text:
package paint

import (
	"context"
	"github.com/sirupsen/logrus"
	"github.com/twitchtv/twirp"
	paintservice "github.com/ykamo001/backend/rpc/paint"
)

type Provider interface {
	FillIn(ctx context.Context, request *paintservice.FillInRequest) (*paintservice.FillInResponse, error)
}

type provider struct {
	logger *logrus.Logger
}

func NewProvider(logger *logrus.Logger) *provider {
	return &provider{
		logger: logger,
	}
}

func (p provider) FillIn(ctx context.Context, request *paintservice.FillInRequest) (*paintservice.FillInResponse, error) {
	entry := p.logger.WithFields(logrus.Fields{
		"id": ctx.Value("id"),
	})

	var matrix [][]string
	for _, row := range request.Matrix {
		var currRow []string
		for _, value := range row.Array {
			currRow = append(currRow, value)
		}
		matrix = append(matrix, currRow)
	}

	picture := NewPicture(matrix, p.logger)
	err := picture.FillIn(ctx, request.Value, request.X, request.Y)
	if err != nil {
		entry.Error("FillIn")
		return &paintservice.FillInResponse{}, twirp.NewError(twirp.Internal, "internal error")
	}

	var grpcMatrix []*paintservice.InternalArray
	for _, row := range picture.values {
		var currRow paintservice.InternalArray
		for _, value := range row {
			currRow.Array = append(currRow.Array, value)
		}
		grpcMatrix = append(grpcMatrix, &currRow)
	}
	return &paintservice.FillInResponse{
		Matrix: grpcMatrix,
	}, nil
}


text:
function(build_mono_benchmark_project solutionname outputname extra_depends)

  set(Mono_FIND_QUIETLY 1)
  find_package(Mono)

  if(MONO_FOUND)

    # Enumerate over all .tt files and apply T4 to them
    SET(numcil_tt_outputs)
    FILE(GLOB_RECURSE files *.tt)

    FOREACH(file ${files})
      SET(src ${file})
      GET_FILENAME_COMPONENT(basename ${file} NAME_WE)
      GET_FILENAME_COMPONENT(targetfolder ${file} PATH)
      SET(dst ${targetfolder}/${basename}.cs)
      ADD_CUSTOM_COMMAND(
        OUTPUT ${dst}
        DEPENDS ${file} ${extra_depends}
        COMMAND ${MONO_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/../../../bridge/NumCIL/buildsupport/TextTransform.exe --out=${dst} ${src}
      )
      SET(numcil_tt_outputs ${numcil_tt_outputs} ${dst})
    ENDFOREACH(file)

    set(build_type "Release")
    if(CMAKE_BUILD_TYPE STREQUAL "Debug")
      set(build_type "Debug")
    endif()

    # Find source files
    file(GLOB_RECURSE SRCS *.cs *.sln *.csproj)
    set(output_binary ${CMAKE_CURRENT_BINARY_DIR}/bin/${build_type}/${outputname})
    add_custom_command(
        OUTPUT ${output_binary}
        COMMAND ${XBUILD_EXECUTABLE} /property:Configuration=${build_type} /property:OutputPath=${CMAKE_CURRENT_BINARY_DIR}/bin/${build_type} ${CMAKE_CURRENT_SOURCE_DIR}/${projname}.sln
        DEPENDS ${SRCS} ${numcil_tt_outputs} numcil_bohrium
    )

    # Add a target, and register a simple name
    add_custom_target(
      numcil_test_${projname} ALL
      DEPENDS numcil_bohrium numcil bhc ${output_binary}
    )

    install(FILES ${output_binary} DESTINATION share/bohrium/benchmark/cil/bin COMPONENT bohrium-numcil)
    install(FILES ${SRCS} DESTINATION share/bohrium/benchmark/cil/${projname} COMPONENT bohrium-numcil)

  else()
    message("Cannot build ${projname} as Mono or xbuild is missing")
  endif()

endfunction(build_mono_benchmark_project)

license_type: permissive

branch_name: refs/heads/master

extension: cmake


text:
@book{mention_research_2021,
	address = {Melbourne (Victoria), Australia},
	edition = {1st},
	title = {From {Research} to {Innovation}: {Exploring} the {Translation} {Journey} with {OpenInnoTrain}},
	isbn = {978-1-922016-75-1},
	url = {https://www.openinnotrain.eu/},
	language = {English},
	publisher = {RMIT University Press},
	editor = {Mention, Anne-Laure and Menichinelli, Massimo},
	year = {2021},
	doi = {10.5281/zenodo.5536932},
}

license: MIT

extension: bib


text:
require xorg-lib-common.inc

DESCRIPTION = "X11 protocol and utility library"
DEPENDS += "libxcb xproto xextproto xtrans libxau kbproto inputproto xf86bigfontproto"

#FILESDIR = "${@os.path.dirname(bb.data.getVar('FILE',d,1))}/libx11"
#SRC_URI += "file://X18NCMSstubs.diff;patch=1 "

PROVIDES = "virtual/libx11"

PE = "1"
PR = "r1"

XORG_PN = "libX11"
LEAD_SONAME = "libX11.so"

SRC_URI += "file://include_fix.patch;patch=1"

EXTRA_OECONF += "--with-keysymdef=${STAGING_INCDIR}/X11/keysymdef.h"
#EXTRA_OECONF += "--disable-xlocale --disable-xcms --with-xcb"
EXTRA_OECONF += "--disable-xcms --with-xcb"

do_compile() {
        (
         unset CC LD CXX CCLD CFLAGS CPPFLAGS LDFLAGS CXXFLAGS
         cd src/util; touch makekeys-makekeys.o ; ${BUILD_CC} ${BUILD_CFLAGS} makekeys.c -o makekeys
         cd ../../
        ) || exit 1
        oe_runmake
}

FILES_${PN} += "${datadir}/X11/XKeysymDB ${datadir}/X11/XErrorDB "

extension: bb


text:
UMMARY = "Startup script for Setting DVC sound module"
LICENSE = "CLOSED"

SRC_URI = "file://init.sh"

S = "${WORKDIR}"

do_install() {
        install -d ${D}/${sysconfdir}/profile.d
        install -m755 ${WORKDIR}/init.sh ${D}/${sysconfdir}/profile.d/audio-init.sh
}


text:
@misc{driscollSchwarzChristoffelToolboxMATLAB1994,
 author = {Driscoll, Tobin A},
 title = {Schwarz-Christoffel Toolbox for MATLAB},
 year = {1994}
}

repository: tobydriscoll/academic-kickstart

repo_name: tobydriscoll/academic-kickstart

gha_license_id: MIT


text:
@article {type-your-key-here,
  author = "Thaís Rocha and Paulo Borba",
  journal = "Empirical Software Engineering",
  title = "Using acceptance tests to predict merge conflict risk",
  year = "2023",
  pages = "?-?"
}

repository: pauloborba/academic-kickstart

repo_name: pauloborba/academic-kickstart


text:
DESCRIPTION = "Default display timings and resolutions for fbset"
LICENSE = "MIT"
PV = "0.1.0"
PR = "r5"

SRC_URI = "file://fb.modes"

do_install() {
    install -d ${D}${sysconfdir}
    install -m 0644 ${WORKDIR}/fb.modes ${D}${sysconfdir}
}

PACKAGE_ARCH = "all"
CONFFILES_${PN} = "${sysconfdir}/fb.modes"

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
# Copyright (C) 2014-2016 GENIVI Alliance
# Released under the MIT license (see COPYING.MIT for the terms)

DESCRIPTION = "GENIVI Development Platform core packagegroup"
LICENSE = "MIT"

inherit packagegroup

RDEPENDS_${PN} += "\
    avahi-daemon \
    cannelloni \
    common-api-c++ \
    common-api-c++-dbus \
    common-api-c++-someip \
    connman \
    connman-client \
    dlt-daemon \
    dlt-daemon-systemd \
    openssh-sftp-server \
    udisks2 \
    udisks2-disk-manager \
"

repository: GENIVI/genivi-dev-platform

repo_name: GENIVI/genivi-dev-platform

gha_language: Shell


text:
Nested crossreferences aren't really allowed (so they create warnings),
and their behavior depends on the order that the entries appear.

@article{grandchild,
    crossref="child",
}

@article{child,
    title="Child title",
    crossref="parent",
}

@article{parent,
    author = "Parent author",
}

@article{parent2,
    author = "Parent author",
}

@article{child2,
    title="Child title",
    crossref="parent2",
}

@article{grandchild2,
    crossref="child2",
}

repository: jneem/bibtex-rs

repo_name: jneem/bibtex-rs


text:
SUMMARY = "Firmware files for QCA6174"
LICENSE = "CLOSED"

inherit allarch

SRC_URI = "http://source.mynonpublic.com/edision/firmware-qca6174.zip"

S = "${WORKDIR}"
PR = "r1"

PACKAGES = "${PN}"
FILES_${PN} += "${nonarch_base_libdir}/firmware"

do_install() {
    install -d ${D}${nonarch_base_libdir}/firmware
    install -m 0644 btfw32.tlv ${D}${nonarch_base_libdir}/firmware/btfw32.tlv

    install -d ${D}${nonarch_base_libdir}/firmware/ath10k/QCA6174/hw3.0
    install -m 0644 board.bin ${D}${nonarch_base_libdir}/firmware/ath10k/QCA6174/hw3.0/board.bin
    install -m 0644 firmware-4.bin ${D}${nonarch_base_libdir}/firmware/ath10k/QCA6174/hw3.0/firmware-4.bin

    install -d ${D}${nonarch_base_libdir}/firmware/wlan
    install -m 0644 bdwlan30.bin ${D}${nonarch_base_libdir}/firmware/bdwlan30.bin
    install -m 0644 otp30.bin ${D}${nonarch_base_libdir}/firmware/otp30.bin
    install -m 0644 qwlan30.bin ${D}${nonarch_base_libdir}/firmware/qwlan30.bin
    install -m 0644 utf30.bin ${D}${nonarch_base_libdir}/firmware/utf30.bin
    install -m 0644 wlan/cfg.dat ${D}${nonarch_base_libdir}/firmware/wlan/cfg.dat
    install -m 0644 wlan/qcom_cfg.ini ${D}${nonarch_base_libdir}/firmware/wlan/qcom_cfg.ini
}

SRC_URI[md5sum] = "f193e6b80752e37234d0a70d56c72ed6"
SRC_URI[sha256sum] = "b86d0160a7b84c3a1da251fd3b591d2828b66b8d050afd9d06327f2768f5ce4d"

repository: avlogic/meta-edision

repo_name: avlogic/meta-edision


text:
package usecase

import (
	"context"
	"errors"
	"reflect"
	"testing"
	"time"

	"github.com/felixa1996/go-plate/domain"
)

type mockAccountRepoFindAll struct {
	domain.AccountRepository

	result []domain.Account
	err    error
}

func (m mockAccountRepoFindAll) FindAll(_ context.Context) ([]domain.Account, error) {
	return m.result, m.err
}

type mockFindAllAccountPresenter struct {
	result []FindAllAccountOutput
}

func (m mockFindAllAccountPresenter) Output(_ []domain.Account) []FindAllAccountOutput {
	return m.result
}

func TestFindAllAccountInteractor_Execute(t *testing.T) {
	t.Parallel()

	tests := []struct {
		name          string
		repository    domain.AccountRepository
		presenter     FindAllAccountPresenter
		expected      []FindAllAccountOutput
		expectedError interface{}
	}{
		{
			name: "Success when returning the account list",
			repository: mockAccountRepoFindAll{
				result: []domain.Account{
					domain.NewAccount(
						"3c096a40-ccba-4b58-93ed-57379ab04680",
						"Test",
						"02815517078",
						125,
						time.Time{},
					),
					domain.NewAccount(
						"3c096a40-ccba-4b58-93ed-57379ab04681",
						"Test",
						"02815517071",
						99999,
						time.Time{},
					),
				},
				err: nil,
			},
			presenter: mockFindAllAccountPresenter{
				result: []FindAllAccountOutput{
					{
						ID:        "3c096a40-ccba-4b58-93ed-57379ab04680",
						Name:      "Test",
						CPF:       "02815517078",
						Balance:   1.25,
						CreatedAt: time.Time{}.String(),
					},
					{
						ID:        "3c096a40-ccba-4b58-93ed-57379ab04681",
						Name:      "Test",
						CPF:       "02815517071",
						Balance:   999.99,
						CreatedAt: time.Time{}.String(),
					},
				},
			},
			expected: []FindAllAccountOutput{
				{
					ID:        "3c096a40-ccba-4b58-93ed-57379ab04680",
					Name:      "Test",
					CPF:       "02815517078",
					Balance:   1.25,
					CreatedAt: time.Time{}.String(),
				},
				{
					ID:        "3c096a40-ccba-4b58-93ed-57379ab04681",
					Name:      "Test",
					CPF:       "02815517071",
					Balance:   999.99,
					CreatedAt: time.Time{}.String(),
				},
			},
		},
		{
			name: "Success when returning the empty account list",
			repository: mockAccountRepoFindAll{
				result: []domain.Account{},
				err:    nil,
			},
			presenter: mockFindAllAccountPresenter{
				result: []FindAllAccountOutput{},
			},
			expected: []FindAllAccountOutput{},
		},
		{
			name: "Error when returning the list of accounts",
			repository: mockAccountRepoFindAll{
				result: []domain.Account{},
				err:    errors.New("error"),
			},
			presenter: mockFindAllAccountPresenter{
				result: []FindAllAccountOutput{},
			},
			expectedError: "error",
			expected:      []FindAllAccountOutput{},
		},
	}

