Chris Sander

Bio: Chris Sander is an academic researcher from Harvard University. The author has contributed to research in topics: Large Hadron Collider & Protein structure. The author has an hindex of 178, co-authored 713 publications receiving 233287 citations. Previous affiliations of Chris Sander include Purdue University & University of Leeds.

Search for trilepton resonances from chargino and neutralino pair production in s =13 TeV pp collisions with the ATLAS detector

Abstract: A search is performed for the electroweak pair production of charginos and associated production of a chargino and neutralino, each of which decays through an $R$-parity-violating coupling into a lepton and a $W$, $Z$, or Higgs boson. The trilepton invariant-mass spectrum is constructed from events with three or more leptons, targeting chargino decays that include an electron or muon and a leptonically decaying $Z$ boson. The analyzed dataset corresponds to an integrated luminosity of 139 fb$^{-1}$ of proton-proton collision data produced by the Large Hadron Collider at a center-of-mass energy of $\sqrt{s}$ = 13 TeV and collected by the ATLAS experiment between 2015 and 2018. The data are found to be consistent with predictions from the Standard Model. The results are interpreted as limits at 95% confidence level on model-independent cross sections for processes beyond the Standard Model. Limits are also set on the production of charginos and neutralinos for a Minimal Supersymmetric Standard Model with an approximate $B$-$L$ symmetry. Charginos and neutralinos with masses between 100 GeV and 1100 GeV are excluded depending on the assumed decay branching fractions into a lepton (electron, muon, or $\tau$-lepton) plus a boson ($W$, $Z$, or Higgs).

Probing color coherence effects in pp collisions at s√=7 TeV

Abstract: A study of color coherence effects in pp collisions at a center-of-mass energy of 7 TeV is presented. The data used in the analysis were collected in 2010 with the CMS detector at the LHC and correspond to an integrated luminosity of 36 inverse picobarns. Events are selected that contain at least three jets and where the two jets with the largest transverse momentum exhibit a back-to-back topology. The measured angular correlation between the second- and third-leading jet is shown to be sensitive to color coherence effects, and is compared to the predictions of Monte Carlo models with various implementations of color coherence. None of the models describe the data satisfactorily.

The Human Genome and High Performance Computing in Molecular Biology

Abstract: Genetic sequences contain the basic instruction code of living systems — a basic book of life. The period 1992–2010 will see the deciphering of much of this information, in many organisms, including that of the human genome. Unfortunately, the code is written in biological assembler language and needs to be deciphered. The translation rules from the basic code to biological function is not yet fully known. Here, computational molecular biology is challenged to make major contributions. The potential benefits to medical science and biotechnology are huge.

AlignmentViewer: Sequence Analysis of Large Protein Families.

Abstract: AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families. The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space. The tool is directly accessible in web browsers without the need for software installation. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, e.g. via EVcouplings.org.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

Abstract: CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

MUSCLE: multiple sequence alignment with high accuracy and high throughput

Abstract: We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using treedependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

Gene Ontology: tool for the unification of biology

Abstract: Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.