User profiles for Y. Mahlich
Yannick MahlichPost-doctoral Associate, Rutgers University Verified email at bromberglab.org Cited by 1260 |
[HTML][HTML] A large-scale evaluation of computational protein function prediction
Automated annotation of protein function is challenging. As the number of sequenced
genomes rapidly grows, the overwhelming majority of protein products can only be annotated …
genomes rapidly grows, the overwhelming majority of protein products can only be annotated …
Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer
… each ligand has a comparable number of alignments (y axis, parenthesis) in the dataset. …
The distance of the alignment from the computed sahle curve along the PID y axis correlates …
The distance of the alignment from the computed sahle curve along the PID y axis correlates …
[HTML][HTML] Homology-based inference sets the bar high for protein function prediction
Background Any method that de novo predicts protein function should do better than random.
More challenging, it also ought to outperform simple homology-based inference. Methods …
More challenging, it also ought to outperform simple homology-based inference. Methods …
HFSP: high speed homology-driven function annotation of proteins
… Pairs of same function proteins (identical annotation for EC) and a given threshold distance
away from the curve along the y-axis were true positives (TP). Pairs that did not have the …
away from the curve along the y-axis were true positives (TP). Pairs that did not have the …
fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks
Microbial functional diversification is driven by environmental factors, ie microorganisms
inhabiting the same environmental niche tend to be more functionally similar than those from …
inhabiting the same environmental niche tend to be more functionally similar than those from …
[HTML][HTML] Fingerprinting cities: differentiating subway microbiome functionality
Background Accumulating evidence suggests that the human microbiome impacts
individual and public health. City subway systems are human-dense environments, where …
individual and public health. City subway systems are human-dense environments, where …
[HTML][HTML] Common sequence variants affect molecular function more than rare variants?
Any two unrelated individuals differ by about 10,000 single amino acid variants (SAVs). Do
these impact molecular function? Experimental answers cannot answer comprehensively, …
these impact molecular function? Experimental answers cannot answer comprehensively, …
Computational approaches for unraveling the effects of variation in the human genome and microbiome
The past two decades of analytical efforts have highlighted how much more remains to be
learned about the human genome and, particularly, its complex involvement in promoting …
learned about the human genome and, particularly, its complex involvement in promoting …
[HTML][HTML] Predicted molecular effects of sequence variants link to system level of disease
… amino acid X at residue n mutated to amino acid Y), we have to find another position (m≠n)
and in silico vary XmY. Then we compare the predicted effect XnY to those predicted for XmY…
and in silico vary XmY. Then we compare the predicted effect XnY to those predicted for XmY…
Learning from the unknown: exploring the range of bacterial functionality
… Choosing different Louvain resolution parameters (x-axis) to establish communities of
functionally similar organisms we can optimize the rate (y-axis) at which any two organisms are …
functionally similar organisms we can optimize the rate (y-axis) at which any two organisms are …