	for _, tt := range tests {
		t.Run(tt.name, func(t *testing.T) {
			var uc = NewFindAllAccountInteractor(tt.repository, tt.presenter, time.Second)

			result, err := uc.Execute(context.Background())
			if (err != nil) && (err.Error() != tt.expectedError) {
				t.Errorf("[TestCase '%s'] Result: '%v' | ExpectedError: '%v'", tt.name, err, tt.expectedError)
			}

			if !reflect.DeepEqual(result, tt.expected) {
				t.Errorf("[TestCase '%s'] Result: '%v' | Expected: '%v'", tt.name, result, tt.expected)
			}
		})
	}
}

branch_name: refs/heads/main

gha_language: Go

extension: go


text:
# Copyright 2023 AVSystem <avsystem@avsystem.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

set(STORED_REQUIRED_DEFINITIONS "${CMAKE_REQUIRED_DEFINITIONS}")
if(NOT APPLE)
    set(CMAKE_REQUIRED_DEFINITIONS
        ${CMAKE_REQUIRED_DEFINITIONS} -D_POSIX_C_SOURCE=200809L)
endif()

include(CheckIncludeFiles)
check_include_files("net/if.h" AVS_COMMONS_HAVE_NET_IF_H)

include(CheckFunctionExists)
check_function_exists(getifaddrs AVS_COMMONS_NET_POSIX_AVS_SOCKET_HAVE_GETIFADDRS)

include(CheckSymbolExists)
check_symbol_exists("gai_strerror" "netdb.h" AVS_COMMONS_NET_POSIX_AVS_SOCKET_HAVE_GAI_STRERROR)
check_symbol_exists("getnameinfo" "netdb.h" AVS_COMMONS_NET_POSIX_AVS_SOCKET_HAVE_GETNAMEINFO)
check_symbol_exists("inet_ntop" "arpa/inet.h" AVS_COMMONS_NET_POSIX_AVS_SOCKET_HAVE_INET_NTOP)
check_symbol_exists("poll" "poll.h" AVS_COMMONS_NET_POSIX_AVS_SOCKET_HAVE_POLL)
check_symbol_exists("recvmsg" "sys/socket.h" AVS_COMMONS_NET_POSIX_AVS_SOCKET_HAVE_RECVMSG)

# When _POSIX_C_SOURCE is defined, but none of _BSD_SOURCE, _SVID_SOURCE and
# _GNU_SOURCE, some toolchains (e.g. default GCC on Ubuntu 16.04 or CentOS 7)
# define IN6_IS_ADDR_V4MAPPED using s6_addr32 symbol that is undefined.
# That makes simple check_symbol_exists() succeed despite it being unusable.
if(NOT DEFINED AVS_COMMONS_NET_POSIX_AVS_SOCKET_HAVE_IN6_IS_ADDR_V4MAPPED)
    message(STATUS "Checking if IN6_IS_ADDR_V4MAPPED is usable")
    file(WRITE ${CMAKE_BINARY_DIR}/CMakeFiles/CMakeTmp/in6_is_addr_v4mapped.c
         "#include <netinet/in.h>\nint main() { struct in6_addr addr = {0}; IN6_IS_ADDR_V4MAPPED(&addr); return 0; }\n")
    try_compile(AVS_COMMONS_NET_POSIX_AVS_SOCKET_HAVE_IN6_IS_ADDR_V4MAPPED
                ${CMAKE_BINARY_DIR}/CMakeFiles/CMakeTmp
                ${CMAKE_BINARY_DIR}/CMakeFiles/CMakeTmp/in6_is_addr_v4mapped.c
                COMPILE_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS})
endif()
if(AVS_COMMONS_NET_POSIX_AVS_SOCKET_HAVE_IN6_IS_ADDR_V4MAPPED)
    message(STATUS "Checking if IN6_IS_ADDR_V4MAPPED is usable - yes")
else()
    message(STATUS "Checking if IN6_IS_ADDR_V4MAPPED is usable - no")
endif()

set(CMAKE_REQUIRED_DEFINITIONS "${STORED_REQUIRED_DEFINITIONS}")

gha_language: C


text:
package config

import "github.com/Unknwon/goconfig"

type Config struct {
	GitterToken string
}

func LoadConfig() *Config {
	config := &Config{}
	cfg, err := goconfig.LoadConfigFile("config.cfg")
	if err != nil {
		panic("Can't load config file")
	}

	// Load gitter.token
	token, err := cfg.GetValue("gitter", "token")
	if err != nil {
		panic("Cant't load config: [gitter] -> token")
	}
	config.GitterToken = token

	return config
}

repository: Diorzz/Gitter-Robot

repo_name: Diorzz/Gitter-Robot


text:
DESCRIPTION = "The SQL::Statement module implements a pure Perl SQL parsing and execution \
engine. While it by no means implements full ANSI standard, it does support \
many features including column and table aliases, built-in and user-defined \
functions, implicit and explicit joins, complex nested search conditions, \
and other features."

SECTION = "libs"
LICENSE = "Artistic-1.0 | GPL-1.0-or-later"
PR = "r0"

MAINTAINER=	"Poky <poky@yoctoproject.org>"
HOMEPAGE=	"https://metacpan.org/release/SQL-Statement"

LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/Artistic-1.0;md5=cda03bbdc3c1951996392b872397b798 \
file://${COMMON_LICENSE_DIR}/GPL-1.0-or-later;md5=30c0b8a5048cc2f4be5ff15ef0d8cf61"

SRC_URI = "https://cpan.metacpan.org/authors/id/R/RE/REHSACK/SQL-Statement-1.414.tar.gz"

SRC_URI[md5sum] = "f93b655aef646b478ccac8d08a7115dd"
SRC_URI[sha256sum] = "dde8bdcfa6a136eedda06519ba0f3efaec085c39db0df9c472dc0ec6cd781a49"
RDEPENDS:${PN} += "clone-perl"
RDEPENDS:${PN} += "module-runtime-perl"
RDEPENDS:${PN} += "params-util-perl"
RRECOMMENDS:${PN} += "math-base-convert-perl"
RRECOMMENDS:${PN} += "perl"
DEPENDS += "math-base-convert-perl-native"
DEPENDS += "perl"
DEPENDS += "test-deep-perl-native"

S = "${WORKDIR}/SQL-Statement-${PV}"

inherit cpan allarch

BBCLASSEXTEND = "native"

repository: rehsack/meta-cpan

repo_name: rehsack/meta-cpan

gha_language: BitBake


text:
require jfsutils.inc

SRC_URI = "cvs://anonymous@jfs.cvs.sourceforge.net/cvsroot/jfs;module=jfsutils"
S = "${WORKDIR}/${PN}"

DEFAULT_PREFERENCE = "-1"


text:
---
---

@string{aps = {American Physical Society,}}

@article{WEI202377,
  abbr={PRL},
  title={Topology-preserving transfer learning for weakly-supervised anomaly detection and segmentation},
  author={Wei, Shenxing and Wei, Xing and Kurniawan, Muhammad Rifki and Ma, Zhiheng and Gong, Yihong},
  abstract={Models pre-trained on the ImageNet dataset are introduced to be exploited for knowledge transfer in numerous downstream computer vision tasks, including the weakly-supervised anomaly detection and segmentation area. Specifically, in anomaly segmentation, the former study shows that representing images with feature maps extracted by pre-trained models significantly improves over previous techniques. This kind of representation method requires both high-quality and task-specific features, but feature extractors obtained from ImageNet directly are very general. One intuition for obtaining stronger features is by transferring a pre-trained model to the target dataset. However, in this paper, we show that under weakly-supervised settings, naïve fine-tune techniques that typically work for supervised learning can lead to catastrophic feature space collapse and reduce performance greatly. Thus, we propose to apply a topology-preserving constraint during transferring. Our method preserves the topology graph to keep the feature space from collapsing under weakly-supervised settings. And then we combine the transferred model with a simple anomaly detection and segmentation baseline for performance evaluation. The experiments show that our method achieves competitive accuracy on several benchmarks meanwhile setting a new state-of-the-art for anomaly detection on CIFAR100/10 and BTAD datasets.},
  journal={Pattern Recognition Letters},
  volume={170},
  pages={77-84},
  issn = {0167-8655},
  year={2023},
  doi={https://doi.org/10.1016/j.patrec.2023.04.019},
  keywords = {Anomaly detection, Transfer learning, Weakly-supervised learning, Topology preservation},
  pdf={https://www.sciencedirect.com/science/article/pii/S0167865523001265},
  dimensions={true},
  selected={true},
  bibtex_show={true},
  preview={anomaly_prl.svg},
}

@article{Kurniawan2021OnlineCL,
  abbr={ArXiv},
  title={Online Continual Learning via Multiple Deep Metric Learning and Uncertainty-guided Episodic Memory Replay - 3rd Place Solution for ICCV 2021 Workshop SSLAD Track 3A Continual Object Classification},
  author={Kurniawan, Muhammad Rifki and Wei, Xing and Gong, Yihong},
  abstract={Online continual learning in the wild is a very difficult task in machine learning. Non-stationarity in online continual learning potentially brings about catastrophic forgetting in neural networks. Specifically, online continual learning for autonomous driving with SODA10M dataset exhibits extra problems on extremely long-tailed distribution with continuous distribution shift. To address these problems, we propose multiple deep metric representation learning via both contrastive and supervised contrastive learning alongside soft labels distillation to improve model generalization. Moreover, we exploit modified class-balanced focal loss for sensitive penalization in class imbalanced and hard-easy samples. We also store some samples under guidance of uncertainty metric for rehearsal and perform online and periodical memory updates. Our proposed method achieves considerable generalization with average mean class accuracy (AMCA) 64.01% on validation and 64.53% AMCA on test set.},
  journal={ArXiv},
  volume={abs/2111.02757},
  year={2021},
  pdf={https://arxiv.org/abs/2111.02757},
  dimensions={true},
  selected={true},
  bibtex_show={true},
  preview={online_cl_sslad.svg},
  code={https://github.com/mrifkikurniawan/sslad},
  slides={https://intip.in/pptxjtusslad3a},
}

@article{doi:10.1063/1.5095287,
  abbr={AIP},
  title={Optimization of neural network based on hybrid method of genetic algorithm and particle swarm optimization for maritime weather forecasting in buoyweather station type II},
  author={Arifin, Syamsul and Mahistha, Dvitiya Srestha Prajna and Ukhti, Magfiroh Fatwaning and Kurniawan, Muhammad Rifki and Aisjah, Aulia Siti},
  abstract={The object the research is to forecast maritime weather variables such wind speed and direction, temperature and wave height for an hour ahead by using artificial intelligence approach. Artificial intelligence is comprised of hybrid neural networks modified by genetic algorithms and particle swarm optimization which are functioned as a model predictor. The hybrid predictor works on every single predictor by weighing both artificial neural network-genetic algorithm (ANN-GA) and artificial neural network-particle swarm optimization (ANN-PSO) which weight is calculated by differential evolution algorithm optimization. When the unsurpassed model is obtained, it will be validated across real-time data that is delivered from type II buoyweather station measurement at the Madura Strait, Java Sea. The prediction results of learning and validation process indicate that the ANN-Hybrid predictor perform more accurate than the ANN-GA and ANN PSO on training and validation. However, the gap of RMSE on real-time test is relatively high compared to validation or training. It can be influenced by the different frequent of weather fluctuation between them. Concurring to real-time test stage, the foremost appropriate variable that predicted by this ANN-Hybrid is temperature.},
  journal={AIP Conference Proceedings},
  volume={2088},
  number={1},
  pages={020035},
  numpages={0},
  year={2019},
  doi={10.1063/1.5095287},
  pdf={https://aip.scitation.org/doi/abs/10.1063/1.5095287},
  dimensions={true},
  selected={false},
  bibtex_show={true},
}

