Sequence assembly demystified
N Nagarajan, M Pop - Nature Reviews Genetics, 2013 - nature.com
Advances in sequencing technologies and increased access to sequencing services have
led to renewed interest in sequence and genome assembly. Concurrently, new applications …
led to renewed interest in sequence and genome assembly. Concurrently, new applications …
[HTML][HTML] Metagenomics-enabled microbial surveillance
KKK Ko, KR Chng, N Nagarajan - Nature Microbiology, 2022 - nature.com
Lessons learnt from the COVID-19 pandemic include increased awareness of the potential
for zoonoses and emerging infectious diseases that can adversely affect human health. …
for zoonoses and emerging infectious diseases that can adversely affect human health. …
Shared decision making and choice for elective surgical care: a systematic review
… Of the 24 studies evaluated in this review, the majority (n = 17) focused their measured
outcomes on the effectiveness of a decision aid without directly assessing doctor-patient …
outcomes on the effectiveness of a decision aid without directly assessing doctor-patient …
[PDF][PDF] Comprehensive characterization of cancer driver genes and mutations
…, EM Liu, L Mularoni, C Rubio-Perez, N Nagarajan… - Cell, 2018 - cell.com
Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced
algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on …
algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on …
Fast and accurate de novo genome assembly from long uncorrected reads
… While the regular DP for pairwise alignment has time complexity of O(3nm), where n and
m are the lengths of the sequences being aligned, the sequence to graph alignment has a …
m are the lengths of the sequences being aligned, the sequence to graph alignment has a …
[HTML][HTML] The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
…, H Albert, ML Wang, YJ Zhu, M Schatz, N Nagarajan… - Nature, 2008 - nature.com
Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional
benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ …
benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ …
[HTML][HTML] Statistical methods for detecting differentially abundant features in clinical metagenomic samples
Numerous studies are currently underway to characterize the microbial communities inhabiting
our world. These studies aim to dramatically expand our understanding of the microbial …
our world. These studies aim to dramatically expand our understanding of the microbial …
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
…, R Petric, ML Hibberd, N Nagarajan - Nucleic acids …, 2012 - academic.oup.com
… for the computation of the pmf in O(N 2 ) time. As N can be large in practice, we aimed to …
to show that Pr n (X=k)=0 for k>n and that entries for n>N − K, k<K − N + n do not affect the …
to show that Pr n (X=k)=0 for k>n and that entries for n>N − K, k<K − N + n do not affect the …
[HTML][HTML] Critical assessment of metagenome interpretation—a benchmark of metagenomics software
Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome
data, but a lack of consensus about benchmarking complicates performance assessment. …
data, but a lack of consensus about benchmarking complicates performance assessment. …
A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer
Tyrosine kinase inhibitors (TKIs) elicit high response rates among individuals with kinase-driven
malignancies, including chronic myeloid leukemia (CML) and epidermal growth factor …
malignancies, including chronic myeloid leukemia (CML) and epidermal growth factor …