User profiles for Y. Mahlich

Yannick Mahlich

Post-doctoral Associate, Rutgers University
Verified email at bromberglab.org
Cited by 1260

[HTML][HTML] A large-scale evaluation of computational protein function prediction

…, M Kiening, D Krompass, C Landerer, Y Mahlich… - Nature …, 2013 - nature.com
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 …

Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer

Y Bromberg, AA Aptekmann, Y Mahlich, L Cook… - Science …, 2022 - science.org
… 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 …

[HTML][HTML] Homology-based inference sets the bar high for protein function prediction

…, M Kiening, D Krompass, C Landerer, Y Mahlich… - BMC …, 2013 - Springer
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 …

HFSP: high speed homology-driven function annotation of proteins

Y Mahlich, M Steinegger, B Rost, Y Bromberg - Bioinformatics, 2018 - academic.oup.com
… 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 …

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks

C Zhu, Y Mahlich, M Miller, Y Bromberg - Nucleic acids research, 2018 - academic.oup.com
Microbial functional diversification is driven by environmental factors, ie microorganisms
inhabiting the same environmental niche tend to be more functionally similar than those from …

[HTML][HTML] Fingerprinting cities: differentiating subway microbiome functionality

…, N Lusskin, Y Mahlich, Y Wang, Z Zeng, Y Bromberg - Biology direct, 2019 - Springer
Background Accumulating evidence suggests that the human microbiome impacts
individual and public health. City subway systems are human-dense environments, where …

[HTML][HTML] Common sequence variants affect molecular function more than rare variants?

Y Mahlich, J Reeb, M Hecht, M Schelling… - Scientific reports, 2017 - nature.com
Any two unrelated individuals differ by about 10,000 single amino acid variants (SAVs). Do
these impact molecular function? Experimental answers cannot answer comprehensively, …

Computational approaches for unraveling the effects of variation in the human genome and microbiome

…, M Miller, Z Zeng, Y Wang, Y Mahlich… - Annual Review of …, 2020 - annualreviews.org
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 …

[HTML][HTML] Predicted molecular effects of sequence variants link to system level of disease

…, M Hecht, Y Mahlich, Y Bromberg… - PLoS computational …, 2016 - journals.plos.org
… 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…

Learning from the unknown: exploring the range of bacterial functionality

Y Mahlich, C Zhu, H Chung, PK Velaga… - Nucleic Acids …, 2023 - academic.oup.com
… 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 …