@article{kurniawanperancangan,
  abbr={Bachelor Thesis},
  title={Perancangan Mobile Predictor Cuaca Maritim Menggunakan Metode Hybrid Logika Fuzzy Tipe 2-Jaringan Syaraf Tiruan dengan Optimasi Algoritma Differential Evolution},
  author={Kurniawan, Muhammad Rifki and Arifin, Syamsul and Aisjah, Aulia Siti},
  journal={AIP Conference Proceedings},
  year={2019},
  doi={10.13140/RG.2.2.27518.84803},
  pdf={https://www.researchgate.net/publication/331837855_Perancangan_Mobile_Predictor_Cuaca_Maritim_Menggunakan_Metode_Hybrid_Logika_Fuzzy_Tipe_2-Jaringan_Syaraf_Tiruan_dengan_Optimasi_Algoritma_Differential_Evolution#fullTextFileContent},
  dimensions={true},
  selected={false},
  bibtex_show={true},
  code={https://github.com/mrifkikurniawan/Maritime-Weather-Forecaster},
}


text:
# Copyright (C) 2016 - 2017 Randy Li <ayaka@soulik.info>
# Released under the GNU GENERAL PUBLIC LICENSE Version 2
# (see COPYING.GPLv2 for the terms)

DEFAULT_PREFERENCE = "-1"

include gstreamer1.0-rockchip.inc

SRCBRANCH ?= "master"
SRCREV = "${AUTOREV}"
SRC_URI = "git://github.com/kraj/gstreamer-rockchip.git;branch=${SRCBRANCH};protocol=https"
SRC_URI_remove = "file://gtk-doc-tweaks.patch"

S = "${WORKDIR}/git"

repository: kraj/meta-rockchip

repo_name: kraj/meta-rockchip


text:
SUMMARY = "testfixtures is a collection of helpers and mock objects that are useful when writing automated tests in Python"

HOMEPAGE = "https://github.com/python/typing"
LICENSE = "Python-2.0"
LIC_FILES_CHKSUM = "file://LICENSE;md5=64fc2b30b67d0a8423c250e0386ed72f"

PYPI_PACKAGE = "typing_extensions"

inherit pypi
inherit setuptools3

SRC_URI[md5sum] = "98510adbacf8ea74f46f98b0a5cbdf73"
SRC_URI[sha256sum] = "2ed632b30bb54fc3941c382decfd0ee4148f5c591651c9272473fea2c6397d95"

BBCLASSEXTEND = "native"

repository: jianchangfeng/meta-ros

repo_name: jianchangfeng/meta-ros


text:
// IDEAS:
// Allow users to change the max counter value (so they can increase the difficulty)

const difficulties = ["Normal", "Elite", "Nightmare", "Any"];

const characters = ["Ao Bai", "Crown Prince", "Qing Yan", "Lei Luo", "Any Character"];

// [challenge, resample weight, chance weight]
// Any challenge with a resample weight of 1 will stop sampling after it is picked
// Increasing the chance weight by 1 increases the chance it will be selected to n+1/total+1
// So if it's 1->2 in a list of 43, all initially at 1, the chance will go from 1/43 to 2/44
// Bear in mind this means that increasing the chance of one, DECREASES the chances of all others by dilution
const challenges = [
  ["Normal Run", 1, 2],
  ["Speedrun", 0.4, 4],
  ["No Dash", 0.5, 3],
  ["No Sound", 0.5, 3],
  ["No Craftsman", 0.3, 4],
  ["No Kermit", 0.3, 4],
  ["No Vaults", 0.3, 4],
  ["All Vaults", 0.1, 4],
  ["No Cursed Chests", 0.3, 4],
  ["All Cursed Chests", 0.3, 4],
  ["No Secondary Skills", 0.3, 4],
  ["No Primary Skills", 0.3, 4],
  ["No Scrolls", 1, 3],
  ["No Acensions", 1, 3],
  ["No Revive", 0.3, 4],
  ["No Manual Reloads", 0.2, 4],
  ["No Elemental Weapons", 0.2, 4],
  ["No Insurance: Try not to break anything", 0.2, 4],
  ["Butterfingers: Always pick up new weapons", 0.2, 3],
  ["Sticky Fingers: Never pick up new weapons", 0.2, 3],
  ["Rebind Hell: Invert Movement Bindings", 1, 3],
  ["Pimm's Curse: Invert mouse buttons, axis, & movement", 1, 1],
  // ["NES Mode: Lowest Resolution", 1, 1], // Sadly this seems to fuck with people's stream setups...which sucks
  ["Kap's Curse: SWORD CAT!", 1, 1],
  ["Foundry Only", 0.5, 5],
  ["Pistols", 0.5, 5],
  ["Submachineguns", 0.3, 5],
  ["Rifles", 0.3, 5],
  ["Shotguns", 0.3, 5],
  ["Snipers", 0.3, 5],
  ["Launchers", 0.3, 5],
  ["Injectors", 0.3, 5],
  ["Melee", 0.3, 2],
  ["Only Fire Weapons", 0.3, 4],
  ["Only Corrosion Weapons", 0.3, 4],
  ["Only Lightning Weapons", 0.3, 4],
  ["Student Loan: Spend money ASAP", 0.5, 4],
  ["No Gemini", 0.1, 4],
  ["OGemini: No reforging", 0.1, 4],
  ["NoUI: Press F10 to play without UI", 0.7, 2],
  ["Backwards movement only", 0.4, 1],
  ["Switch mouse buttons", 0.5, 3],
  ["Change Language", 0.6, 3],
  ["Use a controller", 0.4, 2],
];

// Why in the name of all that is holy do I need to write fisher-yates again just to shuffle an array?
function shuffle(array) {
  let curridx = array.length,  randidx;
  while (0 !== curridx) {
    randidx = Math.floor(Math.random() * curridx);
    curridx--;
    [array[curridx], array[randidx]] = [
      array[randidx], array[curridx]];
  }
  return array;
}

function createWeightedIdxArray(challengeArray) {
  // Calculate total length of array
  // console.log("Creating Weighted Index Array");
  // const reducer = (accumulator, currentValue) => accumulator + currentValue[2];
  // let arrayLength = challengearray.reduce(reducer, 0)
  let i;
  let outarray = [];
  for (i = 0; i < challengeArray.length; i++) {
    outarray = outarray.concat(Array(parseInt(challengeArray[i][2])).fill(i));
  }
  const weightedChallengeIdxs = outarray;
  // console.log(weightedChallengeIdxs);
  return outarray;
}

const weightedChallengeIdxs = createWeightedIdxArray(challenges)  // Create weightedChallengeIdxs in module scope

function findResampleMax(challengeArray) {
  // Find the maximum difficulty value currently allowed by the generator
  const reducer = (accumulator, currentValue) => accumulator + currentValue[1];
  return challengeArray.reduce(reducer, 0)
}

const resampleMax = findResampleMax(challenges) * 0.99  // Allow a bit of headroom just in case
// console.log(findResampleMax(challenges))

function setMaxDifficulty() {
  // Set max of difficulty input when called
  let input = document.getElementById("challengeDifficulty")
  input.setAttribute("max", Math.floor(resampleMax));
}

function removeItem(array, item) {
  return array.filter(i => i !== item);
}

function generateRun(challengeDifficulty) {
  // console.log("Generating new run...")

  // Check whether the supplied difficulty is a positive number
  if (isNaN(challengeDifficulty) || challengeDifficulty <= 0) {
    challengeDifficulty = 1;
  }

  // Check whether the supplied difficulty is greater than the max the generator could generate
  if (challengeDifficulty > resampleMax) {
    challengeDifficulty = resampleMax;
  }
  // console.log(challengeDifficulty)

  // let outstr = ""
  let difficulty = difficulties[Math.floor(Math.random() * difficulties.length)];
  // console.log(difficulty)
  let character = characters[Math.floor(Math.random() * characters.length)];
  // console.log(character)

  let challenge_list = [];
  // JS is not python! deepcopies are hard and don't necessarily happen when you think they do
  // Converting to and from JSON forces a copy and prevents the weightedChallengeIdxs array from being exhausted
  let challengeIdxs = shuffle(JSON.parse(JSON.stringify(weightedChallengeIdxs)));
  // We need to shuffle the array because js arrays do not have a pop command that will take an index to pop.
  // I'm sure all this would be a lot easier if I just learned node.js but that feels ludicrous!

  let counter = 0;
  let randfloat = 1;
  while (counter < randfloat) {
    let challengeIdx = challengeIdxs.pop(); // Get next challenge index
    // console.log(challengeIdx)
    challengeIdxs = removeItem(challengeIdxs, challengeIdx); // Remove all entries of the idx from the index array
    // console.log(challengeIdxs)
    challenge_list.push(challenges[challengeIdx][0]); // Add challenge to list
    counter += challenges[challengeIdx][1];           // Increment counter
    // console.log("Counter: " + counter)
    randfloat = Math.random() * challengeDifficulty;
    // console.log("Randfloat: " + randfloat)
    if (challengeIdxs.length < 1) {
      console.warn("Exhausted Challenge Index Buffer...")
      break;
    }
  }
  // console.log(challenge_list)
  document.getElementById('playerDisplay').innerHTML = "".concat(character, " on ", difficulty, " difficulty");
  document.getElementById('challengeDisplay').innerHTML = challenge_list.join("<br>");
}

gha_language: CSS

extension: js


text:
%%% -*-BibTeX-*-
@article{Liu2015TPAMI,
    author = {Lingqiao Liu and Lei Wang and Chunhua Shen},
    title  = {A Generalized Probabilistic Framework for Compact Codebook Creation},
    journal= {IEEE Transactions on Pattern Analysis and Machine Intelligence},
    volume = {38},
    number = {2},
    year   = {2016},
    url    = {http://doi.org/10.1109/TPAMI.2015.2441069},
    month  = {},
    pages  = {224--237},
    eprint = {1401.7713},
    venue  = {TPAMI},
    project= {},
    note   = {},
}


text:
DESCRIPTION = "64 bit .NET and ASP.NET Core Runtime"
HOMEPAGE = "https://www.microsoft.com/net/core"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://LICENSE.txt;md5=9fc642ff452b28d62ab19b7eea50dfb9"
PV = "3.0-preview9"
PR = "r0"

RPROVIDES_${PN} = "dotnetcore-64"
DEPENDS = "zlib curl"
RDEPENDS_${PN} = "libunwind icu libcurl openssl libgssapi-krb5"

PACKAGECONFIG_pn-curl = 'zlib ipv6 ssl'

# See https://github.com/dotnet/core/tree/master/release-notes for json formatted download details
URL = "https://download.visualstudio.microsoft.com/download/pr/4ca3622d-5ff1-4478-9b7b-5f47cfb7f070/9623cb1f6dea28530695a0fd3032fa30/aspnetcore-runtime-3.0.0-preview9.19424.4-linux-arm64.tar.gz"

# run certUtil -hashfile aspnetcore-runtime-3.0.0-preview9.19424.4-linux-arm64.tar.gz MD5 (or SHA256) to get hashes
SRC_URI =  "${URL};downloadfilename=dotnet-${PV}-linux-arm64.tar.gz"
SRC_URI[md5sum] = "03014fd6ae3ced76774a3e174419259a"
SRC_URI[sha256sum] = "df8a0f1c22f46958588c56caeb7c839855960a4bf0b2f52ebb5a9e694fcdf7ba"

S = "${WORKDIR}"

PACKAGES = "${PN}"

do_configure[noexec] = "1"
do_compile[noexec] = "1"

python do_install () {
    bb.build.exec_func("shell_do_install", d)
    oe.path.make_relative_symlink(d.expand("${D}${bindir}/dotnet"))
}

shell_do_install() {
	install -d ${D}${bindir}

	install -d ${D}/usr/share/dotnet
	install -d ${D}/usr/share/dotnet/host
	install -d ${D}/usr/share/dotnet/shared

	install -m 0755 ${S}/dotnet ${D}/usr/share/dotnet
	install -m 0644 ${S}/LICENSE.txt ${D}/usr/share/dotnet
	install -m 0644 ${S}/ThirdPartyNotices.txt ${D}/usr/share/dotnet

	cp -R --no-dereference --preserve=mode,links -v ${S}/host/. ${D}/usr/share/dotnet/host/
	cp -R --no-dereference --preserve=mode,links -v ${S}/shared/. ${D}/usr/share/dotnet/shared/

	# Symlinks
	ln -s ${D}/usr/share/dotnet/dotnet ${D}${bindir}/dotnet

    # Configure install directory
	mkdir -p ${D}/etc/dotnet && printf '/usr/share/dotnet' > ${D}/etc/dotnet/install_location
}

