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 Higgs Boson Decays into a Z Boson and a Light Hadronically Decaying Resonance Using 13 TeV pp Collision Data from the ATLAS Detector

Abstract: A search for Higgs boson decays into a Z boson and a light resonance in two-lepton plus jet events is performed, using a pp collision dataset with an integrated luminosity of 139 fb^{-1} collected at sqrt[s]=13 TeV by the ATLAS experiment at the CERN LHC. The resonance considered is a light boson with a mass below 4 GeV from a possible extended scalar sector or a charmonium state. Multivariate discriminants are used for the event selection and for evaluating the mass of the light resonance. No excess of events above the expected background is found. Observed (expected) 95% confidence-level upper limits are set on the Higgs boson production cross section times branching fraction to a Z boson and the signal resonance, with values in the range 17-340 pb (16_{-5}^{+6}-320_{-90}^{+130} pb) for the different light spin-0 boson mass and branching fraction hypotheses, and with values of 110 and 100 pb (100_{-30}^{+40} and 100_{-30}^{+40} pb) for the η_{c} and J/ψ hypotheses, respectively.

Direct top-quark decay width measurement in the tt¯ lepton+jets channel at √s=8TeV with the ATLAS experiment

Abstract: This paper presents a direct measurement of the decay width of the top quark using t (t) over bar events in the lepton+jets final state. The data sample was collected by the ATLAS detector at the L ...

Observation and Measurement of Forward Proton Scattering in Association with Lepton Pairs Produced via the Photon Fusion Mechanism at ATLAS

Abstract: The observation of forward proton scattering in association with lepton pairs (e^{+}e^{-}+p or μ^{+}μ^{-}+p) produced via photon fusion is presented. The scattered proton is detected by the ATLAS Forward Proton spectrometer, while the leptons are reconstructed by the central ATLAS detector. Proton-proton collision data recorded in 2017 at a center-of-mass energy of sqrt[s]=13 TeV are analyzed, corresponding to an integrated luminosity of 14.6 fb^{-1}. A total of 57 (123) candidates in the ee+p (μμ+p) final state are selected, allowing the background-only hypothesis to be rejected with a significance exceeding 5 standard deviations in each channel. Proton-tagging techniques are introduced for cross-section measurements in the fiducial detector acceptance, corresponding to σ_{ee+p}=11.0±2.6(stat)±1.2(syst)±0.3(lumi) and σ_{μμ+p}=7.2±1.6(stat)±0.9(syst)±0.2(lumi) fb in the dielectron and dimuon channel, respectively.

Search for new phenomena in final states with b-jets and missing transverse momentum in √s = 13 TeV pp collisions with the ATLAS detector

Abstract: The results of a search for new phenomena in final states with b-jets and missing transverse momentum using 139 fb−1 of proton-proton data collected at a centre-of-mass energy $$ \sqrt{s} $$ = 13 TeV by the ATLAS detector at the LHC are reported The analysis targets final states produced by the decay of a pair-produced supersymmetric bottom squark into a bottom quark and a stable neutralino The analysis also seeks evidence for models of pair production of dark matter particles produced through the decay of a generic scalar or pseudoscalar mediator state in association with a pair of bottom quarks, and models of pair production of scalar third-generation down-type leptoquarks No significant excess of events over the Standard Model background expectation is observed in any of the signal regions considered by the analysis Bottom squark masses below 1270 GeV are excluded at 95% confidence level if the neutralino is massless In the case of nearly mass-degenerate bottom squarks and neutralinos, the use of dedicated secondary-vertex identification techniques permits the exclusion of bottom squarks with masses up to 660 GeV for mass splittings between the squark and the neutralino of 10 GeV These limits extend substantially beyond the regions of parameter space excluded by similar ATLAS searches performed previously

Determination of the parton distribution functions of the proton from ATLAS measurements of differential W± and Z boson production in association with jets

Abstract: This article presents a new set of proton parton distribution functions, ATLASepWZVjet20, produced in an analysis at next-to-next-to-leading order in QCD. The new data sets considered are the measurements of $W^+$ and $W^-$ boson and $Z$ boson production in association with jets in $pp$ collisions at $\sqrt{s} = 8~\mathrm{TeV}$ performed by the ATLAS experiment at the LHC with integrated luminosities of $20.2~\mathrm{fb}^{-1}$ and $19.9~\mathrm{fb}^{-1}$, respectively. The analysis also considers the ATLAS measurements of differential $W^{\pm}$ and $Z$ boson production at $\sqrt{s} = 7~\mathrm{TeV}$ with an integrated luminosity of $4.6~\mathrm{fb}^{-1}$ and deep-inelastic-scattering data from $e^{\pm}p$ collisions at the HERA accelerator. An improved determination of the sea-quark densities at high Bjorken $x$ is shown, while confirming a strange-quark density similar in size to the up- and down-sea-quark densities in the range $x \lesssim 0.02$ found by previous ATLAS analyses.

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.