Institution
La Trobe University
Education•Melbourne, Victoria, Australia•
About: La Trobe University is a education organization based out in Melbourne, Victoria, Australia. It is known for research contribution in the topics: Population & Health care. The organization has 13370 authors who have published 41291 publications receiving 1138269 citations. The organization is also known as: LaTrobe University & LTU.
Papers published on a yearly basis
Papers
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TL;DR: A new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite), is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler.
Abstract: The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler. By combining assembly, split read, and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line, and patient tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods while matching or exceeding their sensitivity. GRIDSS identifies nontemplate sequence insertions, microhomologies, and large imperfect homologies, estimates a quality score for each breakpoint, stratifies calls into high or low confidence, and supports multisample analysis.
214 citations
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TL;DR: What the authors now know about filamentous bacteria inactivated sludge wastewater treatment plants and their identity, ecophysiology and ecological niches and its practical value in better managing activated sludge processes are discussed.
Abstract: Excessive growth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) can cause serious operational problems. With some filaments there may be the problem of bulking, where inadequate flocculation and settling of the biomass in the secondary clarifier results in a carryover of solids with the final treated liquid effluent. Their proliferation often encourages the development of stable foams on the surface of the reactors, and these foams may impact negatively on plant performance and operation. The availability of culture-independent molecular methods now allows us to identify many of the more common filamentous organisms encountered in WWTPs, which are phylogenetically diverse, affiliating to seven separate bacterial phyla. Furthermore, the extensive data published in the past decade on their in situ behaviour from the application of these culture-independent methods have not been summarized or reviewed critically. Hence, here, we attempt to discuss what we now know about their identity, ecophysiology and ecological niches and its practical value in better managing activated sludge processes. Some of this knowledge is already being applied to control and manage full-scale WWTPs better, and the hope is that this review will contribute towards further developments in this field of environmental microbiology.
214 citations
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TL;DR: The predictive model developed can be used to identify people who are likely to have recurrent falls in the 6 months after stroke rehabilitation, with sensitivity and specificity values greater than 80%.
214 citations
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TL;DR: The CBT treatment was associated with significant and sustained improvements in psychological functioning but did not improve fluency; however, the CBT package made no difference to the speech outcomes of those with social phobia.
Abstract: Purpose The aims of the present study were to (a) examine the rate of social phobia among adults who stutter, (b) study the effects of speech restructuring treatment on social anxiety, and (c) stud...
214 citations
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TL;DR: It is concluded that long-term N inputs decreased microbial P-solubilizing and mineralizing capacity while P inputs favored microbial immobilization via altering the microbial functional profiles, providing a novel insight into the regulation of P cycling in sustainable agroecosystems from a microbial perspective.
Abstract: Microorganisms play an important role in soil phosphorus (P) cycling and regulation of P availability in agroecosystems. However, the responses of the functional and ecological traits of P-transformation microorganisms to long-term nutrient inputs are largely unknown. This study used metagenomics to investigate changes in the relative abundance of microbial P-transformation genes at four long-term experimental sites that received various inputs of N and P nutrients (up to 39 years). Long-term P input increased microbial P immobilization by decreasing the relative abundance of the P-starvation response gene (phoR) and increasing that of the low-affinity inorganic phosphate transporter gene (pit). This contrasts with previous findings that low-P conditions facilitate P immobilization in culturable microorganisms in short-term studies. In comparison, long-term nitrogen (N) input significantly decreased soil pH, and consequently decreased the relative abundances of total microbial P-solubilizing genes and the abundances of Actinobacteria, Gammaproteobacteria, and Alphaproteobacteria containing genes coding for alkaline phosphatase, and weakened the connection of relevant key genes. This challenges the concept that microbial P-solubilization capacity is mainly regulated by N:P stoichiometry. It is concluded that long-term N inputs decreased microbial P-solubilizing and mineralizing capacity while P inputs favored microbial immobilization via altering the microbial functional profiles, providing a novel insight into the regulation of P cycling in sustainable agroecosystems from a microbial perspective.
213 citations
Authors
Showing all 13601 results
Name | H-index | Papers | Citations |
---|---|---|---|
Rasmus Nielsen | 135 | 556 | 84898 |
C. N. R. Rao | 133 | 1646 | 86718 |
James Whelan | 128 | 786 | 89180 |
Jacqueline Batley | 119 | 1212 | 68752 |
Eske Willerslev | 115 | 367 | 43039 |
Jonathan E. Shaw | 114 | 629 | 108114 |
Ary A. Hoffmann | 113 | 907 | 55354 |
Mike Clarke | 113 | 1037 | 164328 |
Richard J. Simpson | 113 | 850 | 59378 |
Alan F. Cowman | 111 | 379 | 38240 |
David C. Page | 110 | 509 | 44119 |
Richard Gray | 109 | 808 | 78580 |
David S. Wishart | 108 | 523 | 76652 |
Alan G. Marshall | 107 | 1060 | 46904 |
David A. Williams | 106 | 633 | 42058 |