FILES_${PN} = "\
	${bindir} \
	/usr/share/dotnet/dotnet \
	/usr/share/dotnet/*.txt \
	/usr/share/dotnet/host \
	/usr/share/dotnet/shared \
	/etc/dotnet/install_location \
"

INSANE_SKIP_${PN} = "already-stripped staticdev ldflags libdir file-rdeps"
INHIBIT_PACKAGE_DEBUG_SPLIT = "1"

repository: stevehayles/meta-rpi

repo_name: stevehayles/meta-rpi

branch_name: refs/heads/dunfell


text:
@inproceedings{bukva2020towards,
 author = {Bukva, Alexander and Christopher, Nicholas and Hickey, Jean-Pierre},
 booktitle = {23rd AIAA International Space Planes and Hypersonic Systems and Technologies Conference},
 title = {Towards modelling of thermal protection systems with transpiration cooling},
 year = {2020}
}

repository: mpilab-uw/mpilab

repo_name: mpilab-uw/mpilab


text:
@article{WangDDoSAttackProtection2015,
 author = {Wang, Bing and Zheng, Yao and Lou, Wenjing and Hou, Y. Thomas},
 copyright = {CC0 1.0 Universal Public Domain Dedication},
 file = {/Users/yao/Cloud/Zotero/storage/HJGEB46E/Wang et al. - 2015 - DDoS Attack Protection in the Era of Cloud Computi.pdf},
 journal = {Computer Networks},
 keywords = {journal},
 month = {April},
 number = {C},
 pages = {308--319},
 title = {DDoS Attack Protection in the Era of Cloud Computing and Software-Defined Networking},
 volume = {81},
 year = {2015}
}

repository: brackenw/academic-kickstart

repo_name: brackenw/academic-kickstart


text:
@article{Owen-Smith2012-qp,
 abstract = {Context To interpret spatial utilisation distributions, there is
a need to translate animal locations obtained from global
positioning system (GPS) telemetry into the activities performed
and, hence, benefits derived, from particular places and times
of day. Derived activity patterns also reveal how animals cope
in changing environmental conditions. Aim The aim of our
research was to develop and test an objective, consistent and
biologically faithful method for deriving activity states from
movement rates between successive GPS locations. Methods The
method entails fitting mixtures of component statistical
distributions to the frequency distribution of hourly step
displacements. Breakpoints indicating transitions between
predominant movement modes were identified by fitting
exponential segments. Breakpoints were incorporated as off-sets
for gamma distributions, but not needed for log-normal
distributions. This procedure was applied to movement data for
three large grazing ungulates. Key results Models consistently
distinguished four movement modes interpreted as representing
resting, foraging, mixed movement and travelling activity.
Breakpoints and parameter estimates were consistent among
seasons and herds of each ungulate species. The
exponential-segment model and both mixture models closely
represented observed daily activity patterns. However, some
adjustment of the derived time budgets was needed to be
consistent with observations. Key conclusions Mixture models
provide an objective, reliable and biologically meaningful
procedure for assessing seasonal, annual and spatial variation
in the activity patterns of large ungulates from GPS data.
Implications The method can potentially be applied to other
mobile foragers large enough to carry GPS collars.},
 author = {Owen-Smith, Norman and Goodall, Victoria and Fatti, Paul},
 journal = {Wildl. Res.},
 language = {en},
 month = {July},
 number = {5},
 pages = {452--462},
 publisher = {CSIRO PUBLISHING},
 title = {Applying mixture models to derive activity states of large
herbivores from movement rates obtained using GPS telemetry},
 volume = {39},
 year = {2012}
}

repository: SAEON/academic-kickstart

repo_name: SAEON/academic-kickstart


text:
%
% publications of Mahendra Mariadassou
% (limited to Journal Articles, Proceedings, Book Chapters, and Manuscripts)
% THIS LIST IS NOT COMPLETE
%

% SPECIFIC FIELDS FOR THE WEB PAGES GENERATION ARE:
% - DOI : the DOI of the bib item
% - HAL_ID : the HAL URL of the bib item
% - OPTLINK : the link to a page about the bib item (if not on DOI or HAL)
% - PDF : the link to the PDF of the bib item
% - PP_KIND : the kind of bib item (for sorting based on it) {applied, theoretical}
% - PP_RANK : the rank of the bib item in the year (for sorting based on it)
% - PP_SHORTBOOKTITLE : for conferences/workshops, abbreviation of it

%
%    DOI = {xxxx/xxxx},
%    HAL_ID = {hal-xxxx},
%    OPTLINK = {http://...},
%    PDF = {https://hal.inria.fr/hal-xxxx/document},
%    PP_KIND = {Applied/Theoretical},
%    PP_RANK = {1/2/3...},
%    PP_SHORTBOOKTITLE = {xxx},

% Encoding: UTF-8

%
% ----- PREPRINTS -----
%

@article{goutorbe2022characterizing,
  title={Characterizing the limits of shallow shotgun metagenomics for taxonomic profiling of human gut microbiota in clinical studies},
  author={Goutorbe, Benoit and Abraham, Anne-Laure and Mariadassou, Mahendra and Plauzolles, Anne and Bidaut, Ghislain and Halfon, Philippe and Schbath, Sophie},
  year={2022},
  journal={submitted to mSystems},
  volume={under revision}
}

%
% ----- POSTER -----
%

%
% ----- ARTICLES -----
%

%% ----------- 2023 --------------

@article{mariadassou2023microbiota,
  title={Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd},
  author={Mariadassou, Mahendra and Nouvel, Laurent X and Constant, Fabienne and Morgavi, Diego P and Rault, Lucie and Barbey, Sarah and Helloin, Emmanuelle and Rué, Olivier and Schbath, Sophie and Launay, Frederic and Sandra, Olivier and Lefebvre, Rachel and Le Loir, Yves and Germon, Pierre and Citti, Christine and Even, Sergine},
  journal={Animal Microbiome},
  volume={5},
  number={1},
  pages={1--17},
  year={2023},
  doi = {10.1186/s42523-023-00252-w},
  url = {https://doi.org/10.1186/s42523-023-00252-w},
  pdf = {https://animalmicrobiome.biomedcentral.com/counter/pdf/10.1186/s42523-023-00252-w.pdf},
  publisher={BioMed Central}
}

%% ----------- 2022 --------------

@article {Richter2022,
title = {Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems},
author = {Richter, Daniel J and Watteaux, Romain and Vannier, Thomas and Leconte, Jade and Frémont, Paul and Reygondeau, Gabriel and Maillet, Nicolas and Henry, Nicolas and Benoit, Gaëtan and Da Silva, Ophélie and Delmont, Tom O and Fernàndez-Guerra, Antonio and Suweis, Samir and Narci, Romain and Berney, Cédric and Eveillard, Damien and Gavory, Frederick and Guidi, Lionel and Labadie, Karine and Mahieu, Eric and Poulain, Julie and Romac, Sarah and Roux, Simon and Dimier, Céline and Kandels, Stefanie and Picheral, Marc and Searson, Sarah and Tara Oceans Coordinators and Pesant, Stéphane and Aury, Jean-Marc and Brum, Jennifer R and Lemaitre, Claire and Pelletier, Eric and Bork, Peer and Sunagawa, Shinichi and Lombard, Fabien and Karp-Boss, Lee and Bowler, Chris and Sullivan, Matthew B and Karsenti, Eric and Mariadassou, Mahendra and Probert, Ian and Peterlongo, Pierre and Wincker, Patrick and de Vargas, Colomban and Ribera d'Alcalà, Maurizio and Iudicone, Daniele and Jaillon, Olivier},
volume = 11,
year = 2022,
month = {aug},
pub_date = {2022-08-03},
pages = {e78129},
citation = {eLife 2022;11:e78129},
doi = {10.7554/eLife.78129},
url = {https://doi.org/10.7554/eLife.78129},
journal = {eLife},
issn = {2050-084X},
pdf = {https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNzgxMjkvZWxpZmUtNzgxMjktdjEucGRmP2Nhbm9uaWNhbFVyaT1odHRwczovL2VsaWZlc2NpZW5jZXMub3JnL2FydGljbGVzLzc4MTI5/elife-78129-v1.pdf?_hash=84cJGQ8IyGlmYH01ZvsbITElPXHN6qOAs3LCEKQkWOk%3D}
}

@article{Ngo2022,
author = {Ngo, Vuong Quoc Hoang and Enault, François and Midoux, Cédric and Mariadassou, Mahendra and Chapleur, Olivier and Mazéas, Laurent and Loux, Valentin and Bouchez, Théodore and Krupovic, Mart and Bize, Ariane},
title = {Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics},
journal = {Environmental Microbiology},
volume = {24},
number = {10},
pages = {4853--4868},
year = {2022},
publisher = {Wiley},
month = jul,
doi = {https://doi.org/10.1111/1462-2920.16120},
url = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.16120},
eprint = {https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.16120},
pdf = {https://sfamjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16120}
}

@inBook{bastide:hal-03762880,
  TITLE = {{Modèles d'évolution de caractères continus}},
  AUTHOR = {Bastide, Paul and Mariadassou, Mahendra and Robin, Stéphane},
  editor    = {Gilles Didier and Stéphane Guindon},
  URL = {https://hal.archives-ouvertes.fr/hal-03762880},
  BOOKTITLE = {{Modèles et méthodes pour l'évolution biologique}},
  PUBLISHER = {{ISTE Group}},
  PAGES = {47 - 85},
  YEAR = {2022},
  MONTH = Jul,
  DOI = {10.51926/iste.9069.ch3},
  KEYWORDS = {modèle d'évolution ; traits quantitatifs ; méthodes phylogénétiques comparatives ; mouvement brownien ; processus d'Ornstein-Uhlenbeck ; calcul de vraisemblance},
  PDF = {https://hal.archives-ouvertes.fr/hal-03762880/file/chapitre_hal.pdf},
  HAL_ID = {hal-03762880},
  HAL_VERSION = {v1}
}

@InBook{Chiquet2022,
  title   = {The Poisson Log-Normal Model: A Generic Framework for Analyzing Joint Abundance Distributions},
  pages     = {157--180},
  booktitle     = {Statistical Approaches for Hidden Variables in Ecology},
  publisher = {Wiley-ISTE},
  year      = {2022},
  author    = {Julien Chiquet and Marie-Josée Cros and Mahendra Mariadassou and Nathalie Peyrard and Stéphane Robin},
  editor    = {Olivier Gimenez and Nathalie Peyrard},
  month     = dec,
  isbn      = {9781789450477},
  optlink   = {https://www.amazon.com/dp/1789450470/}
}

@InBook{Chiquet2022,
  title   = {Le modèle Poisson log-normal pour l'analyse de distributions jointes d'abondance},
  pages     = {175--199},
  booktitle     = {Approches statistiques pour les variables cachées en écologie},
  publisher = {ISTE group},
  year      = {2022},
  author    = {Julien Chiquet and Marie-Josée Cros and Mahendra Mariadassou and Nathalie Peyrard and Stéphane Robin},
  editor    = {Olivier Gimenez and Nathalie Peyrard},
  month     = aug,
  isbn      = {9781789480474},
  optlink   = {https://www.amazon.fr/Approches-statistiques-variables-cach%C3%A9es-%C3%A9cologie/dp/1789480477}
}

@article{10.1158/1055-9965.EPI-21-0188,
    author = {Zouiouich, Semi and Mariadassou, Mahendra and Rué, Olivier and Vogtmann, Emily and Huybrechts, Inge and Severi, Gianluca and Boutron-Ruault, Marie-Christine and Senore, Carlo and Naccarati, Alessio and Mengozzi, Giulio and Kozlakidis, Zisis and Jenab, Mazda and Sinha, Rashmi and Gunter, Marc J. and Leclerc, Marion},
    title = "{Comparison of Fecal Sample Collection Methods for Microbial Analysis Embedded within Colorectal Cancer Screening Programs}",
    journal = {Cancer Epidemiology, Biomarkers & Prevention},
    volume = {31},
    number = {2},
    pages = {305-314},
    year = {2022},
    month = {02},
    issn = {1055-9965},
    doi = {10.1158/1055-9965.EPI-21-0188},
    url = {https://doi.org/10.1158/1055-9965.EPI-21-0188},
    pdf = {https://aacrjournals.org/cebp/article-pdf/31/2/305/3035218/305.pdf},
}

