce K. Tan…
    Citation: Genome Medicine 2021 13:157
  42. A complex set of perturbations occur in cytokines and hormones in the etiopathogenesis of obesity and related cardiometabolic conditions such as type 2 diabetes (T2D). Evidence for the genetic regulation of th...

    Authors: Karlijn A. C. Meeks, Amy R. Bentley, Mateus H. Gouveia, Guanjie Chen, Jie Zhou, Lin Lei, Adebowale A. Adeyemo, Ayo P. Doumatey and Charles N. Rotimi
    Citation: Genome Medicine 2021 13:156
  43. Malignancies are molecularly complex and become more resistant with each line of therapy. We hypothesized that offering matched, individualized combination therapies to patients with treatment-naïve, advanced ...

    Authors: Jason K. Sicklick, Shumei Kato, Ryosuke Okamura, Hitendra Patel, Mina Nikanjam, Paul T. Fanta, Michael E. Hahn, Pradip De, Casey Williams, Jessica Guido, Benjamin M. Solomon, Rana R. McKay, Amy Krie, Sarah G. Boles, Jeffrey S. Ross, J. Jack Lee…
    Citation: Genome Medicine 2021 13:155
  44. Authors: Bing Yao, Tao Gui, Xiangwei Zeng, Yexuan Deng, Zhi Wang, Ying Wang, Dongjun Yang, Qixiang Li, Peipei Xu, Ruifeng Hu, Xinyu Li, Bing Chen, Jin Wang, Ke Zen, Haitao Li, Melissa J. Davis…
    Citation: Genome Medicine 2021 13:154

    The original article was published in Genome Medicine 2021 13:58

  45. Deep learning is a subdiscipline of artificial intelligence that uses a machine learning technique called artificial neural networks to extract patterns and make predictions from large data sets. The increasin...

    Authors: Khoa A. Tran, Olga Kondrashova, Andrew Bradley, Elizabeth D. Williams, John V. Pearson and Nicola Waddell
    Citation: Genome Medicine 2021 13:152
  46. Rapid advances in the past decade have shown that dysbiosis of the gut microbiome is a key hallmark of rheumatoid arthritis (RA). Yet, the relationship between the gut microbiome and clinical improvement in RA...

    Authors: Vinod K. Gupta, Kevin Y. Cunningham, Benjamin Hur, Utpal Bakshi, Harvey Huang, Kenneth J. Warrington, Veena Taneja, Elena Myasoedova, John M. Davis III and Jaeyun Sung
    Citation: Genome Medicine 2021 13:149
  47. Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently ...

    Authors: Aline Cuénod, Daniel Wüthrich, Helena M. B. Seth-Smith, Chantal Ott, Christian Gehringer, Frédéric Foucault, Roxanne Mouchet, Ali Kassim, Gunturu Revathi, Deborah R. Vogt, Stefanie von Felten, Stefano Bassetti, Sarah Tschudin-Sutter, Timm Hettich, Götz Schlotterbeck, Christina Homberger…
    Citation: Genome Medicine 2021 13:150

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