@article{bichat2022hierarchical,
  title={Hierarchical correction of p-values via an ultrametric tree running Ornstein-Uhlenbeck process},
  author={Bichat, Antoine and Ambroise, Christophe and Mariadassou, Mahendra},
  journal={Computational Statistics},
  volume={37},
  number={3},
  pages={995--1013},
  year={2022},
  publisher={Springer},
  url = {http://link.springer.com/article/10.1007/s00180-021-01148-6},
  doi = {10.1007/s00180-021-01148-6},
  pdf = {https://link.springer.com/content/pdf/10.1007/s00180-021-01148-6.pdf}
}

%% ----------- 2021 --------------

@article{Selle2021,
title = {Food allergy prevention in progeny by prebiotic supplementation during pregnancy in a preclinical study},
author = {Amandine Selle and Carole Brosseau and Angéline Duval and Grégory Bouchaud and Anais Rousseaux and Aurélia Bruneau and Claire Cherbuy and Mahendra Mariadassou and Véronique Cariou and Sebastien Barbarot and Marie Bodinier},
journal={Frontiers in Immunology},
volume={12},
pages={4832},
year={2022},
url={https://www.frontiersin.org/article/10.3389/fimmu.2021.745535},
doi={10.3389/fimmu.2021.745535},
pdf = {https://www.frontiersin.org/articles/10.3389/fimmu.2021.745535/pdf}
}

@Article{nu13113865,
AUTHOR = {Jollet, Maxence and Nay, Kevin and Chopard, Angèle and Bareille, Marie-Pierre and Beck, Arnaud and Ollendorff, Vincent and Vernus, Barbara and Bonnieu, Anne and Mariadassou, Mahendra and Rué, Olivier and Derbré, Frédéric and Goustard, Bénédicte and Koechlin-Ramonatxo, Christelle},
TITLE = {Does Physical Inactivity Induce Significant Changes in Human Gut Microbiota? New Answers Using the Dry Immersion Hypoactivity Model},
JOURNAL = {Nutrients},
VOLUME = {13},
YEAR = {2021},
NUMBER = {11},
ARTICLE-NUMBER = {3865},
URL = {https://www.mdpi.com/2072-6643/13/11/3865},
ISSN = {2072-6643},
DOI = {10.3390/nu13113865},
pdf = {https://www.mdpi.com/2072-6643/13/11/3865/pdf}
}

@article{Zhang2021,
title = {Glucose but not fructose alters the  intestinal paracellular permeability in association with gut inflammation and dysbiosis in mice},
author = {Xufei Zhang and Magali Monnoye and Mahendra Mariadassou and Fabienne Beguet-Crespel and Nicolas Lapaque and Christine Heberden and Veronique Douard},
year = {2021},
journal = {Frontiers in Immunology},
url = {https://www.frontiersin.org/article/10.3389/fimmu.2021.742584},
doi = {10.3389/fimmu.2021.742584},
volume = {12},
pages = {4479},
pdf = {https://www.frontiersin.org/articles/10.3389/fimmu.2021.742584/pdf}
}

@article{leclerc2021,
 title = {Nitric Oxide impacts human gut microbiota diversity and functionalities},
 journal = {mSystems},
 author = {Marion Leclerc and Cassandre Bedu-Ferrari and Lucie Etienne Mesmin and Mahendra Mariadassou and Lucie Lebreuilly and Seav Ly Tran and Laurence Brazeau and Camille Mayeur and Julien Delmas and Olivier Rué and Sylvain Denis and Stéphanie Blanquet-Diot and and Nalini Ramarao},
 year = {2021},
 doi = {10.1128/mSystems.00558-21},
 volume = {6},
 issue = {5},
 pages = {e00558-21},
 pdf = {https://journals.asm.org/doi/pdf/10.1128/mSystems.00558-21?download=true}
}

@article{FROGS2,
    author = {Bernard, Maria and Rué, Olivier and Mariadassou, Mahendra and Pascal, Géraldine},
    title = "{FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers}",
    journal = {Briefings in Bioinformatics},
    year = {2021},
    month = {08},
    issn = {1477-4054},
    doi = {10.1093/bib/bbab318},
    url = {https://doi.org/10.1093/bib/bbab318},
    pdf = {https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbab318/39805849/bbab318.pdf?guestAccessKey=c3c28079-333a-432e-9d9e-b4c37da8284d}
}

@article{Lejal2021,
  doi = {10.1186/s40168-021-01051-8},
  url = {https://doi.org/10.1186/s40168-021-01051-8},
  pdf = {https://microbiomejournal.biomedcentral.com/track/pdf/10.1186/s40168-021-01051-8.pdf},
  year = {2021},
  month = jul,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {9},
  number = {1},
  author = {E. Lejal and J. Chiquet and J. Aubert and S. Robin and A. Estrada-Pe{\~{n}}a and O. Rue and C. Midoux and M. Mariadassou and X. Bailly and A. Cougoul and P. Gasqui and J. F. Cosson and K. Chalvet-Monfray and M. Vayssier-Taussat and T. Pollet},
  title = {Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions},
  journal = {Microbiome}
}

@article{CAMARGO2021112631,
title = {Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions},
journal = {Journal of Environmental Management},
volume = {291},
pages = {112631},
year = {2021},
issn = {0301-4797},
doi = {10.1016/j.jenvman.2021.112631},
url = {https://www.sciencedirect.com/science/article/pii/S0301479721006939},
pdf = {https://www.sciencedirect.com/science/article/pii/S0301479721006939/pdfft?isDTMRedir=true&download=true},
author = {Franciele Pereira Camargo and Isabel Kimiko Sakamoto and Tiago Palladino Delforno and Mahendra Mariadassou and Valentin Loux and Cédric Midoux and Iolanda Cristina Silveira Duarte and Edson Luiz Silva and Ariane Bize and Maria Bernadete Amâncio Varesche},
keywords = {Rotational central composite design, Shotgun metagenomics, Carbohydrate-active enzymes, Kyoto encyclopedia of genes and genomes, KEGG Orthology database}
}

@ARTICLE{10.3389/falgy.2021.667562,
AUTHOR={Aydin, Malik and Weisser, Cornelius and Rué, Olivier and Mariadassou, Mahendra and Maaß, Sandra and Behrendt, Ann-Kathrin and Jaszczyszyn, Yan and Heilker, Tatje and Spaeth, Maximilian and Vogel, Silvia and Lutz, Sören and Ahmad-Nejad, Parviz and Graf, Viktoria and Bellm, Aliyah and Weisser, Christoph and Naumova, Ella A. and Arnold, Wolfgang H. and Ehrhardt, Anja and Meyer-Bahlburg, Almut and Becher, Dörte and Postberg, Jan and Ghebremedhin, Beniam and Wirth, Stefan},
TITLE={The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network},
JOURNAL={Frontiers in Allergy},
VOLUME={2},
PAGES={11},
YEAR={2021},
URL={https://www.frontiersin.org/article/10.3389/falgy.2021.667562},
DOI={10.3389/falgy.2021.667562},
ISSN={2673-6101},
pdf = {https://www.frontiersin.org/articles/10.3389/falgy.2021.667562/pdf}
}

@article{chiquet2021,
title = {The Poisson-lognormal model as a versatile framework for the joint analysis of species abundances},
author = {Chiquet, Julien and Mariadassou, Mahendra and Robin, Stephane},
VOLUME={9},
PAGES={188},
YEAR={2021},
URL={https://www.frontiersin.org/article/10.3389/fevo.2021.588292},
DOI={10.3389/fevo.2021.588292},
pdf = {https://www.frontiersin.org/articles/10.3389/fevo.2021.588292/pdf},
journal = {Frontiers in Ecology and Evolution}
}

@article{Bize2021,
  doi = {10.1186/s12864-021-07471-y},
  url = {https://doi.org/10.1186/s12864-021-07471-y},
  pdf = {https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-021-07471-y.pdf},
  year = {2021},
  month = mar,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {22},
  number = {1},
  author = {Ariane Bize and C{\'{e}}dric Midoux and Mahendra Mariadassou and Sophie Schbath and Patrick Forterre and Violette Da Cunha},
  title = {Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history},
  HAL_ID = {hal-03176011},
  journal = {BMC Genomics}
}

@article{Mariadassou2021,
title = {Unraveling the history of the genus Gallus through whole genome sequencing},
journal = {Molecular Phylogenetics and Evolution},
volume = {158},
pages = {107044},
year = {2021},
issn = {1055-7903},
doi = {https://doi.org/10.1016/j.ympev.2020.107044},
url = {https://www.sciencedirect.com/science/article/pii/S105579032030316X},
author = {Mahendra Mariadassou and Marie Suez and Sanbandam Sathyakumar and Alain Vignal and Mariangela Arca and Pierre Nicolas and Thomas Faraut and Diane Esquerré and Masahide Nishibori and Agathe Vieaud and Chih-Feng Chen and Hung {Manh Pham} and Yannick Roman and Frédéric Hospital and Tatiana Zerjal and Xavier Rognon and Michèle Tixier-Boichard},
keywords = {Chicken genomics, Hybridization, Introgression, Domestication},
pdf = {https://www.sciencedirect.com/science/article/pii/S105579032030316X/pdfft?md5=b12dc00280157f06a65823c9ff4eda74&pid=1-s2.0-S105579032030316X-main.pdf}
}

%%% ---------- 2020  -------------

@article{dauge2020,
title = {A probiotic mixture induces anxiolytic-and antidepressive-like effects in Fischer and maternally deprived Long Evans rats},
author = {Daugé, Valérie Marie and Philippe, Catherine and Mariadassou, Mahendra and Rué, Olivier and Martin, Jean-Charles and Rossignol, Marie-Noelle and Dourmap, Nathalie and Svilar, Ljubica and Tourniaire, Franck and Monnoye, Magali and Jardet, Deborah and Bangratz, Marie and Holowacz, Sophie and Rabot, Sylvie and Naudon, Laurent},
journal={Frontiers in Behavioral Neuroscience},
volume={14},
pages={214},
year={2020},
url={https://www.frontiersin.org/article/10.3389/fnbeh.2020.581296},
doi={10.3389/fnbeh.2020.581296},
ISSN={1662-5153},
pdf={https://www.frontiersin.org/article/10.3389/fnbeh.2020.581296/pdf}
}

@article{Canon2020,
 author = {Canon, Fanny and Mariadassou, Mahendra and Maillard, Marie-Bernadette and Falentin, Hélène and Parayre, Sandrine and Madec, Marie-Noëlle and Valence, Florence and Henry, Gwénaële and Laroute,
Valérie and Daveran-Mingot, Marie-Line and Cocaign-Bousquet, Muriel and Thierry, Anne and Gagnaire, Valérie},
 title  = {Function-driven design of lactic acid bacteria co-cultures to produce new fermented food associating milk and lupin},
 year   = {2020},
 journal   = {Frontiers in Microbiology},
 doi = {10.3389/fmicb.2020.584163},
 url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.584163},
 pdf = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.584163/pdf},
 volume = {11},
 pages = {2850},
 ISSN = {1664-302X}
}

@article{mariadassou2019consistency,
  title={Consistency and Asymptotic Normality of Stochastic Block Models Estimators from Sampled Data},
  author={Mariadassou, Mahendra and Tabouy, Timoth{\'e}e},
  volume={14},
  pages={3672--3704},
  number={2},
  journal={Electronic Journal of Statistics},
  doi = {10.1214/20-EJS1750},
  URL = {https://projecteuclid.org/euclid.ejs/1601949675},
  pdf = {https://projecteuclid.org/download/pdfview_1/euclid.ejs/1601949675},
  year={2020}
}

@article{Mariadassou2020,
  author = {Mariadassou, Mahendra and Ramayo-Caldas, Yuliaxis and Charles, Mathieu and Fémenia, Maureen and
Renand, Gilles and Rocha, Dominique},
  title = {Detection of selection signatures in Limousin cattle using whole-genome resequencing},
  journal = {Animal Genetics},
  year = {2020},
  volume = {},
  number = {},
  pages = {},
  keywords = {Limousin breed, polymorphisms, signature of selection, whole-genome resequencing},
  doi = {10.1111/age.12982},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/age.12982},
  pdf = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/age.12982}
}

@article{Lejal2020,
	author = {Lejal, Emilie and Estrada-Pe{\~n}a, Agust{\'\i}n and Marsot, Maud and Cosson, Jean-Fran{\c c}ois and Ru{\'e}, Olivier and Mariadassou, Mahendra and Midoux, C{\'e}dric and Vayssier-Taussat, Muriel and Pollet, Thomas},
	title = {Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis},
	elocation-id = {714030},
	year = {2020},
	volume={11},
	pages={1093},
	doi = {10.3389/fmicb.2020.01093},
	URL = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.01093},
	pdf = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.01093/pdf},
	journal = {Frontiers in Microbiology},
	ISSN={1664-302X}
}

@article{Bichat2020,
title = {Incorporating phylogenetic information in microbiome abundance studies has no effect on detection power and FDR control},
author = {Bichat, Antoine and Plassais, Jonathan and Ambroise, Christophe and Mariadassou, Mahendra},
year = {2020},
volume={11},
pages={649},
url={https://www.frontiersin.org/article/10.3389/fmicb.2020.00649},
ISSN={1664-302X},
doi = {10.3389/fmicb.2020.00649},
pdf = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.00649/pdf},
journal = {Frontiers in Microbiology},
}

@article{Naudon2020,
title = "First step of odorant detection in the olfactory epithelium and olfactory preferences differ according to the microbiota profile in mice",
journal = "Behavioural Brain Research",
volume = "384",
pages = "112549",
year = "2020",
issn = "0166-4328",
doi = "https://doi.org/10.1016/j.bbr.2020.112549",
url = "http://www.sciencedirect.com/science/article/pii/S0166432819314950",
pdf = {https://www.sciencedirect.com/science/article/pii/S0166432819314950/pdfft?md5=b6f53e61c9d0b52087b7e9f410ca7d66&pid=1-s2.0-S0166432819314950-main.pdf},
author = "Laurent Naudon and Adrien François and Mahendra Mariadassou and Magali Monnoye and Catherine Philippe and Aurélia Bruneau and Marie Dussauze and Olivier Rué and Sylvie Rabot and Nicolas Meunier",
keywords = "Olfaction, Microbiota, Olfactory epithelium",
}

@article{Brault2020,
  TITLE = {{Consistency and Asymptotic Normality of Latent Blocks Model Estimators}},
  AUTHOR = {Brault, Vincent and Keribin, Christine and Mariadassou, Mahendra},
  URL = {https://hal.archives-ouvertes.fr/hal-01511960},
   JOURNAL = {Electron. J. Statist.},
  FJOURNAL = {Electronic Journal of Statistics},
      YEAR = {2020},
    VOLUME = {14},
    NUMBER = {1},
     PAGES = {1234-1268},
      ISSN = {1935-7524},
       DOI = {10.1214/20-EJS1695},
      SICI = {1935-7524(2020)14:1<1234:CAANOL>2.0.CO;2-7},
  KEYWORDS = {Latent Block Model ; asymptotic normality ; Maximum Likelihood Estimate ; Concentration Inequality},
  PDF = {https://hal.archives-ouvertes.fr/hal-01511960/file/bj-BraultKeribinMariadassou.pdf},
  HAL_ID = {hal-01511960},
  HAL_VERSION = {v1},
}

@article{Safari2020,
author = {Zahra Safari and Aurélia Bruneau and Magali Monnoye and Mahendra Mariadassou and Catherine Philippe and Kurt Zatloukal and Philippe Gérard},
title = {Murine Genetic Background Overcomes Gut Microbiota Changes to Explain Metabolic Response to High-Fat Diet},
journal = {Nutrients},
year = {2020},
doi = {https://doi.org/10.3390/nu12020287},
url = {https://www.mdpi.com/2072-6643/12/2/287/htm},
pdf = {https://www.mdpi.com/2072-6643/12/2/287/pdf},
volume = {12},
pages = {287}
}

%%% ---------- 2019  -------------

@article{Wenden2019,
author = {B. Wenden and M. Mariadassou and F. Chmielewski and Y. Vitasse},
title = {Shifts in the temperature-sensitive periods for spring phenology in European beech and pedunculate oak clones across latitudes and over recent decades},
journal = {Global Change Biology},
year = {2019},
doi = {https://doi.org/10.1111/gcb.14918},
pdf = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/gcb.14918},
volume = {26},
issue = {5},
pages = {1808--1819}
}

@article{Vila2019,
 author = {M. Vila Nova and K. Durimel and K. La and A. Felten and P. Bessières and M.-Y. Mistou and M. Mariadassou and N. Radomski},
 title = {Genetic and metabolic signatures of \emph{Salmonella enterica subsp. {E}nterica} associated to animal sources at the pangenomic scale},
 year = {2019},
 volume = {20},
 pages = {814},
 journal = {BMC Genomics},
 doi = {doi:10.1186/s12864-019-6188-x},
 url = {https://doi.org/10.1186/s12864-019-6188-x},
 pdf = {https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-019-6188-x}
}

@article{guide_pratique_metab,
title = {Guide pratique à destination des biologistes, bioinformaticiens et statisticiens qui souhaitent s’initier aux analyses métabarcoding},
author = {Falentin, Hélène and Auer, Lucas and Mariadassou, Mahendra and Pascal, Géraldine and Rué, Olivier and Dugat-Bony, Éric and Delbès, Céline and Nicolas, Aurélie and Rifa, Étienne and Mondy, Samuel
and Le Boulch, Malo and Cauquil, Laurent and Hernandez-Raquet, Guillermina and Terrat, Sébastien and Abraham, Anne-Laure},
year = {2019},
journal = {Les Cahiers Techniques de l'INRA},
volume = {97},
optlink = {https://www6.inra.fr/cahier_des_techniques/Les-Cahiers-parus/Les-N-reguliers/2019/Cahier-N-97/Art4-ct97-2019},
pdf = {https://www6.inra.fr/cahier_des_techniques/content/download/5278/53753/version/2/file/CT97_Art4_Falentin+et+al.pdf}
}

@article{Safari2019,
title = "Steatosis and gut microbiota dysbiosis induced by high fat diet are reversed by one-week chow diet administration",
journal = "Nutrition Research",
year = "2019",
issn = "0271-5317",
volume = "71",
pages = "72--88",
doi = "https://doi.org/10.1016/j.nutres.2019.09.004",
url = "http://www.sciencedirect.com/science/article/pii/S0271531719304270",
pdf = {https://www.sciencedirect.com/science/article/pii/S0271531719304270/pdf?md5=db74ea2145f6141bcf6c83ddf8c5fb7d&pid=1-s2.0-S0271531719304270-main.pdf},
author = "Zahra Safari and Magali Monnoye and Peter M. Abuja and Mahendra Mariadassou and Karl Kashofer and Philippe Gérard and Kurt Zatloukal",
keywords = "Reversibility, Microbiome, Liver Steatosis, NAFLD, High Fat Diet, Diet Switch",
}

@article{Lemaitre2019,
    author = {Benoit, Gaetan and Mariadassou, Mahendra and Robin, Stéphane and Schbath, Sophie and Peterlongo, Pierre and Lemaitre, Claire},
    title = "{SimkaMin: fast and resource frugal de novo comparative metagenomics}",
    journal = {Bioinformatics},
    year = {2019},
    month = {09},
    abstract = "{De novo comparative metagenomics is one of the most straightforward ways to analyze large sets of metagenomics data. Latest methods use the fraction of shared k-mers to estimate genomic similarity between read sets. However, those methods, while extremely efficient, are still limited by computational needs for practical usage outside of large computing facilities.We present SimkaMin, a quick comparative metagenomics tool with low disk and memory footprints, thanks to an efficient data subsampling scheme used to estimate Bray-Curtis and Jaccard dissimilarities. One billion metagenomic reads can be analyzed in less than 3 minutes, with tiny memory (1.09 GB) and disk (≈0.3 GB) requirements and without altering the quality of the downstream comparative analyses, making of SimkaMin a tool perfectly tailored for very large-scale metagenomic projects.https://github.com/GATB/simka}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btz685},
    url = {https://doi.org/10.1093/bioinformatics/btz685},
    note = {btz685},
    eprint = {http://oup.prod.sis.lan/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz685/29520698/btz685.pdf},
    pdf = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz685/29520698/btz685.pdf?guestAccessKey=b5eee976-0096-4a93-8f5e-de6e74103088}
}

@Article{Chiquet2019,
  title = 	 {Variational Inference for sparse network reconstruction from count data},
  author = 	 {Chiquet, Julien and Robin, Stephane and Mariadassou, Mahendra},
  booktitle = 	 {Proceedings of the 36th International Conference on Machine Learning},
  pages = 	 {1162--1171},
  year = 	 {2019},
  editor = 	 {Chaudhuri, Kamalika and Salakhutdinov, Ruslan},
  volume = 	 {97},
  series = 	 {Proceedings of Machine Learning Research},
  address = 	 {Long Beach, California, USA},
  month = 	 {June},
  publisher = 	 {PMLR},
  pdf = 	 {http://proceedings.mlr.press/v97/chiquet19a/chiquet19a.pdf},
  optlink = 	 {http://proceedings.mlr.press/v97/chiquet19a.html}
}

@article{Nay2019,
author = {Nay, Kevin and Jollet, Maxence and Goustard, Benedicte and Baati, Narjes and Vernus, Barbara and Pontones, Maria and Lefeuvre-Orfila, Luz and Bendavid, Claude and Rué, Olivier and Mariadassou, Mahendra and Bonnieu, Anne and Ollendorff, Vincent and Lepage, Patricia and Derbré, Frédéric and Koechlin-Ramonatxo, Christelle},
title = {Gut bacteria are critical for optimal muscle function: a potential link with glucose homeostasis},
journal = {American Journal of Physiology-Endocrinology and Metabolism},
volume = {317},
number = {1},
pages = {E158-E171},
year = {2019},
doi = {10.1152/ajpendo.00521.2018},
note ={PMID: 31039010},
pdf = {https://www.physiology.org/doi/pdf/10.1152/ajpendo.00521.2018},
URL = {https://doi.org/10.1152/ajpendo.00521.2018},
eprint = {https://doi.org/10.1152/ajpendo.00521.2018}
}

@article{Zhang2019,
author = {Zhang, Xufei and Grosfeld, Alexandra and Williams, Edek and Vasiliauskas, Daniel and Barretto, Sharon and Smith, Lorraine and Mariadassou, Mahendra and Philippe, Catherine and Devime, Fabienne and Melchior, Chloé and Gourcerol, Guillaume and Dourmap, Nathalie and Lapaque, Nicolas and Larraufie, Pierre and Blottière, Hervé M. and Herberden, Christine and Gerard, Philippe and Rehfeld, Jens F. and Ferraris, Ronaldo P. and Fritton, J. Christopher and Ellero-Simatos, Sandrine and Douard, Veronique},
title = {Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism},
journal = {The FASEB Journal},
volume = {33},
pages = {7126 - 7142},
year = {2019},
doi = {10.1096/fj.201801526RR},
note ={PMID: 30939042},
pdf = {https://www.fasebj.org/doi/pdf/10.1096/fj.201801526RR},
URL = {https://doi.org/10.1096/fj.201801526RR},
eprint = {https://doi.org/10.1096/fj.201801526RR}
}

@Article{Delforno2019,
title = "Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater",
journal = "Science of The Total Environment",
volume = "649",
pages = "482 - 494",
year = "2019",
issn = "0048-9697",
doi = "10.1016/j.scitotenv.2018.08.328",
url = "http://www.sciencedirect.com/science/article/pii/S0048969718332996",
author = "Tiago P. Delforno and Thais Z. Macedo and Cédric Midoux and Gileno V. Lacerda and Olivier Rué and Mahendra Mariadassou and Valentin Loux and Maria B.A. Varesche and Théodore Bouchez and Ariane Bize and Valéria M. Oliveira",
pdf   = "https://www.sciencedirect.com/science/article/pii/S0048969718332996/pdfft?md5=4d93013993cd24f1821587eab8198ad1&pid=1-s2.0-S0048969718332996-main.pdf"
}

@InBook{Mariadassou2018,
  title = "Tree Evaluation and Robustness Testing",
  editor = "Shoba Ranganathan and Michael Gribskov and Kenta Nakai and Christian Schönbach",
  booktitle = "Encyclopedia of Bioinformatics and Computational Biology",
  publisher = "Academic Press",
  address = "Oxford",
  pages = "736 - 745",
  year = "2019",
  isbn = "978-0-12-811432-2",
  doi = "10.1016/B978-0-12-809633-8.20259-8",
  url = "http://www.sciencedirect.com/science/article/pii/B9780128096338202598",
  pdf = "https://www.sciencedirect.com/science/article/pii/B9780128096338202598/pdfft?md5=eb60d2910602e5597274430d499a8b56&pid=3-s2.0-B9780128096338202598-main.pdf",
  author = "Mahendra Mariadassou and Avner Bar-Hen and Hirohisa Kishino",
  keywords = "Bootstrap, Model misspecification, Outlier detection, Phylogenetic inference, Robustness, Tree distances"
}

%%% ---------- 2018  -------------

@Article{Bastide2018,
    Title                    = {Inference of Adaptive Shifts for Multivariate Correlated Traits},
    Author                   = {Bastide, Paul and Ané, Cécile and Robin, Stéphane and Mariadassou, Mahendra},
    Journal                  = {Systematic Biology},
    volume = {67},
    number = {4},
    pages = {662-680},
    year = {2018},
    Doi                      = {10.1093/sysbio/syy005},
    PDF                      = {https://www.biorxiv.org/content/early/2017/06/05/146191.full.pdf},
    Owner                    = {mmariadasso},
    Timestamp                = {2018.02.17},
    Url                      = {http://dx.doi.org/10.1093/sysbio/syy005}
}

@article{Chiquet2018,
  TITLE = {{Variational inference for probabilistic Poisson PCA}},
  AUTHOR = {Chiquet, Julien and Mariadassou, Mahendra and Robin, Stéphane},
  URL = {https://hal.archives-ouvertes.fr/hal-01608912},
  Journal = {Ann. Appl. Stat.},
  Volume = {4},
  PAGES = {2674--2698},
  YEAR = {2018},
  KEYWORDS = { variational inference ; probabilistic PCA  ; poisson-lognormal model ; count data},
  PDF = {https://hal.archives-ouvertes.fr/hal-01608912/file/variational_%7BCE66C6D5-8A36-4981-BF8A-04F537890B08%7D.pdf},
  HAL_ID = {hal-01608912},
  Doi = {10.1214/18-AOAS1177}
}

@Article{Cornuault2018,
  Title                    = {{Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes}},
  Author                   = {Cornuault, Jeffrey K. and Petit, Marie-Agn{\`e}s and Mariadassou, Mahendra and Benevides, Leandro and Moncaut, Elisabeth and Langella, Philippe and Sokol, Harry and De Paepe, Marianne},
  Journal                  = {{Microbiome}},
  Year                     = {2018},
  Volume                   = {6},
  Pages                    = {65},
  Doi                      = {10.1186/s40168-018-0452-1},
  PDF                      = {https://microbiomejournal.biomedcentral.com/track/pdf/10.1186/s40168-018-0452-1},
  Hal_id                   = {hal-01774632},
  Hal_version              = {v1},
  Publisher                = {{ BioMed Central}},
  Url                      = {http://hal.upmc.fr/hal-01774632}
}

@Article{Escudie2018,
  Title                    = {FROGS: Find, Rapidly, OTUs with Galaxy Solution},
  Author                   = {Escudié, Frédéric and Auer, Lucas and Bernard, Maria and Mariadassou, Mahendra and Cauquil, Laurent and Vidal, Katia and Maman, Sarah and Hernandez-Raquet, Guillermina and Combes, Sylvie and Pascal, Géraldine},
  Journal                  = {Bioinformatics},
  Year                     = {2018},
  Number                   = {8},
  Pages                    = {1287-1294},
  Volume                   = {34},
  Doi                      = {10.1093/bioinformatics/btx791},
  PDF                      = {https://academic.oup.com/bioinformatics/article-pdf/34/8/1287/25120139/btx791.pdf?guestAccessKey=a3b4c7f6-d18e-43a0-971e-8f6422c67f56},
  Url                      = {http://dx.doi.org/10.1093/bioinformatics/btx791}
}

@inproceedings{MCR18,
author = {Mariadassou, Mahendra. and Chiquet, Julien. and Robin, Stéphane.},
title= {Probabilistic PCA for count data in microbial ecology},
booktitle   = {Proceedings of the 2018 JOBIM edition},
year= {2018},
pages     = {30 -- 32},
url       = {https://jobim2018.sciencesconf.org/data/pages/Book_JOBIM2018_V3.pdf}
}

%%% ---------- 2017  -------------

@Article{Auer2017,
  Title                    = {Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description},
  Author                   = {Auer, Lucas and Mariadassou, Mahendra and O'Donohue, Michael and Klopp, Christophe and Hernandez-Raquet, Guillermina},
    Journal                  = {Molecular Ecology Resources},
    Year                     = {2017},
    Volume                   = {17},
    Number                   = {6},
    Pages                    = {e122-e132},
    Doi                      = {10.1111/1755-0998.12700},
    ISSN                     = {1755-0998},
    Keywords                 = {16SrRNA, Illumina, metabarcoding, microbial diversity, singleton filtering},
    Owner                    = {mmariadasso},
    Timestamp                = {2017.08.03},
    Url                      = {http://dx.doi.org/10.1111/1755-0998.12700},
    PDF                      = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.12700}
  }

@Article{Bastide2017,
    Title                    = {Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree},
    Author                   = {Bastide, Paul and Mariadassou, Mahendra and Robin, Stéphane},
    Journal                  = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
    Year                     = {2017},
    Number                   = {4},
    Pages                    = {1067--1093},
    Volume                   = {79},
    Doi                      = {10.1111/rssb.12206},
    ISSN                     = {1467-9868},
    Keywords                 = {Adaptive shifts, Change point detection, Model selection, Ornstein–Uhlenbeck process, Phylogeny, Random process on tree},
    PDF                      = {https://rss.onlinelibrary.wiley.com/doi/epdf/10.1111/rssb.12206},
    Url                      = {http://dx.doi.org/10.1111/rssb.12206}
}

@Article{Deutsch2017,
  Title                    = {Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study},
  Author                   = {Stéphanie-Marie Deutsch and Mahendra Mariadassou and Pierre Nicolas and Sandrine Parayre and Rozenn Le Guellec and Victoria Chuat and Vincent Peton and Caroline Le Maréchal and Julien Burati and Valentin Loux and Valérie Briard-Bion and Julien Jardin and Coline Plé and Benoît Foligné and Gwénaël Jan and Hélène Falentin},
  Journal                  = {Scientific Reports},
  Year                     = {2017},
  Pages                    = {46409},
  Volume                   = {7},
  Doi                      = {10.1038/srep46409},
  PDF                      = {https://www.nature.com/articles/srep46409.pdf}
}

@Article{ElKafsi2017,
  Title                    = {Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue},
  Author                   = {El Kafsi, Hela and Loux, Valentin and Mariadassou, Mahendra and Blin, Camille and Chiapello, Hélène and Abraham, Anne-Laure and Maguin, Emmanuelle and van de Guchte, Maarten},
  Journal                  = {Scientific Reports},
  Year                     = {2017},
  Pages                    = {44331},
  Volume                   = {7},
  Doi                      = {10.1038/srep44331},
  PDF                      = {https://www.nature.com/articles/srep44331.pdf},
  ISSN                     = {2045-2322},
  Publisher                = {Springer Nature},
  Url                      = {http://dx.doi.org/10.1038/srep44331}
}

@Article{Segovia2017,
  Title                    = {OH1 from Orf Virus: A New Tyrosine Phosphatase that Displays Distinct Structural Features and Triple Substrate Specificity},
  Author                   = {Danilo Segovia and Ahmed Haouz and Darío Porley and Natalia Olivero and Mariano Martínez and Mahendra Mariadassou and Mabel Berois and Gwenaëlle André-Leroux and Andrea Villarino},
  Journal                  = {Journal of Molecular Biology},
  Year                     = {2017},
  Number                   = {18},
  Pages                    = {2816 - 2824},
  Volume                   = {429},
  Crossref                 = {2018},
  Doi                      = {10.1016/j.jmb.2017.07.017},
  ISSN                     = {0022-2836},
  pdf                      = {https://www.sciencedirect.com/science/article/pii/S0022283617303674/pdfft?isDTMRedir=true&download=true},
  Keywords                 = {crystallography, Orf virus, tyrosine phosphatase, phosphatidylinositol},
  Timestamp                = {2018.02.17},
  Url                      = {http://www.sciencedirect.com/science/article/pii/S0022283617303674}
}

@InProceedings{Wenden2017a,
  Title                    = {Statistical analysis of trends in sweet cherry flowering data across Europe},
  Author                   = {Wenden, B. and Mariadassou, M and Campoy, J.A. and Quero-Garcia, J. and Dirlewanger, E.},
  Year                     = {2017},
  Pages                    = {215--220},
  Volume                   = {1160},
  Booktitle                = {Acta Horticulturae},
  doi                      = {10.17660/ActaHortic.2017.1160.31}
}

@InProceedings{Wenden2017b,
  Title                    = {Sweet cherry phenology in the context of climate change: A systems biology approach},
  Author                   = {Wenden, Bénédicte and Mariadassou, M},
  Year                     = {2017},
  Pages                    = {31-38},
  Volume                   = {1162},
  Booktitle                = {Acta Horticulturae},
  doi                      = {10.17660/ActaHortic.2017.1162.6}
}

%%% ---------- 2016  -------------

@Article{Alard2016,
  Title                    = {Beneficial metabolic effects of selected probiotics on diet-induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota},
  Author                   = {Alard, Jeanne and Lehrter, Véronique and Rhimi, Moez and Mangin, Irène and Peucelle, Véronique and Abraham, Anne-Laure and Mariadassou, Mahendra and Maguin, Emmanuelle and Waligora-Dupriet, Anne-Judith and Pot, Bruno and Wolowczuk, Isabelle and Grangette, Corinne},
  Journal                  = {Environmental Microbiology},
  Year                     = {2016},
  journal = {Environmental Microbiology},
  volume = {18},
  number = {5},
  pages = {1484-1497},
  doi = {10.1111/1462-2920.13181},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.13181},
  ISSN                     = {1462-2920},
  Pmid                     = {26689997},
  PDF                      = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.13181}
}

@Article{Benoit2016,
  Title                    = {Multiple comparative metagenomics using multiset \textit{k}-mer counting},
  Author                   = {Benoit, Gaëtan and Peterlongo, Pierre and Mariadassou, Mahendra and Drezen, Erwan and Schbath, Sophie and Lavenier, Dominique and Lemaitre, Claire},
  Journal                  = {PeerJ Computer Science},
  Year                     = {2016},
  Pages                    = {e94},
  Volume                   = {2},
  Doi                      = {10.7717/peerj-cs.94},
  ISSN                     = {2376-5992},
  Keywords                 = {Comparative metagenomics, k-mer, k-mer counting, Metagenomic, Large scale, Ecological distance, Ngs},
  PDF                      = {https://peerj.com/articles/cs-94.pdf},
  Url                      = {https://doi.org/10.7717/peerj-cs.94}
}

@Article{Francois2016,
  Title                    = {Olfactory epithelium changes in germfree mice},
  Author                   = {Adrien François and Denise Grebert and Moez Rhimi and Mahendra Mariadassou and Laurent Naudon and Sylvie Rabot and Nicolas Meunier},
  Journal                  = {Scientific Reports},
  Year                     = {2016},
  Pages                    = {24687},
  Volume                   = {6},
  Doi                      = {10.1038/srep24687},
  PDF                      = {https://www.nature.com/articles/srep24687.pdf}
}

@Article{Metzger2016,
  Title                    = {The Red Queen lives: Epistasis between linked resistance loci},
  Author                   = {Metzger, César M. J. A. and Luijckx, Pepijn and Bento, Gilberto and Mariadassou, Mahendra and Ebert, Dieter},
  Journal                  = {Evolution},
  Year                     = {2016},
  Number                   = {2},
  Pages                    = {480--487},
  Volume                   = {70},
  Doi                      = {10.1111/evo.12854},
  ISSN                     = {1558-5646},
  Url                      = {http://dx.doi.org/10.1111/evo.12854},
  PDF                      = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/evo.12854}
}

%%% ---------- 2015  -------------

@Article{Brault2015,
  Title                    = {Co-clustering through Latent Bloc Model: a Review},
  Author                   = {Brault, Vincent and Mariadassou, Mahendra},
  Journal                  = {Journal de la SFdS},
  Year                     = {2015},
  Number                   = {3},
  Pages                    = {120--139},
  Volume                   = {156},
  PDF                      = {http://journal-sfds.fr/article/view/474/448},
  optlink                      = {http://revues-sfds.math.cnrs.fr/index.php/J-SFdS/article/view/474}
}

@Article{Goelzer2015,
  Title                    = {Quantitative prediction of genome-wide resource allocation in bacteria},
  Author                   = {Anne Goelzer and Jan Muntel and Victor Chubukov and Matthieu Jules and Eric Prestel and Rolf Nölker and Mahendra Mariadassou and Stéphane Aymerich and Michael Hecker and Philippe Noirot and Dörte Becher and Vincent Fromion},
  Journal                  = {Metabolic Engineering},
  Year                     = {2015},
  Pages                    = {232 - 243},
  Volume                   = {32},
  Doi                      = {10.1016/j.ymben.2015.10.003},
  ISSN                     = {1096-7176},
  Keywords                 = {Resource allocation},
  Url                      = {http://www.sciencedirect.com/science/article/pii/S1096717615001317}
}

@Article{Loux2015,
  Title                    = {Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii},
  Author                   = {Loux, Valentin
    and Mariadassou, Mahendra
    and Almeida, Sintia
    and Chiapello, Hélène
    and Hammani, Amal
    and Buratti, Julien
    and Gendrault, Annie
    and Barbe, Valérie
    and Aury, Jean-Marc
    and Deutsch, Stéphanie-Marie
    and Parayre, Sandrine
    and Madec, Marie-Noëlle
    and Chuat, Victoria
    and Jan, Gwenaël
    and Peterlongo, Pierre
    and Azevedo, Vasco
    and Le Loir, Yves
    and Falentin, Hélène},
  Journal                  = {BMC Genomics},
  Year                     = {2015},
  Number                   = {1},
  Pages                    = {296},
  Volume                   = {16},
  Doi                      = {10.1186/s12864-015-1467-7},
  PDF                      = {https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-015-1467-7},
  ISSN                     = {1471-2164},
  Url                      = {http://dx.doi.org/10.1186/s12864-015-1467-7}
}

@Article{Mariadassou2015a,
  Title                    = {Convergence of the groups posterior distribution in latent or stochastic block models},
  Author                   = {Mariadassou, Mahendra and Matias, Catherine},
  Journal                  = {Bernoulli},
  Year                     = {2015},
  Month                    = {02},
  Number                   = {1},
  Pages                    = {537--573},
  Volume                   = {21},
  Doi                      = {10.3150/13-BEJ579},
  PDF                      = {https://projecteuclid.org/download/pdfview_1/euclid.bj/1426597081},
  Fjournal                 = {Bernoulli},
  Publisher                = {Bernoulli Society for Mathematical Statistics and Probability},
  Url                      = {http://dx.doi.org/10.3150/13-BEJ579}
}

@Article{Mariadassou2015,
  Title                    = {Microbial ecosystems are dominated by specialist taxa},
  Author                   = {Mariadassou, Mahendra and Pichon, Samuel and Ebert, Dieter},
  Journal                  = {Ecology Letters},
  Year                     = {2015},
  Number                   = {9},
  Pages                    = {974--982},
  Volume                   = {18},
  Doi                      = {10.1111/ele.12478},
  PDF                      = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/ele.12478},
  ISSN                     = {1461-0248},
  Url                      = {http://dx.doi.org/10.1111/ele.12478},
  OPTLINK                  = {http://genome.jouy.inra.fr/~mmariadasso/website/source/specificity_methods.tar.gz}
}

@Article{Roulin2015,
  Title                    = {High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation?},
  Author                   = {Roulin, Anne C. and Mariadassou, Mahendra and Hall, Matthew D. and Walser, Jean-Claude and Haag, Christoph and Ebert, Dieter},
  Journal                  = {Evolution},
  Year                     = {2015},
  Number                   = {10},
  Pages                    = {2747--2756},
  Volume                   = {69},
  Doi                      = {10.1111/evo.12770},
  PDF                      = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/evo.12770},
  ISSN                     = {1558-5646},
  Url                      = {http://dx.doi.org/10.1111/evo.12770}
}

%%% ---------- 2014  -------------

@Article{Mariadassou2014,
  Title                    = {Identification of amino acids in mitochondrially encoded proteins that correlate with lifespan.},
  Author                   = {Mariadassou, Mahendra and Pellay, Fran{\c{c}}ois-Xavier},
  Journal                  = {Exp Gerontol},
  Year                     = {2014},
  Pages                    = {53--58},
  Volume                   = {56},
  Doi                      = {10.1016/j.exger.2014.03.009},
  PDF                      = {},
  Pmid                     = {24657631},
  Url                      = {http://dx.doi.org/10.1016/j.exger.2014.03.009}
}

@Article{SantosRocha2014,
  Title                    = {Local and Systemic Immune Mechanisms Underlying the Anti-Colitis Effects of the Dairy Bacterium \textit{Lactobacillus delbrueckii}},
  Author                   = {Santos Rocha, Clarissa AND Gomes-Santos, Ana Cristina AND Garcias Moreira, Thais AND de Azevedo, Marcela AND Diniz Luerce, Tessalia AND Mariadassou, Mahendra AND Longaray Delamare, Ana Paula AND Langella, Philippe AND Maguin, Emmanuelle AND Azevedo, Vasco AND Caetano de Faria, Ana Maria AND Miyoshi, Anderson AND van de Guchte, Maarten},
  Journal                  = {PLoS ONE},
  Year                     = {2014},
  Number                   = {1},
  Pages                    = {e85923},
  Volume                   = {9},
  Doi                      = {10.1371/journal.pone.0085923},
  PDF                      = {https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0085923&type=printable},
  Publisher                = {Public Library of Science},
  Url                      = {http://dx.doi.org/10.1371%2Fjournal.pone.0085923}
}

%%% ---------- 2013  -------------

@Article{Gibrat2013,
  Title                    = {Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods.},
  Author                   = {Gibrat, Jean-François and Mariadassou, Mahendra and Boudinot, Pierre and Delmas, Bernard},
  Journal                  = {BMC Evol Biol},
  Year                     = {2013},
  Pages                    = {154},
  Volume                   = {13},
  Doi                      = {10.1186/1471-2148-13-154},
  PDF                      = {https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/1471-2148-13-154},
  Pmid                     = {23865988},
  Url                      = {http://dx.doi.org/10.1186/1471-2148-13-154}
}

%%% ---------- 2012  -------------

@Article{Mariadassou2012,
  Title                    = {Taxon influence index: assessing taxon-induced incongruities in phylogenetic inference.},
  Author                   = {Mahendra Mariadassou and Avner Bar-Hen and Hirohisa Kishino},
  Journal                  = {Syst Biol},
  Year                     = {2012},
  Number                   = {2},
  Pages                    = {337--345},
  Volume                   = {61},
  Doi                      = {10.1093/sysbio/syr129},
  PDF                      = {https://academic.oup.com/sysbio/article-pdf/61/2/337/24563223/syr129.pdf},
  Pmid                     = {22228800},
  Url                      = {http://dx.doi.org/10.1093/sysbio/syr129},
  OPTLINK                  = {http://genome.jouy.inra.fr/~mmariadasso/website/source/TaxonInfluenceIndex.tar.gz}
}

%%% ---------- 2011  -------------

@Article{Szczepankowska2011,
  Title                    = {Phylogenetic and complementation analysis of a single-stranded DNA binding protein family from lactococcal phages indicates a non-bacterial origin.},
  Author                   = {Agnieszka K Szczepankowska and Eric Prestel and Mahendra Mariadassou and Jacek K Bardowski and Elena Bidnenko},
  Journal                  = {PLoS One},
  Year                     = {2011},
  Number                   = {11},
  Pages                    = {e26942},
  Volume                   = {6},
  Doi                      = {10.1371/journal.pone.0026942},
  PDF                      = {https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0026942&type=printable},
  Pii                      = {PONE-D-11-14025},
  Pmid                     = {22073223},
  Url                      = {http://dx.doi.org/10.1371/journal.pone.0026942}
}

%%% ---------- 2010  -------------

@Article{Mariadassou2010,
  Title                    = {Uncovering latent structure in valued graphs: A variational approach},
  Author                   = {Mariadassou, Mahendra and Robin, Stéphane and Vacher, Corinne},
  Journal                  = {The Annals of Applied Statistics},
  Year                     = {2010},
  Month                    = {06},
  Number                   = {2},
  Pages                    = {715--742},
  Volume                   = {4},
  Journal                  = {Ann. Appl. Stat.},
  Doi                      = {10.1214/10-AOAS361},
  PDF                      = {https://projecteuclid.org/download/pdfview_1/euclid.aoas/1280842137},
  Publisher                = {The Institute of Mathematical Statistics},
  Url                      = {http://dx.doi.org/10.1214/10-AOAS361}
}

%%% ---------- 2009  -------------

@Article{Mariadassou2009,
  Title                    = {Concentration inequality for evolutionary trees},
  Author                   = {Mariadassou, Mahendra and Bar-Hen, A.},
  Journal                  = {Journal of Multivariate Analysis},
  Year                     = {2009},
  Pages                    = {2055--2064},
  Volume                   = {100},
  Doi                      = {10.1016/j.jmva.2009.02.015},
  PDF                      = {https://www.sciencedirect.com/science/article/pii/S0047259X09000499/pdfft?md5=88a8e5ccfce29decee3861fd5ff6e7a4&pid=1-s2.0-S0047259X09000499-main.pdf},
}

%%% ---------- 2008  -------------

@Article{Bar-Hen2008,
    Title                    = {Influence function for robust phylogenetic reconstructions.},
    Author                   = {Avner Bar-Hen and Mahendra Mariadassou and Marie-Anne Poursat and Philippe Vandenkoornhuyse},
    Journal                  = {Mol Biol Evol},
    Year                     = {2008},

    Month                    = {May},
    Number                   = {5},
    Pages                    = {869--873},
    Volume                   = {25},
    Doi                      = {10.1093/molbev/msn030},
    PDF                      = {https://academic.oup.com/mbe/article-pdf/25/5/869/4031426/msn030.pdf},
    Keywords                 = {Data Interpretation, Statistical; Evolution; Fungi; Likelihood Functions; Phylogeny; Software; Statistics as Topic},
    Pmid                     = {18263606},
    Url                      = {http://dx.doi.org/10.1093/molbev/msn030}
    }


text:
@InProceedings{chung15,
  supplementary = {Supplementary:chung15-supp.pdf},
  title = {Gated Feedback Recurrent Neural Networks},
  author = {Junyoung Chung and Caglar Gulcehre and Kyunghyun Cho and Yoshua Bengio},
  pages = {2067-2075},
  abstract = {In this work, we propose a novel recurrent neural network (RNN) architecture. The proposed RNN, gated-feedback RNN (GF-RNN), extends the existing approach of stacking multiple recurrent layers by allowing and controlling signals flowing from upper recurrent layers to lower layers using a global gating unit for each pair of layers. The recurrent signals exchanged between layers are gated adaptively based on the previous hidden states and the current input. We evaluated the proposed GF-RNN with different types of recurrent units, such as tanh, long short-term memory and gated recurrent units, on the tasks of character-level language modeling and Python program evaluation. Our empirical evaluation of different RNN units, revealed that in both tasks, the GF-RNN outperforms the conventional approaches to build deep stacked RNNs. We suggest that the improvement arises because the GF-RNN can adaptively assign different layers to different timescales and layer-to-layer interactions (including the top-down ones which are not usually present in a stacked RNN) by learning to gate these interactions.},
}

repository: mreid/papersite

repo_name: mreid/papersite

gha_language: TeX


text:
require vpnc.inc

PR = "r1"

SRC_URI = "http://www.unix-ag.uni-kl.de/~massar/vpnc/vpnc-${PV}.tar.gz"


text:
LICENSE = GPL
SECTION = "x11/utils"
PR = "r2"

inherit gnome gettext

DEPENDS = "gtk+ libgnomeui libbonoboui gnome-vfs gconf gettext libglade \
	libgnomeprint libgnomeprintui gnome-common"

EXTRA_OECONF = "--disable-schemas-install"

SRC_URI += "file://aclocal-lossage.patch;patch=1 \
	file://desktop.patch;patch=1"

repository: BackupTheBerlios/openslug-svn

repo_name: BackupTheBerlios/openslug-svn


text:
SECTION = "libs"
LICENSE = "LGPL"
PRIORITY = "optional"
DEPENDS = "libsvg cairo"
DESCRIPTION = "SVG rendering library"

SRC_URI = "http://cairographics.org/snapshots/libsvg-cairo-${PV}.tar.gz"

inherit autotools pkgconfig

do_stage () {
	oe_runmake install DESTDIR="" bindir=${STAGING_BINDIR} includedir=${STAGING_INCDIR} libdir=${STAGING_LIBDIR} prefix=${STAGING_DIR}
}

repository: jdegges/gumstix-pip-oe

repo_name: jdegges/gumstix-pip-oe


text:
@ARTICLE{8709849,
	author={J. T. {Zhou} and H. {Zhang} and D. {Jin} and X. {Peng} and Y. {Xiao} and Z. {Cao}},
	journal={IEEE Transactions on Neural Networks and Learning Systems},
	title={RoSeq: Robust Sequence Labeling},
	year={2019},
	pages={1-11},
	doi={10.1109/TNNLS.2019.2911236},
	ISSN={2162-237X}
}

url: https://raw.githubusercontent.com/shaolinliu/DL-NLP-Readings/158df66b1d84f9d982d659d8ae5d7476a5911cba/Bibtex/RoSeq - Robust Sequence Labeling.bib

repository: shaolinliu/DL-NLP-Readings

repo_name: shaolinliu/DL-NLP-Readings

filename: RoSeq - Robust Sequence Labeling.bib